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commit/galaxy-central: greg: Add an additional filter to correct improper image declarations so they will be displayed in tool config help sections or reqdme files contained in tool shed repositories.
by commits-noreply＠bitbucket.org 04 Oct '13

04 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/836b6a16e5a9/ Changeset: 836b6a16e5a9 User: greg Date: 2013-10-04 16:13:44 Summary: Add an additional filter to correct improper image declarations so they will be displayed in tool config help sections or reqdme files contained in tool shed repositories. Affected #: 1 file diff -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac -r 836b6a16e5a9e499c0a07b23b69c25a3f17eba98 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1519,7 +1519,9 @@ route_to_images = '/repository/static/images/%s' % encoded_repository_id # We used to require $PATH_TO_IMAGES, but we now eliminate it if it's used. text = text.replace( '$PATH_TO_IMAGES', '' ) - # We can eliminate the default setting of /static/images since the routs will properly display images contained in that directory. + # Eliminate the invalid setting of ./static/images since the routes will properly display images contained in that directory. + text = text.replace( './static/images', '' ) + # Eliminate the default setting of /static/images since the routes will properly display images contained in that directory. text = text.replace( '/static/images', '' ) # Use regex to instantiate routes into the defined image paths. for match in re.findall( '.. image:: (?!http)/?(.+)', text ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Enhance the framework that display images declared in the help section of Galaxy tool configs contained in tool shed repositories to also work in README files with a .rst extension that are contained in repositories. Remote images that are available view http requests are supported as are any relative path for locating the image if it is contained within the repository hierarchy. The previously required $PATH_TO_IMAGES is no longer required, and is ignored if us
by commits-noreply＠bitbucket.org 04 Oct '13

04 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1bb04279216e/ Changeset: 1bb04279216e User: greg Date: 2013-10-04 16:04:25 Summary: Enhance the framework that display images declared in the help section of Galaxy tool configs contained in tool shed repositories to also work in README files with a .rst extension that are contained in repositories. Remote images that are available view http requests are supported as are any relative path for locating the image if it is contained within the repository hierarchy. The previously required $PATH_TO_IMAGES is no longer required, and is ignored if used. The following image declarations are all supported: .. image:: http://www.animalphotos.me/mammal/mammal-wcat_files/wildcat7.jpg .. image:: https://raw.github.com/peterjc/picobio/769e4a77194587207f50707939db42b9f04b… .. image:: $PATH_TO_IMAGES/count_modes.png .. image:: count_modes.png .. image:: /deep/Phyca11_example_output.png Affected #: 11 files diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -11,6 +11,7 @@ import shutil import sys import tempfile +import threading import traceback import types import urllib @@ -1333,19 +1334,16 @@ help_header = "" help_footer = "" if self.help is not None: - # Handle tool help image display for tools that are contained in repositories that are in the tool shed or installed into Galaxy. - # When tool config files use the special string $PATH_TO_IMAGES, the following code will replace that string with the path on disk. - if self.repository_id and self.help.text.find( '$PATH_TO_IMAGES' ) >= 0: - if self.app.name == 'galaxy': - repository = self.sa_session.query( self.app.model.ToolShedRepository ).get( self.app.security.decode_id( self.repository_id ) ) - if repository: - path_to_images = '/tool_runner/static/images/%s' % self.repository_id - self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) - elif self.app.name == 'tool_shed': - repository = self.sa_session.query( self.app.model.Repository ).get( self.app.security.decode_id( self.repository_id ) ) - if repository: - path_to_images = '/repository/static/images/%s' % self.repository_id - self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) + if self.repository_id and self.help.text.find( '.. image:: ' ) >= 0: + # Handle tool help image display for tools that are contained in repositories in the tool shed or installed into Galaxy. + lock = threading.Lock() + lock.acquire( True ) + try: + self.help.text = shed_util_common.set_image_paths( self.app, self.repository_id, self.help.text ) + except Exception, e: + log.exception( "Exception in parse_help, so images may not be properly displayed:\n%s" % str( e ) ) + finally: + lock.release() help_pages = self.help.findall( "page" ) help_header = self.help.text try: diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -46,8 +46,12 @@ atexit.register( app.shutdown ) # Create the universe WSGI application webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' ) - # The following route will handle displaying tool shelp images for tools contained in repositories installed from the tool shed. - webapp.add_route( '/tool_runner/static/images/:repository_id/:image_file', controller='tool_runner', action='display_tool_help_image_in_repository', repository_id=None, image_file=None ) + # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. + webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + controller='admin_toolshed', + action='display_image_in_repository', + repository_id=None, + image_file=None ) webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -285,6 +285,28 @@ status=status ) @web.expose + def display_image_in_repository( self, trans, **kwd ): + """ + Open an image file that is contained in an installed tool shed repository or that is referenced by a URL for display. The + image can be defined in either a README.rst file contained in the repository or the help section of a Galaxy tool config that + is contained in the repository. The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer + required, and is now ignored. + .. image:: https://raw.github.com/galaxy/some_image.png + .. image:: $PATH_TO_IMAGES/some_image.png + .. image:: /static/images/some_image.gif + .. image:: some_image.jpg + .. image:: /deep/some_image.png + """ + repository_id = kwd.get( 'repository_id', None ) + relative_path_to_image_file = kwd.get( 'image_file', None ) + if repository_id and relative_path_to_image_file: + repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + repo_files_dir = repository.repo_files_directory( trans.app ) + path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file ) + return open( path_to_file, 'r' ) + return None + + @web.expose @web.require_admin def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -98,22 +98,6 @@ **vars ) @web.expose - def display_tool_help_image_in_repository( self, trans, **kwd ): - repository_id = kwd.get( 'repository_id', None ) - image_file = kwd.get( 'image_file', None ) - if repository_id and image_file: - repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) - repo_files_dir = os.path.join( repository.repo_files_directory( trans.app ) ) - default_path = os.path.abspath( os.path.join( repo_files_dir, 'static', 'images', image_file ) ) - if os.path.exists( default_path ): - return open( default_path, 'r' ) - else: - path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, image_file ) - if os.path.exists( path_to_file ): - return open( path_to_file, 'r' ) - return None - - @web.expose def rerun( self, trans, id=None, from_noframe=None, **kwd ): """ Given a HistoryDatasetAssociation id, find the job and that created diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -69,8 +69,12 @@ webapp.add_route( '/view/{owner}', controller='repository', action='sharable_owner' ) webapp.add_route( '/view/{owner}/{name}', controller='repository', action='sharable_repository' ) webapp.add_route( '/view/{owner}/{name}/{changeset_revision}', controller='repository', action='sharable_repository_revision' ) - # The following route will handle displaying tool shelp images for tools contained in repositories. - webapp.add_route( '/repository/static/images/:repository_id/:image_file', controller='repository', action='display_tool_help_image_in_repository', repository_id=None, image_file=None ) + # Handle displaying tool help images and README file images for tools contained in repositories. + webapp.add_route( '/repository/static/images/:repository_id/:image_file', + controller='repository', + action='display_image_in_repository', + repository_id=None, + image_file=None ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='repository', action='index' ) webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -666,7 +666,7 @@ # Update repository files for browsing. suc.update_repository( repo ) changeset_revision = repository.tip( trans.app ) - metadata = self.get_metadata( trans, id, changeset_revision ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, changeset_revision, metadata_only=True ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repository=repository, @@ -897,7 +897,10 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) - metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + id, + repository.tip( trans.app ), + metadata_only=True ) if trans.user and trans.user.email: return trans.fill_template( "/webapps/tool_shed/repository/contact_owner.mako", repository=repository, @@ -1015,6 +1018,27 @@ status=status ) ) @web.expose + def display_image_in_repository( self, trans, **kwd ): + """ + Open an image file that is contained in repository or that is referenced by a URL for display. The image can be defined in + either a README.rst file contained in the repository or the help section of a Galaxy tool config that is contained in the repository. + The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer required, and is now ignored. + .. image:: https://raw.github.com/galaxy/some_image.png + .. image:: $PATH_TO_IMAGES/some_image.png + .. image:: /static/images/some_image.gif + .. image:: some_image.jpg + .. image:: /deep/some_image.png + """ + repository_id = kwd.get( 'repository_id', None ) + relative_path_to_image_file = kwd.get( 'image_file', None ) + if repository_id and relative_path_to_image_file: + repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repo_files_dir = os.path.join( repository.repo_path( trans.app ), repository.name ) + path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file ) + return open( path_to_file, 'r' ) + return None + + @web.expose def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -1023,7 +1047,10 @@ if message: status = 'error' tool_state = tool_util.new_state( trans, tool, invalid=False ) - metadata = self.get_metadata( trans, repository_id, changeset_revision ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + repository_id, + changeset_revision, + metadata_only=True ) try: return trans.fill_template( "/webapps/tool_shed/repository/tool_form.mako", repository=repository, @@ -1052,22 +1079,6 @@ status='error' ) ) @web.expose - def display_tool_help_image_in_repository( self, trans, **kwd ): - repository_id = kwd.get( 'repository_id', None ) - image_file = kwd.get( 'image_file', None ) - if repository_id and image_file: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) - repo_files_dir = os.path.join( repository.repo_path( trans.app ), repository.name ) - default_path = os.path.abspath( os.path.join( repo_files_dir, 'static', 'images', image_file ) ) - if os.path.exists( default_path ): - return open( default_path, 'r' ) - else: - path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, image_file ) - if os.path.exists( path_to_file ): - return open( path_to_file, 'r' ) - return None - - @web.expose def download( self, trans, repository_id, changeset_revision, file_type, **kwd ): """Download an archive of the repository files compressed as zip, gz or bz2.""" # FIXME: thgis will currently only download the repository tip, no matter which installable changeset_revision is being viewed. @@ -1571,12 +1582,6 @@ pubdate=strftime( '%a, %d %b %Y %H:%M:%S UT', gmtime() ), items=functional_test_results ) - def get_metadata( self, trans, repository_id, changeset_revision ): - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) - if repository_metadata and repository_metadata.metadata: - return repository_metadata.metadata - return None - @web.json def get_readme_files( self, trans, **kwd ): """ @@ -2409,7 +2414,10 @@ avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) display_reviews = util.string_as_bool( kwd.get( 'display_reviews', False ) ) rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) - metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + id, + repository.tip( trans.app ), + metadata_only=True ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, @@ -2806,7 +2814,10 @@ 'has_metadata' : has_metadata } # Make sure we'll view latest changeset first. changesets.insert( 0, change_dict ) - metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + id, + repository.tip( trans.app ), + metadata_only=True ) return trans.fill_template( '/webapps/tool_shed/repository/view_changelog.mako', repository=repository, metadata=metadata, @@ -2839,7 +2850,7 @@ diffs = [] for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ): diffs.append( suc.to_html_string( diff ) ) - metadata = self.get_metadata( trans, id, ctx_str ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, ctx_str, metadata_only=True ) # For rendering the prev button. if ctx_parent: ctx_parent_rev = ctx_parent.rev() diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1072,13 +1072,15 @@ """Get repository metadata from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) -def get_repository_metadata_by_repository_id_changeset_revision( trans, id, changeset_revision ): - """Get a specified metadata record for a specified repository.""" - return trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), - trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ - .first() - +def get_repository_metadata_by_repository_id_changeset_revision( trans, id, changeset_revision, metadata_only=False ): + """Get a specified metadata record for a specified repository in the tool shed.""" + if metadata_only: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + if repository_metadata and repository_metadata.metadata: + return repository_metadata.metadata + return None + return suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + def get_repository_metadata_revisions_for_review( repository, reviewed=True ): repository_metadata_revisions = [] metadata_changeset_revision_hashes = [] diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/tool_shed/util/readme_util.py --- a/lib/tool_shed/util/readme_util.py +++ b/lib/tool_shed/util/readme_util.py @@ -1,7 +1,11 @@ import logging import os +import threading +from mako.template import Template from galaxy import eggs +from galaxy import web from galaxy.util import json +from galaxy.util import rst_to_html from galaxy.util import unicodify import tool_shed.util.shed_util_common as suc from tool_shed.util import common_util @@ -34,13 +38,39 @@ full_path_to_readme_file = os.path.abspath( os.path.join( tool_path, relative_path_to_readme_file ) ) else: full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file ) + text = None try: f = open( full_path_to_readme_file, 'r' ) text = unicodify( f.read() ) f.close() - readme_files_dict[ readme_file_name ] = suc.size_string( text ) except Exception, e: log.exception( "Error reading README file '%s' from disk: %s" % ( str( relative_path_to_readme_file ), str( e ) ) ) + text = None + if text: + text_of_reasonable_length = suc.size_string( text ) + if text_of_reasonable_length.find( '.. image:: ' ) >= 0: + # Handle image display for README files that are contained in repositories in the tool shed or installed into Galaxy. + lock = threading.Lock() + lock.acquire( True ) + try: + text_of_reasonable_length = suc.set_image_paths( trans.app, + trans.security.encode_id( repository.id ), + text_of_reasonable_length ) + except Exception, e: + log.exception( "Exception in build_readme_files_dict, so images may not be properly displayed:\n%s" % str( e ) ) + finally: + lock.release() + if readme_file_name.endswith( '.rst' ): + text_of_reasonable_length = Template( rst_to_html( text_of_reasonable_length ), + input_encoding='utf-8', + output_encoding='utf-8', + default_filters=[ 'decode.utf8' ], + encoding_errors='replace' ) + text_of_reasonable_length = text_of_reasonable_length.render( static_path=web.url_for( '/static' ), + host_url=web.url_for( '/', qualified=True ) ) + else: + text_of_reasonable_length = suc.to_html_string( text_of_reasonable_length ) + readme_files_dict[ readme_file_name ] = text_of_reasonable_length else: # We must be in the tool shed and have an old changeset_revision, so we need to retrieve the file contents from the repository manifest. ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1,5 +1,6 @@ import logging import os +import re import shutil import string import tempfile @@ -1504,6 +1505,28 @@ """Return a reversed list of changesets in the repository changelog up to and including the included_upper_bounds_changeset_revision.""" return reversed_lower_upper_bounded_changelog( repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision ) +def set_image_paths( app, encoded_repository_id, text ): + """ + Handle tool help image display for tools that are contained in repositories in the tool shed or installed into Galaxy as well as image + display in repository README files. This method will determine the location of the image file and return the path to it that will enable + the caller to open the file. + """ + if text: + if app.name == 'galaxy': + route_to_images = '/admin_toolshed/static/images/%s' % encoded_repository_id + else: + # We're in the tool shed. + route_to_images = '/repository/static/images/%s' % encoded_repository_id + # We used to require $PATH_TO_IMAGES, but we now eliminate it if it's used. + text = text.replace( '$PATH_TO_IMAGES', '' ) + # We can eliminate the default setting of /static/images since the routs will properly display images contained in that directory. + text = text.replace( '/static/images', '' ) + # Use regex to instantiate routes into the defined image paths. + for match in re.findall( '.. image:: (?!http)/?(.+)', text ): + text = text.replace( match, match.replace( '/', '%2F' ) ) + text = re.sub( '.. image:: (?!http)/?(.+)', '.. image:: %s/\\1' % route_to_images, text ) + return text + def set_only_if_compiling_contained_td( repository, required_repository ): """Return True if the received required_repository is only needed to compile a tool dependency defined for the received repository.""" # This method is called only from Galaxy when rendering repository dependencies for an installed tool shed repository. diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -584,12 +584,7 @@ </%def><%def name="render_readme( readme, pad, parent, row_counter )"> - <% - from tool_shed.util.shed_util_common import to_html_string - from galaxy.util import rst_to_html - encoded_id = trans.security.encode_id( readme.id ) - render_rst = readme.name.endswith( '.rst' ) - %> + <% encoded_id = trans.security.encode_id( readme.id ) %><tr class="datasetRow" %if parent is not None: parent="${parent}" @@ -597,11 +592,7 @@ id="libraryItem-rr-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="readme_files"> - %if render_rst: - <tr><td>${ rst_to_html( readme.text ) }</td></tr> - %else: - <tr><td>${ to_html_string( readme.text ) }</td></tr> - %endif + <tr><td>${ readme.text }</td></tr></table></td></tr> diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac test/tool_shed/functional/test_1140_tool_help_images.py --- a/test/tool_shed/functional/test_1140_tool_help_images.py +++ b/test/tool_shed/functional/test_1140_tool_help_images.py @@ -109,10 +109,10 @@ In the center tool panel, look for the image string similar to the following string where the encoded_repository_id is previously determined as the installed ToolShedRepository id: - src="/tool_runner/static/images/<id>/count_modes.png" + src="/admin_toolshed/static/images/<id>/count_modes.png" ''' repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) - image_path = 'src="/tool_runner/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) + image_path = 'src="/admin_toolshed/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) # The repository uploaded in this test should only define one tool, which should be the tool that contains a link to an image. repository_metadata = repository.metadata tool_id = repository_metadata[ 'tools' ][ 0 ][ 'guid' ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: to_dict fixes.
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/288203bc6e4e/ Changeset: 288203bc6e4e User: jgoecks Date: 2013-10-04 00:38:23 Summary: to_dict fixes. Affected #: 1 file diff -r 8f2b1130bc523ba60731eb4c5cecfb004e7f9b1b -r 288203bc6e4eac539ad2008ca088530cf2250cee lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2351,7 +2351,7 @@ self.tags.append(new_swta) def to_dict( self, view='collection', value_mapper = None ): - rval = super( StoredWorkflow, self ).to_dict(self, view=view, value_mapper = value_mapper) + rval = super( StoredWorkflow, self ).to_dict( view=view, value_mapper = value_mapper ) tags_str_list = [] for tag in self.tags: tag_str = tag.user_tname @@ -3912,7 +3912,7 @@ return [ tool_version.tool_id for tool_version in self.get_versions( app ) ] def to_dict( self, view='element' ): - rval = super( ToolVersion, self ).to_dict( self, view ) + rval = super( ToolVersion, self ).to_dict( view=view ) rval['tool_name'] = self.tool_id for a in self.parent_tool_association: rval['parent_tool_id'] = a.parent_id Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Enhance handling of downloaded compressed files based on their internal directory structure. Add rename_to attribute to the move_file action.
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8f2b1130bc52/ Changeset: 8f2b1130bc52 User: Dave Bouvier Date: 2013-10-03 20:17:19 Summary: Enhance handling of downloaded compressed files based on their internal directory structure. Add rename_to attribute to the move_file action. Affected #: 3 files diff -r 84781f00ff8e57848397177511b77a400055b59f -r 8f2b1130bc523ba60731eb4c5cecfb004e7f9b1b lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -284,7 +284,8 @@ elif action_type == 'move_file': td_common_util.move_file( current_dir=current_dir, source=os.path.join( action_dict[ 'source' ] ), - destination_dir=os.path.join( action_dict[ 'destination' ] ) ) + destination=os.path.join( action_dict[ 'destination' ] ), + rename_to=action_dict[ 'rename_to' ] ) elif action_type == 'set_environment': # Currently the only action supported in this category is "environment_variable". # Build a command line from the prior_installation_required, in case an environment variable is referenced diff -r 84781f00ff8e57848397177511b77a400055b59f -r 8f2b1130bc523ba60731eb4c5cecfb004e7f9b1b lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -464,7 +464,7 @@ is_binary_download = True else: is_binary_download = False - elif action_elem: + elif action_elem is not None: # We were provided with a single <action> element to perform certain actions after a platform-specific tarball was downloaded. elems = [ action_elem ] else: @@ -550,11 +550,7 @@ action_dict[ 'directory' ] = action_elem.text else: continue - elif action_type in [ 'move_directory_files', 'move_file' ]: - # <action type="move_file"> - # <source>misc/some_file</source> - # <destination>$INSTALL_DIR/bin</destination> - # </action> + elif action_type == 'move_directory_files': # <action type="move_directory_files"> # <source_directory>bin</source_directory> # <destination_directory>$INSTALL_DIR/bin</destination_directory> @@ -563,6 +559,14 @@ move_elem_text = evaluate_template( move_elem.text ) if move_elem_text: action_dict[ move_elem.tag ] = move_elem_text + elif action_type == 'move_file': + # <action type="move_file" rename_to="new_file_name"> + # <source>misc/some_file</source> + # <destination>$INSTALL_DIR/bin</destination> + # </action> + action_dict[ 'source' ] = evaluate_template( action_elem.find( 'source' ).text ) + action_dict[ 'destination' ] = evaluate_template( action_elem.find( 'destination' ).text ) + action_dict[ 'rename_to' ] = action_elem.get( 'rename_to' ) elif action_type == 'set_environment': # <action type="set_environment"> # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> diff -r 84781f00ff8e57848397177511b77a400055b59f -r 8f2b1130bc523ba60731eb4c5cecfb004e7f9b1b lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -12,6 +12,109 @@ log = logging.getLogger( __name__ ) + +class CompressedFile( object ): + + def __init__( self, file_path, mode='r' ): + if istar( file_path ): + self.file_type = 'tar' + elif iszip( file_path ) and not isjar( file_path ): + self.file_type = 'zip' + self.file_name = os.path.splitext( file_path )[ 0 ] + if self.file_name.endswith( '.tar' ): + self.file_name = os.path.splitext( self.file_name )[ 0 ] + self.type = self.file_type + method = 'open_%s' % self.file_type + if hasattr( self, method ): + self.archive = getattr( self, method )( file_path, mode ) + else: + raise NameError( 'File type %s specified, no open method found.' % self.file_type ) + + def extract( self, path ): + full_path = self.extraction_path( path ) + self.archive.extractall( full_path ) + return full_path + + def extraction_path( self, path ): + '''Determine the path to which the archive should be extracted.''' + contents = self.getmembers() + extraction_path = path + if len( contents ) == 1: + # The archive contains a single file, return the extraction path. + if self.isfile( contents[ 0 ] ): + extraction_path = os.path.join( path, self.file_name ) + else: + # Sort filenames within the archive by length, because if the shortest path entry in the archive is a directory, + # and the next entry has the directory prepended, then everything following that entry must be within that directory. + # For example, consider tarball for BWA 0.5.9: + # bwa-0.5.9.tar.bz2: + # bwa-0.5.9/ + # bwa-0.5.9/bwt.c + # bwa-0.5.9/bwt.h + # bwa-0.5.9/Makefile + # bwa-0.5.9/bwt_gen/ + # bwa-0.5.9/bwt_gen/Makefile + # bwa-0.5.9/bwt_gen/bwt_gen.c + # bwa-0.5.9/bwt_gen/bwt_gen.h + # When sorted by length, one sees a directory at the root of the tarball, and all other tarball contents as + # children of that directory. + filenames = sorted( [ self.getname( item ) for item in contents ], cmp=lambda a,b: cmp( len( a ), len( b ) ) ) + parent_name = filenames[ 0 ] + parent = self.getmember( parent_name ) + first_child = filenames[ 1 ] + if first_child.startswith( parent_name ) and parent is not None and self.isdir( parent ): + extraction_path = os.path.join( path, self.getname( parent ) ) + else: + extraction_path = os.path.join( path, self.file_name ) + if not os.path.exists( extraction_path ): + os.makedirs( extraction_path ) + return os.path.abspath( extraction_path ) + + def getmembers_tar( self ): + return self.archive.getmembers() + + def getmembers_zip( self ): + return self.archive.infolist() + + def getname_tar( self, item ): + return item.name + + def getname_zip( self, item ): + return item.filename + + def getmember( self, name ): + for member in self.getmembers(): + if self.getname( member ) == name: + return member + + def getmembers( self ): + return getattr( self, 'getmembers_%s' % self.type )() + + def getname( self, member ): + return getattr( self, 'getname_%s' % self.type )( member ) + + def isdir( self, member ): + return getattr( self, 'isdir_%s' % self.type )( member ) + + def isdir_tar( self, member ): + return member.isdir() + + def isdir_zip( self, member ): + if member.filename.endswith( os.sep ): + return True + return False + + def isfile( self, member ): + if not self.isdir( member ): + return True + return False + + def open_tar( self, filepath, mode ): + return tarfile.open( filepath, mode ) + + def open_zip( self, filepath, mode ): + return zipfile.ZipFile( filepath, mode ) + def clean_tool_shed_url( base_url ): if base_url: if base_url.find( '://' ) > -1: @@ -92,30 +195,6 @@ dir = url_download( work_dir, downloaded_filename, url, extract=False ) return downloaded_filename -def extract_tar( file_name, file_path ): - if isgzip( file_name ) or isbz2( file_name ): - # Open for reading with transparent compression. - tar = tarfile.open( file_name, 'r:*', errorlevel=0 ) - else: - tar = tarfile.open( file_name, errorlevel=0 ) - tar.extractall( path=file_path ) - tar.close() - -def extract_zip( archive_path, extraction_path ): - # TODO: change this method to use zipfile.Zipfile.extractall() when we stop supporting Python 2.5. - if not zipfile_ok( archive_path ): - return False - zip_archive = zipfile.ZipFile( archive_path, 'r' ) - for name in zip_archive.namelist(): - uncompressed_path = os.path.join( extraction_path, name ) - if uncompressed_path.endswith( '/' ): - if not os.path.isdir( uncompressed_path ): - os.makedirs( uncompressed_path ) - else: - file( uncompressed_path, 'wb' ).write( zip_archive.read( name ) ) - zip_archive.close() - return True - def format_traceback(): ex_type, ex, tb = sys.exc_info() return ''.join( traceback.format_tb( tb ) ) @@ -232,12 +311,18 @@ destination_file = os.path.join( destination_directory, file_name ) shutil.move( source_file, destination_file ) -def move_file( current_dir, source, destination_dir ): +def move_file( current_dir, source, destination, rename_to=None ): source_file = os.path.abspath( os.path.join( current_dir, source ) ) - destination_directory = os.path.join( destination_dir ) - if not os.path.isdir( destination_directory ): + if rename_to is not None: + destination_file = rename_to + destination_directory = os.path.join( destination ) + destination_path = os.path.join( destination_directory, destination_file ) + else: + destination_directory = os.path.join( destination ) + destination_path = os.path.join( destination_directory, source_file ) + if not os.path.exists( destination_directory ): os.makedirs( destination_directory ) - shutil.move( source_file, destination_directory ) + shutil.move( source_file, destination_path ) def parse_package_elem( package_elem, platform_info_dict=None, include_after_install_actions=True ): """ @@ -340,19 +425,6 @@ continue return actions_elem_tuples -def tar_extraction_directory( file_path, file_name ): - """Try to return the correct extraction directory.""" - file_name = file_name.strip() - extensions = [ '.tar.gz', '.tgz', '.tar.bz2', '.tar', '.zip' ] - for extension in extensions: - if file_name.find( extension ) > 0: - dir_name = file_name[ :-len( extension ) ] - if os.path.exists( os.path.abspath( os.path.join( file_path, dir_name ) ) ): - return dir_name - if os.path.exists( os.path.abspath( os.path.join( file_path, file_name ) ) ): - return os.path.abspath( file_path ) - raise ValueError( 'Could not find path to file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) ) - def url_download( install_dir, downloaded_file_name, download_url, extract=True ): file_path = os.path.join( install_dir, downloaded_file_name ) src = None @@ -374,32 +446,14 @@ if dst: dst.close() if extract: - if istar( file_path ): - # <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> - extract_tar( file_path, install_dir ) - dir = tar_extraction_directory( install_dir, downloaded_file_name ) - elif isjar( file_path ): - dir = os.path.curdir - elif iszip( file_path ): - # <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-to…</action> - zip_archive_extracted = extract_zip( file_path, install_dir ) - dir = zip_extraction_directory( install_dir, downloaded_file_name ) + if istar( file_path ) or iszip( file_path ): + archive = CompressedFile( file_path ) + extraction_path = archive.extract( install_dir ) else: - dir = os.path.abspath( install_dir ) + extraction_path = os.path.abspath( install_dir ) else: - dir = os.path.abspath( install_dir ) - return dir - -def zip_extraction_directory( file_path, file_name ): - """Try to return the correct extraction directory.""" - files = [ filename for filename in os.listdir( file_path ) if not filename.endswith( '.zip' ) ] - if len( files ) > 1: - return os.path.abspath( file_path ) - elif len( files ) == 1: - # If there is only on file it should be a directory. - if os.path.isdir( os.path.join( file_path, files[ 0 ] ) ): - return os.path.abspath( os.path.join( file_path, files[ 0 ] ) ) - raise ValueError( 'Could not find directory for the extracted file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) ) + extraction_path = os.path.abspath( install_dir ) + return extraction_path def zipfile_ok( path_to_archive ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Trackster: Fix cell content if metadata is inconsistent
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/84781f00ff8e/ Changeset: 84781f00ff8e User: guerler Date: 2013-10-03 19:21:59 Summary: Trackster: Fix cell content if metadata is inconsistent Affected #: 1 file diff -r a1c04a1b716a2c83f821b08f5ca18ace27fcfe21 -r 84781f00ff8e57848397177511b77a400055b59f static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -183,7 +183,7 @@ var column_types = this.model.get_metadata('column_types'); if (colspan !== undefined) { $cell.attr('colspan', colspan).addClass('stringalign'); - } else if (index < column_types.length) { + } else if (column_types !== undefined && index < column_types.length) { if (column_types[index] === 'str' || column_types === 'list') { /* Left align all str columns, right align the rest */ $cell.addClass('stringalign'); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Trackster: Fix cell content if metadata is inconsistent
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a1c04a1b716a/ Changeset: a1c04a1b716a User: guerler Date: 2013-10-03 19:11:43 Summary: Trackster: Fix cell content if metadata is inconsistent Affected #: 1 file diff -r e55c7a4a88e076f163949381937d38d11e48c74a -r a1c04a1b716a2c83f821b08f5ca18ace27fcfe21 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -179,17 +179,17 @@ // -- Helper functions. -- _renderCell: function(cell_contents, index, colspan) { + var $cell = $('<td>').text(cell_contents); var column_types = this.model.get_metadata('column_types'); if (colspan !== undefined) { - return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); + $cell.attr('colspan', colspan).addClass('stringalign'); + } else if (index < column_types.length) { + if (column_types[index] === 'str' || column_types === 'list') { + /* Left align all str columns, right align the rest */ + $cell.addClass('stringalign'); + } } - else if (column_types[index] === 'str' || column_types === 'list') { - /* Left align all str columns, right align the rest */ - return $('<td>').addClass('stringalign').text(cell_contents); - } - else { - return $('<td>').text(cell_contents); - } + return $cell; }, _renderRow: function(line) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Update universe sample with new inactivity box content default text
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e55c7a4a88e0/ Changeset: e55c7a4a88e0 User: dannon Date: 2013-10-03 18:18:50 Summary: Update universe sample with new inactivity box content default text Affected #: 1 file diff -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd -r e55c7a4a88e076f163949381937d38d11e48c74a universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -299,7 +299,7 @@ # Used for warning box for inactive accounts (unable to run jobs). # In use only if activation_grace_period is set. -#inactivity_box_content = Your account has not been activated yet. Please activate your account by verifying your email address. For now you can access everything at Galaxy but your jobs won't run. +#inactivity_box_content = Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address. # -- Display sites Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Fix grid_base.mako url_base parameters (grids need to be refactored), continue integration of new modal
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2fed7f7b23fd/ Changeset: 2fed7f7b23fd User: guerler Date: 2013-10-03 18:09:35 Summary: Fix grid_base.mako url_base parameters (grids need to be refactored), continue integration of new modal Affected #: 4 files diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -255,7 +255,8 @@ }); // Initialize ratings. - $('.community_rating_star').rating({}); + if ($('.community_rating_star').length !== 0) + $('.community_rating_star').rating({}); // Initialize item menu operations. make_popup_menus(); diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -20,47 +20,7 @@ data: filters, error: function() { alert( "Grid failed" ); }, success: function(table_html) { - show_modal( - "Select datasets for new tracks", - table_html, - { - "Cancel": function() { - hide_modal(); - }, - "Add": function() { - var requests = []; - $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { - var data = { - data_type: 'track_config', - 'hda_ldda': 'hda' - }, - id = $(this).val(); - if ($(this).attr("name") !== "id") { - data.hda_ldda = 'ldda'; - } - requests[requests.length] = $.ajax({ - url: add_track_async_url + "/" + id, - data: data, - dataType: "json" - }); - }); - // To preserve order, wait until there are definitions for all tracks and then add - // them sequentially. - $.when.apply($, requests).then(function() { - // jQuery always returns an Array for arguments, so need to look at first element - // to determine whether multiple requests were made and consequently how to - // map arguments to track definitions. - var track_defs = (arguments[0] instanceof Array ? - $.map(arguments, function(arg) { return arg[0]; }) : - [ arguments[0] ] - ); - success_fn(track_defs); - }); - hide_modal(); - } - } - ); - /*Galaxy.modal.show({ + Galaxy.modal.show({ title : "Select datasets for new tracks", body : table_html, buttons : @@ -100,7 +60,7 @@ Galaxy.modal.hide(); } } - });*/ + }); } }); }; diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -86,7 +86,7 @@ // Create grid. var grid = new Grid({ - url_base: location.pathname, + url_base: '${trans.request.path_url}', async: is_true('${grid.use_async}'), async_ops: async_ops, categorical_filters: categorical_filters, @@ -102,6 +102,12 @@ // Initialize grid objects on load. // FIXME: use a grid view object eventually. $(document).ready(function() { + + // strip protocol and domain + var url = grid.get('url_base'); + url = url.replace(/^.*\/\/[^\/]+/, ''); + grid.set('url_base', url); + init_grid_elements(); init_grid_controls(); // Initialize text filters to select text on click and use normal font when user is typing. diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -152,38 +152,6 @@ </script></%def> -<%def name="overlay( title='', content='', visible=False )"> - <%def name="title()"></%def> - <%def name="content()"></%def> - - <% - if visible: - display = "style='display: block;'" - overlay_class = "in" - else: - display = "style='display: none;'" - overlay_class = "" - %> - - <div id="top-modal" class="modal fade ${overlay_class}" ${display}> - <div id="top-modal-backdrop" class="modal-backdrop fade ${overlay_class}" style="z-index: -1"></div> - <div id="top-modal-dialog" class="modal-dialog"> - <div class="modal-content"> - <div class="modal-header"> - <button type='button' class='close' style="display: none;">×</button> - <h4 class='title'>${title}</h4> - </div> - <div class="modal-body">${content}</div> - <div class="modal-footer"> - <div class="buttons" style="float: right;"></div> - <div class="extra_buttons" style=""></div> - <div style="clear: both;"></div> - </div> - </div> - </div> - </div> -</%def> - ## document <html><head> @@ -214,7 +182,6 @@ %if self.galaxy_config['message_box']: <div id="messagebox" class="panel-message"></div> %endif - ${self.overlay()} ## left panel %if self.galaxy_config['left_panel']: <div id="left"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: activation feature tweaks
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b714089d888c/ Changeset: b714089d888c User: martenson Date: 2013-10-03 17:18:59 Summary: activation feature tweaks Affected #: 2 files diff -r becb2b5d2d0690fa5217a8101c6d0b5f8c6dc99d -r b714089d888cad2942ba3edcd968532f07b56143 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -133,7 +133,7 @@ self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.activation_email = kwargs.get( 'activation_email', None ) - self.user_activation_on = kwargs.get( 'user_activation_on', None ) + self.user_activation_on = string_as_bool( kwargs.get( 'user_activation_on', False ) ) self.activation_grace_period = kwargs.get( 'activation_grace_period', None ) self.inactivity_box_content = kwargs.get( 'inactivity_box_content', None ) self.registration_warning_message = kwargs.get( 'registration_warning_message', None ) diff -r becb2b5d2d0690fa5217a8101c6d0b5f8c6dc99d -r b714089d888cad2942ba3edcd968532f07b56143 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -670,8 +670,10 @@ user = trans.app.model.User( email=email ) user.set_password_cleartext( password ) user.username = username - if trans.app.config.user_activation_on: # Do not set the active flag in case activation is OFF. + if trans.app.config.user_activation_on: user.active = False + else: + user.active = True # Activation is off, every new user is active by default. trans.sa_session.add( user ) trans.sa_session.flush() trans.app.security_agent.create_private_user_role( user ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Remove reference to removed select field in the repository write permission form.
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/becb2b5d2d06/ Changeset: becb2b5d2d06 User: Dave Bouvier Date: 2013-10-03 16:45:39 Summary: Remove reference to removed select field in the repository write permission form. Affected #: 1 file diff -r 54673424aa68129d1bae517db268d571feb73fae -r becb2b5d2d0690fa5217a8101c6d0b5f8c6dc99d test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -723,7 +723,6 @@ post_submit_strings_not_displayed=[] ): self.display_manage_repository_page( repository ) self.check_for_strings( strings_displayed, strings_not_displayed ) - tc.fv( "user_access", "allow_push", '-Select one' ) for username in usernames: tc.fv( "user_access", "allow_push", '+%s' % username ) tc.submit( 'user_access_button' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Clean up migration stage functional test script, add check strings for stage 8.
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/54673424aa68/ Changeset: 54673424aa68 User: Dave Bouvier Date: 2013-10-03 16:15:42 Summary: Clean up migration stage functional test script, add check strings for stage 8. Affected #: 1 file diff -r a3c0180445385eb708e03304769599a8c9cc2760 -r 54673424aa68129d1bae517db268d571feb73fae test/tool_shed/functional/test_1400_review_migration_stages.py --- a/test/tool_shed/functional/test_1400_review_migration_stages.py +++ b/test/tool_shed/functional/test_1400_review_migration_stages.py @@ -20,14 +20,26 @@ def test_0005_load_migration_stages_page( self ): '''Load the migration page and check for the appropriate migration stages.''' - stages = [ - 'emboss_5', 'emboss_datatypes', 'emboss', '5.0.0', '0002_tools.sh', - 'freebayes', '0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8', 'samtools', '0.1.18', 'FreeBayes requires g++', - 'ncurses', 'zlib', '0003_tools.sh', - 'ncbi_blast_plus', 'blast_datatypes', 'blast+', '2.2.26+', 'blast.ncbi.nlm.nih.gov', 'NCBI BLAST+ tools', '0004_tools.sh', - 'bwa_wrappers', '0.5.9', 'zlib and libpthread', 'Map with BWA for Illumina', '0005_tools.sh', - 'picard', '1.56.0', 'FASTQ to BAM', '0006_tools.sh', - 'lastz', '1.02.00', 'bowtie', '0.12.7', 'Map with Bowtie for Illumina', 'Bowtie requires libpthread', '0007_tools.sh' - ] + stages = [] + migration_message_strings = [ 'The Emboss 5.0.0 tools have been eliminated', + 'The freebayes tool has been eliminated', + 'The NCBI BLAST+ tools', + 'The tools "Map with BWA for Illumina"', + 'FASTQ to BAM, SAM to FASTQ, BAM ', + 'Map with Bowtie for Illumina, ', + 'BAM-to-SAM converts BAM format' ] + migrated_repository_names = [ 'emboss_5', 'emboss_datatypes', 'freebayes', 'ncbi_blast_plus', + 'blast_datatypes', 'bwa_wrappers', 'picard', 'lastz', + 'lastz_paired_reads', 'bowtie_color_wrappers', 'bowtie_wrappers', + 'xy_plot', 'bam_to_sam' ] + migrated_tool_dependencies = [ 'emboss', '5.0.0', 'freebayes', '0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8', + 'samtools', '0.1.18', 'blast+', '2.2.26+', 'bwa', '0.5.9', 'picard', '1.56.0', + 'lastz', '1.02.00', 'bowtie', '0.12.7', 'FreeBayes requires g++', 'ncurses', 'zlib', + 'zlib and libpthread', 'blast.ncbi.nlm.nih.gov', 'fastx_toolkit', '0.0.13', + 'samtools', '0.1.16', 'cufflinks', '2.1.1', 'R', '2.11.0' ] + migration_scripts = [ '0002_tools.sh', '0003_tools.sh', '0004_tools.sh', '0005_tools.sh', '0006_tools.sh', + '0007_tools.sh', '0008_tools.sh' ] + stages.extend( migration_scripts + migrated_tool_dependencies + migrated_repository_names ) + stages.extend( migration_message_strings ) self.load_galaxy_tool_migrations_page( strings_displayed=stages ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Eliminate the problematic "Select one" option from select fields.
by commits-noreply＠bitbucket.org 02 Oct '13

02 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3c018044538/ Changeset: a3c018044538 User: greg Date: 2013-10-02 22:44:48 Summary: Eliminate the problematic "Select one" option from select fields. Affected #: 1 file diff -r e262ddfe44c34200bac86dfab64c7acbdc5c54a3 -r a3c0180445385eb708e03304769599a8c9cc2760 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -756,13 +756,6 @@ refresh_on_change=refresh_on_change, refresh_on_change_values=refresh_on_change_values, size=size ) - if display is None and initial_value == 'none': - # Only insert an initial "Select one" option if we are not displaying check boxes - # or radio buttons and we have not received an initial_value other than 'none'. - if selected_value == initial_value: - select_field.add_option( 'Select one', initial_value, selected=True ) - else: - select_field.add_option( 'Select one', initial_value ) for obj in objs: if label_attr == 'self': # Each obj is a string Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Fix links in masterhead
by commits-noreply＠bitbucket.org 02 Oct '13

02 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e262ddfe44c3/ Changeset: e262ddfe44c3 User: guerler Date: 2013-10-02 19:34:52 Summary: Fix links in masterhead Affected #: 1 file diff -r 99e18f8868470f48a6a5d91070019d9bfc801f7e -r e262ddfe44c34200bac86dfab64c7acbdc5c54a3 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -51,7 +51,7 @@ <ul class="nav navbar-nav" border="0" cellspacing="0"> - <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='', menu_options=None )"> + <%def name="tab( id, display, href, onclick=False, target='_parent', visible=True, extra_class='', menu_options=None )"> ## Create a tab at the top of the panels. menu_options is a list of 2-elements lists of [name, link] ## that are options in the menu. @@ -61,8 +61,6 @@ extra = "" if extra_class: cls += " " + extra_class - ##if self.active_view == id: - ## cls += " active" if menu_options: cls += " dropdown" a_cls += " dropdown-toggle" @@ -88,7 +86,11 @@ ${menu_item[0]} %elif len ( menu_item ) == 2: <% name, link = menu_item %> - <a href="${link}">${name}</a> + %if onclick: + <a href="${link}" onclick="Galaxy.frame_manager.frame_new({title: '${name}', type: 'url', content: '${link}'}); return false;">${name}</a> + %else: + <a href="${link}">${name}</a> + %endif %else: <% name, link, target = menu_item %><a target="${target}" href="${link}">${name}</a> @@ -105,7 +107,7 @@ ${tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) )} ## Workflow tab. - ${tab( "workflow", _("Workflow"), "javascript:Galaxy.frame_manager.frame_new({title: 'Workflow', type: 'url', content: '" + h.url_for( controller='/workflow', action='index' ) + "'});")} + ${tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) )} ## 'Shared Items' or Libraries tab. <% @@ -135,10 +137,10 @@ ## Visualization menu. <% menu_options = [ - [_('New Track Browser'), "javascript:Galaxy.frame_manager.frame_new({title: 'Trackster', type: 'url', content: '" + h.url_for( controller='/visualization', action='trackster' ) + "'});"], - [_('Saved Visualizations'), "javascript:Galaxy.frame_manager.frame_new({ type: 'url', content : '" + h.url_for( controller='/visualization', action='list' ) + "'});" ] + [_('New Track Browser'), h.url_for( controller='/visualization', action='trackster' )], + [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' )] ] - tab( "visualization", _("Visualization"), "javascript:Galaxy.frame_manager.frame_new({title: 'Trackster', type: 'url', content: '" + h.url_for( controller='/visualization', action='list' ) + "'});", menu_options=menu_options ) + tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list' ), menu_options=menu_options, onclick=True ) %> ## Cloud menu. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Fix links in masterhead, continue integration of new modal
by commits-noreply＠bitbucket.org 02 Oct '13

02 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/99e18f886847/ Changeset: 99e18f886847 User: guerler Date: 2013-10-02 19:23:22 Summary: Fix links in masterhead, continue integration of new modal Affected #: 8 files diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -416,49 +416,54 @@ error: function() { alert( ( "Could not add this dataset to browser" ) + '.' ); }, success: function(table_html) { var parent = window.parent; + parent.Galaxy.modal.show({ + title : "View Data in a New or Saved Visualization", + buttons :{ + "Cancel": function(){ + parent.Galaxy.modal.hide(); + }, + "View in saved visualization": function(){ + // Show new modal with saved visualizations. + parent.Galaxy.modal.show( + { + title: "Add Data to Saved Visualization", + body: table_html, + buttons :{ + "Cancel": function(){ + parent.Galaxy.modal.hide(); + }, + "Add to visualization": function(){ + $(parent.document).find('input[name=id]:checked').each(function(){ + // hide + parent.Galaxy.modal.hide(); + + var vis_id = $(this).val(); + dataset_params.id = vis_id; + + // add widget + parent.Galaxy.frame_manager.frame_new({ + title : "Trackster", + type : "url", + content : vis_url + "/trackster?" + $.param(dataset_params) + }); + }); + } + } + }); + }, + "View in new visualization": function(){ + // hide + parent.Galaxy.modal.hide(); + + var url = vis_url + "/trackster?" + $.param(dataset_params); - parent.show_modal( ( "View Data in a New or Saved Visualization" ), "", { - "Cancel": function() { - parent.hide_modal(); - }, - "View in saved visualization": function() { - // Show new modal with saved visualizations. - parent.show_modal( ( "Add Data to Saved Visualization" ), table_html, { - "Cancel": function() { - parent.hide_modal(); - }, - "Add to visualization": function() { - $(parent.document).find('input[name=id]:checked').each(function() { - var vis_id = $(this).val(); - dataset_params.id = vis_id; - - // add widget - parent.Galaxy.frame_manager.frame_new( - { - title : "Trackster", - type : "url", - content : vis_url + "/trackster?" + $.param(dataset_params) - }); - - // hide - parent.hide_modal(); - }); - } - }); - }, - "View in new visualization": function() { - var url = vis_url + "/trackster?" + $.param(dataset_params); - - // add widget - parent.Galaxy.frame_manager.frame_new( - { - title : "Trackster", - type : "url", - content : url - }); - - // hide - parent.hide_modal(); + // add widget + parent.Galaxy.frame_manager.frame_new({ + title : "Trackster", + type : "url", + content : url + }); + } } }); } diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -635,67 +635,77 @@ * @returns function that displays modal, loads trackster */ //TODO: should be imported from trackster.js -function create_trackster_action_fn(vis_url, dataset_params, dbkey) { - return function() { - var listTracksParams = {}; - if (dbkey){ - // list_tracks seems to use 'f-dbkey' (??) - listTracksParams[ 'f-dbkey' ] = dbkey; - } - $.ajax({ - url: vis_url + '/list_tracks?' + $.param( listTracksParams ), - dataType: "html", - error: function() { alert( _l( "Could not add this dataset to browser" ) + '.' ); }, - success: function(table_html) { - var parent = window.parent; +//TODO: This function is redundant and also exists in data.js + // create action + function create_trackster_action_fn (vis_url, dataset_params, dbkey) { + return function() { + var listTracksParams = {}; + if (dbkey){ + // list_tracks seems to use 'f-dbkey' (??) + listTracksParams[ 'f-dbkey' ] = dbkey; + } + $.ajax({ + url: vis_url + '/list_tracks?' + $.param( listTracksParams ), + dataType: "html", + error: function() { alert( ( "Could not add this dataset to browser" ) + '.' ); }, + success: function(table_html) { + var parent = window.parent; + parent.Galaxy.modal.show({ + title : "View Data in a New or Saved Visualization", + buttons :{ + "Cancel": function(){ + parent.Galaxy.modal.hide(); + }, + "View in saved visualization": function(){ + // Show new modal with saved visualizations. + parent.Galaxy.modal.show( + { + title: "Add Data to Saved Visualization", + body: table_html, + buttons :{ + "Cancel": function(){ + parent.Galaxy.modal.hide(); + }, + "Add to visualization": function(){ + $(parent.document).find('input[name=id]:checked').each(function(){ + // hide + parent.Galaxy.modal.hide(); + + var vis_id = $(this).val(); + dataset_params.id = vis_id; + + // add widget + parent.Galaxy.frame_manager.frame_new({ + title : "Trackster", + type : "url", + content : vis_url + "/trackster?" + $.param(dataset_params) + }); + }); + } + } + }); + }, + "View in new visualization": function(){ + // hide + parent.Galaxy.modal.hide(); + + var url = vis_url + "/trackster?" + $.param(dataset_params); - parent.show_modal( _l( "View Data in a New or Saved Visualization" ), "", { - "Cancel": function() { - parent.hide_modal(); - }, - "View in saved visualization": function() { - // Show new modal with saved visualizations. - parent.show_modal( _l( "Add Data to Saved Visualization" ), table_html, { - "Cancel": function() { - parent.hide_modal(); - }, - "Add to visualization": function() { - $(parent.document).find('input[name=id]:checked').each(function() { - var vis_id = $(this).val(); - dataset_params.id = vis_id; - - // hide modal - parent.hide_modal(); - - // add widget - Galaxy.frame_manager.frame_new( - { - title : "Trackster", - type : "url", - content : vis_url + "/trackster?" + $.param(dataset_params) - }); + // add widget + parent.Galaxy.frame_manager.frame_new({ + title : "Trackster", + type : "url", + content : url }); } - }); - }, - "View in new visualization": function() { - // hide modal - parent.hide_modal(); + } + }); + } + }); + return false; + }; + } - // add widget - Galaxy.frame_manager.frame_new( - { - title : "Trackster", - type : "url", - content : vis_url + "/trackster?" + $.param(dataset_params) - }); - } - }); - } - }); - return false; - }; -} //============================================================================== //return { diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e static/scripts/utils/config.js --- a/static/scripts/utils/config.js +++ b/static/scripts/utils/config.js @@ -245,9 +245,13 @@ if (this.$el.children().length === 0) { this.render(); } - show_modal("Configure", drawable.config.build_form(), { - "Cancel": cancel_fn, - "OK": ok_fn + Galaxy.modal.show({ + title: "Configure", + body: drawable.config.build_form(), + buttons: { + "Cancel": cancel_fn, + "OK": ok_fn + } }); }, diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e static/scripts/viz/trackster/filters.js --- a/static/scripts/viz/trackster/filters.js +++ b/static/scripts/viz/trackster/filters.js @@ -596,15 +596,19 @@ $.getJSON(run_tool_url, url_params, function(response) { if (response.error) { // General error. - show_modal("Filter Dataset", - "Error running tool " + tool_id, - { "Close" : hide_modal } ); + Galaxy.modal.show({ + title: "Filter Dataset", + body : "Error running tool " + tool_id, + buttons : { "Close" : Galaxy.modal.hide() } + }); } else if (filters.length === 0) { // No more filters to run. - show_modal("Filtering Dataset", - "Filter(s) are running on the complete dataset. Outputs are in dataset's history.", - { "Close" : hide_modal } ); + Galaxy.modal.show({ + title: "Filtering Dataset", + body: "Filter(s) are running on the complete dataset. Outputs are in dataset's history.", + buttons: { "Close" : Galaxy.modal.hide() } + }); } else { // More filters to run. diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -20,7 +20,47 @@ data: filters, error: function() { alert( "Grid failed" ); }, success: function(table_html) { - Galaxy.modal.show({ + show_modal( + "Select datasets for new tracks", + table_html, + { + "Cancel": function() { + hide_modal(); + }, + "Add": function() { + var requests = []; + $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { + var data = { + data_type: 'track_config', + 'hda_ldda': 'hda' + }, + id = $(this).val(); + if ($(this).attr("name") !== "id") { + data.hda_ldda = 'ldda'; + } + requests[requests.length] = $.ajax({ + url: add_track_async_url + "/" + id, + data: data, + dataType: "json" + }); + }); + // To preserve order, wait until there are definitions for all tracks and then add + // them sequentially. + $.when.apply($, requests).then(function() { + // jQuery always returns an Array for arguments, so need to look at first element + // to determine whether multiple requests were made and consequently how to + // map arguments to track definitions. + var track_defs = (arguments[0] instanceof Array ? + $.map(arguments, function(arg) { return arg[0]; }) : + [ arguments[0] ] + ); + success_fn(track_defs); + }); + hide_modal(); + } + } + ); + /*Galaxy.modal.show({ title : "Select datasets for new tracks", body : table_html, buttons : @@ -60,7 +100,7 @@ Galaxy.modal.hide(); } } - }); + });*/ } }); }; diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -102,10 +102,11 @@ }); ## load galaxy js-modules - require(['galaxy.master', 'galaxy.frame', 'galaxy.upload'], function(master, frame, upload) + require(['galaxy.master', 'galaxy.frame', 'galaxy.modal', 'galaxy.upload'], function(master, frame, modal, upload) { Galaxy.master = new master.GalaxyMaster(); Galaxy.frame_manager = new frame.GalaxyFrameManager(); + Galaxy.modal = new modal.GalaxyModal(); ##Galaxy.upload = new upload.GalaxyUpload(); }); </script> diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -63,7 +63,7 @@ <ul class="nav navbar-nav" border="0" cellspacing="0"> - <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='', menu_options=None )"> + <%def name="tab( id, display, href, onclick=False, target='_parent', visible=True, extra_class='', menu_options=None )"> ## Create a tab at the top of the panels. menu_options is a list of 2-elements lists of [name, link] ## that are options in the menu. @@ -100,7 +100,11 @@ ${menu_item[0]} %elif len ( menu_item ) == 2: <% name, link = menu_item %> - <a href="${link}">${name}</a> + %if onclick: + <a href="${link}" onclick="Galaxy.frame_manager.frame_new({title: '${name}', type: 'url', content: '${link}'}); return false;">${name}</a> + %else: + <a href="${link}">${name}</a> + %endif %else: <% name, link, target = menu_item %><a target="${target}" href="${link}">${name}</a> @@ -117,7 +121,7 @@ ${tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) )} ## Workflow tab. - ${tab( "workflow", _("Workflow"), "javascript:Galaxy.frame_manager.frame_new({title: 'Workflow', type: 'url', content: '" + h.url_for( controller='/workflow', action='index' ) + "'});")} + ${tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) )} ## 'Shared Items' or Libraries tab. <% @@ -147,10 +151,10 @@ ## Visualization menu. <% menu_options = [ - [_('New Track Browser'), "javascript:Galaxy.frame_manager.frame_new({title: 'Trackster', type: 'url', content: '" + h.url_for( controller='/visualization', action='trackster' ) + "'});"], - [_('Saved Visualizations'), "javascript:Galaxy.frame_manager.frame_new({ type: 'url', content : '" + h.url_for( controller='/visualization', action='list' ) + "'});" ] + [_('New Track Browser'), h.url_for( controller='/visualization', action='trackster' )], + [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' )] ] - tab( "visualization", _("Visualization"), "javascript:Galaxy.frame_manager.frame_new({title: 'Trackster', type: 'url', content: '" + h.url_for( controller='/visualization', action='list' ) + "'});", menu_options=menu_options ) + tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list' ), menu_options=menu_options, onclick=True ) %> ## Cloud menu. diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -152,6 +152,38 @@ </script></%def> +<%def name="overlay( title='', content='', visible=False )"> + <%def name="title()"></%def> + <%def name="content()"></%def> + + <% + if visible: + display = "style='display: block;'" + overlay_class = "in" + else: + display = "style='display: none;'" + overlay_class = "" + %> + + <div id="top-modal" class="modal fade ${overlay_class}" ${display}> + <div id="top-modal-backdrop" class="modal-backdrop fade ${overlay_class}" style="z-index: -1"></div> + <div id="top-modal-dialog" class="modal-dialog"> + <div class="modal-content"> + <div class="modal-header"> + <button type='button' class='close' style="display: none;">×</button> + <h4 class='title'>${title}</h4> + </div> + <div class="modal-body">${content}</div> + <div class="modal-footer"> + <div class="buttons" style="float: right;"></div> + <div class="extra_buttons" style=""></div> + <div style="clear: both;"></div> + </div> + </div> + </div> + </div> +</%def> + ## document <html><head> @@ -182,7 +214,7 @@ %if self.galaxy_config['message_box']: <div id="messagebox" class="panel-message"></div> %endif - + ${self.overlay()} ## left panel %if self.galaxy_config['left_panel']: <div id="left"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: activation config settings made better
by commits-noreply＠bitbucket.org 02 Oct '13

02 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0fc6c5554877/ Changeset: 0fc6c5554877 User: martenson Date: 2013-10-02 15:39:40 Summary: activation config settings made better Affected #: 3 files diff -r 0026e8e49df4273dc9bebcf3475e1873e5e808f3 -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -132,7 +132,7 @@ self.admin_users = kwargs.get( "admin_users", "" ) self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) - self.admin_email = kwargs.get( 'admin_email', None ) + self.activation_email = kwargs.get( 'activation_email', None ) self.user_activation_on = kwargs.get( 'user_activation_on', None ) self.activation_grace_period = kwargs.get( 'activation_grace_period', None ) self.inactivity_box_content = kwargs.get( 'inactivity_box_content', None ) @@ -143,10 +143,10 @@ if self.blacklist_location is not None: self.blacklist_file = resolve_path( kwargs.get( 'blacklist_file', None ), self.root ) try: - with open(self.blacklist_file) as blacklist: - self.blacklist_content = [ line.rstrip() for line in blacklist.readlines() ] + with open( self.blacklist_file ) as blacklist: + self.blacklist_content = [ line.rstrip() for line in blacklist.readlines() ] except IOError: - print ( "CONFIGURATION ERROR: Can't open supplied blacklist file from path: " + str( self.blacklist_file ) ) + print ( "CONFIGURATION ERROR: Can't open supplied blacklist file from path: " + str( self.blacklist_file ) ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None ) self.smtp_password = kwargs.get( 'smtp_password', None ) diff -r 0026e8e49df4273dc9bebcf3475e1873e5e808f3 -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -491,12 +491,12 @@ message = "No such user (please note that login is case sensitive)" elif user.deleted: message = "This account has been marked deleted, contact your local Galaxy administrator to restore the account." - if trans.app.config.admin_email is not None: - message += 'Contact: %s' % trans.app.config.admin_email + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to elif user.external: message = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it." - if trans.app.config.admin_email is not None: - message += 'Contact: %s' % trans.app.config.admin_email + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to elif not user.check_password( password ): message = "Invalid password" elif trans.app.config.user_activation_on and not user.active: # activation is ON and the user is INACTIVE @@ -536,8 +536,8 @@ message = 'This account has not been activated yet. The activation link has been sent again. Please check your email address %s.<br>' % email else: message = 'This account has not been activated yet but we are unable to send the activation link. Please contact your local Galaxy administrator.' - if trans.app.config.admin_email is not None: - message += 'Contact: %s' % trans.app.config.admin_email + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to return message def is_outside_grace_period ( self, trans, create_time ): @@ -591,8 +591,8 @@ is_admin = cntrller == 'admin' and trans.user_is_admin if not trans.app.config.allow_user_creation and not trans.user_is_admin(): message = 'User registration is disabled. Please contact your local Galaxy administrator for an account.' - if trans.app.config.admin_email is not None: - message += 'Contact: %s' % trans.app.config.admin_email + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to status = 'error' else: if not refresh_frames: @@ -733,8 +733,8 @@ success = True else: message = 'Unable to send activation email, please contact your local Galaxy administrator.' - if trans.app.config.admin_email is not None: - message += 'Contact: %s' % trans.app.config.admin_email + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to success = False else: # User activation is OFF, proceed without sending the activation email. message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) ) @@ -752,7 +752,7 @@ "Activation link: %s \n\n" "Your Galaxy Team" % ( email, activation_link )) to = email - frm = trans.app.config.admin_email + frm = trans.app.config.activation_email subject = 'How to activate your Galaxy account' try: util.send_mail( frm, to, subject, body, trans.app.config ) diff -r 0026e8e49df4273dc9bebcf3475e1873e5e808f3 -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -269,11 +269,11 @@ # Datasets in an error state include a link to report the error. Those reports # will be sent to this address. Error reports are disabled if no address is set. +# Also this email is shown as a contact to user in case of Galaxy misconfiguration and other events user may encounter. #error_email_to = None -# Administrator's email is shown to user in case of Galaxy misconfiguration or a generic error. -# It is also used as a sender for the account activation mail. -#admin_email = None +# Activation email is used as a sender ('from' field) for the account activation mail. +#activation_email = None # E-mail domains blacklist is used for filtering out users that are using disposable email address # during the registration. If their address domain matches any domain in the BL they are refused the registration. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Handle errors when attempting to set metadata on a tool shed repository that contains a file with a .ga extension but turns out to not be a valid exported Galaxy workflow.
by commits-noreply＠bitbucket.org 02 Oct '13

02 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0026e8e49df4/ Changeset: 0026e8e49df4 User: greg Date: 2013-10-02 15:17:52 Summary: Handle errors when attempting to set metadata on a tool shed repository that contains a file with a .ga extension but turns out to not be a valid exported Galaxy workflow. Affected #: 1 file diff -r e416f8c710b63d7fc9f682539929e9823c26f041 -r 0026e8e49df4273dc9bebcf3475e1873e5e808f3 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -710,8 +710,16 @@ fp = open( relative_path, 'rb' ) workflow_text = fp.read() fp.close() - exported_workflow_dict = json.from_json_string( workflow_text ) - if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + if workflow_text: + valid_exported_galaxy_workflow = True + try: + exported_workflow_dict = json.from_json_string( workflow_text ) + except Exception, e: + log.exception( "Skipping file %s since it does not seem to be a valid exported Galaxy workflow: %s" \ + % str( relative_path ), str( e ) ) + valid_exported_galaxy_workflow = False + if valid_exported_galaxy_workflow and \ + 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) # Handle any data manager entries metadata_dict = generate_data_manager_metadata( app, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Remove toolForm styling from response box in cloudlaunch; strip unused page styles
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e416f8c710b6/ Changeset: e416f8c710b6 User: dannon Date: 2013-10-01 23:32:17 Summary: Remove toolForm styling from response box in cloudlaunch; strip unused page styles Affected #: 1 file diff -r addd90e5adcd54cb5d78204093fba5519b95e059 -r e416f8c710b63d7fc9f682539929e9823c26f041 templates/webapps/galaxy/cloud/index.mako --- a/templates/webapps/galaxy/cloud/index.mako +++ b/templates/webapps/galaxy/cloud/index.mako @@ -13,41 +13,9 @@ ${parent.stylesheets()} ${h.css( "autocomplete_tagging" )} <style type="text/css"> - #new_history_p{ - line-height:2.5em; - margin:0em 0em .5em 0em; - } - #new_history_cbx{ - margin-right:.5em; - } - #new_history_input{ - display:none; - line-height:1em; - } - #ec_button_container{ - float:right; - } #hidden_options{ display:none; } - div.toolForm{ - margin-top: 10px; - margin-bottom: 10px; - } - div.toolFormTitle{ - cursor:pointer; - } - .title_ul_text{ - text-decoration:underline; - } - .step-annotation { - margin-top: 0.25em; - font-weight: normal; - font-size: 97%; - } - .workflow-annotation { - margin-bottom: 1em; - } #loading_indicator{ position:fixed; top:40px; @@ -285,7 +253,7 @@ </div></form></div> - <div id="responsePanel" class="toolForm" style="display:none;"> + <div id="responsePanel" style="display:none;"><div id="launchPending">Launch Pending, please be patient.</div><div id="launchSuccess" style="display:none;"><div id="keypairInfo" style="display:none;margin-bottom:20px;"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: style: Allow text in buttons to be wrapped
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/addd90e5adcd/ Changeset: addd90e5adcd User: james_taylor Date: 2013-10-01 22:55:54 Summary: style: Allow text in buttons to be wrapped Affected #: 3 files diff -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 -r addd90e5adcd54cb5d78204093fba5519b95e059 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -753,6 +753,7 @@ .affix{position:fixed} .navbar-fixed-top .navbar-brand{font-family:Verdana;font-weight:bold;font-size:160%} pre{overflow:auto;word-wrap:normal;white-space:pre} +.btn{white-space:normal} .dropdown-menu{max-width:auto} input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex} .modal-dialog{width:690px} @@ -1219,7 +1220,7 @@ select,input,textarea{font:inherit} .form-row select,.form-row textarea,.form-row input[type="text"],.form-row input[type="file"],.form-row input[type="password"]{max-width:90%} textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:1.428571429;border:1px solid #aaa;padding:3px} -input[type="submit"],button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}input[type="submit"]:focus,button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} +input[type="submit"],button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;white-space:normal;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}input[type="submit"]:focus,button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} input[type="submit"]:hover,button:hover,input[type="submit"]:focus,button:focus{color:#333;text-decoration:none} input[type="submit"]:active,button:active,input[type="submit"].active,button.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],button[disabled],fieldset[disabled] input[type="submit"],fieldset[disabled] button{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} @@ -1323,7 +1324,7 @@ .state-fg-ok{color:#66AA66} .state-fg-error{color:#AA6666} .state-fg-deleted{color:#3399FF} -button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} +button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;white-space:normal;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} button:hover,button:focus{color:#333;text-decoration:none} button:active,button.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} button.disabled,button[disabled],fieldset[disabled] button{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} @@ -1333,7 +1334,7 @@ button:hover,button:focus,button:active,button.active,.open .dropdown-togglebutton{color:#333;background-color:#dedede;border-color:#a1a1a1} button:active,button.active,.open .dropdown-togglebutton{background-image:none} button.disabled,button[disabled],fieldset[disabled] button,button.disabled:hover,button[disabled]:hover,fieldset[disabled] button:hover,button.disabled:focus,button[disabled]:focus,fieldset[disabled] button:focus,button.disabled:active,button[disabled]:active,fieldset[disabled] button:active,button.disabled.active,button[disabled].active,fieldset[disabled] button.active{background-color:#f2f2f2;border-color:#bfbfbf} -.action-button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}.action-button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} +.action-button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;white-space:normal;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}.action-button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} .action-button:hover,.action-button:focus{color:#333;text-decoration:none} .action-button:active,.action-button.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} .action-button.disabled,.action-button[disabled],fieldset[disabled] .action-button{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} @@ -1346,7 +1347,7 @@ a.action-button{color:#333;text-decoration:none} .action-button>img{vertical-align:middle} .action-button:active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} -.menubutton{padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;border:1px solid transparent;border-radius:3px;white-space:nowrap;user-select:none;color:#333;background-color:#f2f2f2;border-color:#bfbfbf;display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none}.menubutton:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} +.menubutton{padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;border:1px solid transparent;border-radius:3px;white-space:nowrap;user-select:none;white-space:normal;color:#333;background-color:#f2f2f2;border-color:#bfbfbf;display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none}.menubutton:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} .menubutton:hover,.menubutton:focus{color:#333;text-decoration:none} .menubutton:active,.menubutton.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} .menubutton.disabled,.menubutton[disabled],fieldset[disabled] .menubutton{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} @@ -1361,7 +1362,7 @@ .menubutton a{text-decoration:none} .menubutton .label,.menubutton>label{position:relative;display:inline-block;border-right:none;text-decoration:none;text-align:left;max-height:2.857142858;line-height:1.428571429;overflow:hidden;text-overflow:ellipsis} .menubutton.popup .label{border-right:solid #bfbfbf 1px;padding-right:6px} -.menubutton.popup,.menubutton.popup.split{padding-right:18px}.menubutton.popup:after,.menubutton.popup.split:after{margin-top:6px;position:absolute;right:6px;display:inline-block;width:0;height:0;margin-left:2px;vertical-align:middle;border-top:4px solid #000;border-right:4px solid transparent;border-left:4px solid transparent;border-bottom:0 dotted;content:""}.btn-default .menubutton.popup:after,.btn-default .menubutton.popup.split:after{border-top-color:#333} +.menubutton.popup,.menubutton.popup.split{padding-right:18px}.menubutton.popup:after,.menubutton.popup.split:after{top:45%;position:absolute;right:6px;display:inline-block;width:0;height:0;margin-left:2px;vertical-align:middle;border-top:4px solid #000;border-right:4px solid transparent;border-left:4px solid transparent;border-bottom:0 dotted;content:""}.btn-default .menubutton.popup:after,.btn-default .menubutton.popup.split:after{border-top-color:#333} .btn-primary .menubutton.popup:after,.btn-primary .menubutton.popup.split:after,.btn-success .menubutton.popup:after,.btn-success .menubutton.popup.split:after,.btn-warning .menubutton.popup:after,.btn-warning .menubutton.popup.split:after,.btn-danger .menubutton.popup:after,.btn-danger .menubutton.popup.split:after,.btn-info .menubutton.popup:after,.btn-info .menubutton.popup.split:after{border-top-color:#fff} div.popmenu-wrapper{position:absolute;top:100%;z-index:20000}div.popmenu-wrapper ul.dropdown-menu{display:block;position:relative;float:none} ul.dropdown-menu a{text-decoration:none} diff -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 -r addd90e5adcd54cb5d78204093fba5519b95e059 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -1229,7 +1229,7 @@ &.popup, &.popup.split { padding-right: 18px; &:after { - margin-top: 6px; + top: 45%; position: absolute; right: 6px; .caret(); diff -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 -r addd90e5adcd54cb5d78204093fba5519b95e059 static/style/src/less/galaxy_bootstrap/overrides.less --- a/static/style/src/less/galaxy_bootstrap/overrides.less +++ b/static/style/src/less/galaxy_bootstrap/overrides.less @@ -11,11 +11,15 @@ white-space: pre; } - .btn.hover { @btn:hover(); } +// Allow text in buttons to wrap +.btn { + white-space: normal; +} + .dropdown-menu { max-width: auto; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dadd5cd688ff/ Changeset: dadd5cd688ff User: dannon Date: 2013-10-01 14:19:42 Summary: Fix tab in RequestIDMiddleware Affected #: 1 file diff -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 -r dadd5cd688ff53b50bdf01304acfb75f96b8e408 lib/galaxy/web/framework/middleware/request_id.py --- a/lib/galaxy/web/framework/middleware/request_id.py +++ b/lib/galaxy/web/framework/middleware/request_id.py @@ -8,5 +8,5 @@ def __init__( self, app, global_conf=None ): self.app = app def __call__( self, environ, start_response ): - environ['request_id'] = uuid.uuid1().hex - return self.app( environ, start_response ) \ No newline at end of file + environ['request_id'] = uuid.uuid1().hex + return self.app( environ, start_response ) https://bitbucket.org/galaxy/galaxy-central/commits/a5764a397a98/ Changeset: a5764a397a98 User: dannon Date: 2013-10-01 21:56:26 Summary: Force send_redirect to encode the url as utf-8. This should resolve all uwsgi unicode issues Affected #: 1 file diff -r dadd5cd688ff53b50bdf01304acfb75f96b8e408 -r a5764a397a989eb30e890d974c04f877ff169b0b lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py +++ b/lib/galaxy/web/framework/base.py @@ -379,7 +379,7 @@ """ Send an HTTP redirect response to (target `url`) """ - raise httpexceptions.HTTPFound( url, headers=self.wsgi_headeritems() ) + raise httpexceptions.HTTPFound( url.encode('utf-8'), headers=self.wsgi_headeritems() ) def wsgi_headeritems( self ): """ https://bitbucket.org/galaxy/galaxy-central/commits/1d49fb745d2f/ Changeset: 1d49fb745d2f User: dannon Date: 2013-10-01 21:56:34 Summary: Merge Affected #: 46 files diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -15,6 +15,13 @@ deprecated_tip_str = '' return '<img src="/static/images/icon_error_sml.gif" %s/>' % deprecated_tip_str +def generate_includes_workflows_img_str( include_mouse_over=False ): + if include_mouse_over: + deprecated_tip_str = 'class="icon-button" title="This repository contains exported workflows"' + else: + deprecated_tip_str = '' + return '<img src="/static/images/fugue/gear.png" %s/>' % deprecated_tip_str + def generate_latest_revision_img_str( include_mouse_over=False ): if include_mouse_over: latest_revision_tip_str = 'class="icon-button" title="This is the latest installable revision of this repository"' @@ -60,6 +67,8 @@ tool_shed_status_str += generate_revision_updates_img_str( include_mouse_over=True ) if tool_shed_repository.upgrade_available: tool_shed_status_str += generate_revision_upgrades_img_str( include_mouse_over=True ) + if tool_shed_repository.includes_workflows: + tool_shed_status_str += generate_includes_workflows_img_str( include_mouse_over=True ) else: tool_shed_status_str = generate_unknown_img_str( include_mouse_over=True ) return tool_shed_status_str @@ -211,7 +220,11 @@ use_paging = False def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ) + return trans.sa_session.query( self.model_class ) \ + .order_by( self.model_class.table.c.tool_shed, + self.model_class.table.c.name, + self.model_class.table.c.owner, + self.model_class.table.c.ctx_rev ) @property def legend( self ): @@ -219,6 +232,7 @@ legend_str += '%s  A newer installable revision is available for this repository<br/>' % generate_revision_upgrades_img_str() legend_str += '%s  This is the latest installable revision of this repository<br/>' % generate_latest_revision_img_str() legend_str += '%s  This repository is deprecated in the Tool Shed<br/>' % generate_deprecated_repository_img_str() + legend_str += '%s  This repository contains exported workflows<br/>' % generate_includes_workflows_img_str() legend_str += '%s  Unable to get information from the Tool Shed<br/>' % generate_unknown_img_str() return legend_str diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -133,7 +133,7 @@ # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision> relative_clone_dir = os.path.join( self.tool_shed, 'repos', owner, name, changeset_revision ) clone_dir = os.path.join( self.tool_path, relative_clone_dir ) - if not self.__isinstalled( clone_dir ): + if not self.__iscloned( clone_dir ): repository_clone_url = os.path.join( self.tool_shed_url, 'repos', owner, name ) relative_install_dir = os.path.join( relative_clone_dir, name ) install_dir = os.path.join( clone_dir, name ) @@ -478,7 +478,15 @@ tool_shed_repository.name, tool_shed_repository.installed_changeset_revision ) clone_dir = os.path.join( self.tool_path, relative_clone_dir ) - if self.__isinstalled( clone_dir ): + cloned_ok = self.__iscloned( clone_dir ) + is_installed = False + # Any of the following states should count as installed in this context. + if tool_shed_repository.status in [ self.app.model.ToolShedRepository.installation_status.INSTALLED, + self.app.model.ToolShedRepository.installation_status.ERROR, + self.app.model.ToolShedRepository.installation_status.UNINSTALLED, + self.app.model.ToolShedRepository.installation_status.DEACTIVATED ]: + is_installed = True + if cloned_ok and is_installed: print "Skipping automatic install of repository '", tool_shed_repository.name, "' because it has already been installed in location ", clone_dir else: repository_clone_url = os.path.join( self.tool_shed_url, 'repos', tool_shed_repository.owner, tool_shed_repository.name ) @@ -489,9 +497,10 @@ tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) - suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) - cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) - if cloned_ok: + if not cloned_ok: + suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) + cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) + if cloned_ok and not is_installed: self.handle_repository_contents( tool_shed_repository=tool_shed_repository, repository_clone_url=repository_clone_url, relative_install_dir=relative_install_dir, @@ -592,7 +601,7 @@ return True return False - def __isinstalled( self, clone_dir ): + def __iscloned( self, clone_dir ): full_path = os.path.abspath( clone_dir ) if os.path.exists( full_path ): for root, dirs, files in os.walk( full_path ): diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py --- a/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py +++ b/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py @@ -6,45 +6,49 @@ 3: Compute Motif Frequencies For All Motifs motif by motif 4: Compute Motif Frequencies in indel flanking regions 5: CTD analysis of chemicals, diseases, or genes -6: Delete Overlapping Indels from a chromosome indels file -7: Separate pgSnp alleles into columns -8: Draw Stacked Bar Plots for different categories and different criteria -9: Length Distribution chart -10: FASTA Width formatter -11: RNA/DNA converter -12: Draw quality score boxplot -13: Quality format converter (ASCII-Numeric) -14: Filter by quality -15: FASTQ to FASTA converter -16: Remove sequencing artifacts -17: Barcode Splitter -18: Clip adapter sequences -19: Collapse sequences -20: Draw nucleotides distribution chart -21: Compute quality statistics -22: Rename sequences -23: Reverse- Complement -24: Trim sequences -25: FunDO human genes associated with disease terms -26: HVIS visualization of genomic data with the Hilbert curve -27: Fetch Indels from 3-way alignments -28: Identify microsatellite births and deaths -29: Extract orthologous microsatellites for multiple (>2) species alignments -30: Mutate Codons with SNPs -31: Pileup-to-Interval condenses pileup format into ranges of bases -32: Filter pileup on coverage and SNPs -33: Filter SAM on bitwise flag values -34: Merge BAM Files merges BAM files together -35: Generate pileup from BAM dataset -36: SAM-to-BAM converts SAM format to BAM format -37: Convert SAM to interval -38: flagstat provides simple stats on BAM files -39: MPileup SNP and indel caller -40: rmdup remove PCR duplicates -41: Slice BAM by provided regions -42: Split paired end reads -43: T Test for Two Samples -44: Plotting tool for multiple series and graph types. +6: Cuffcompare +7: Cuffdiff +8: Cufflinks +9: Cuffmerge +10: Delete Overlapping Indels from a chromosome indels file +11: Separate pgSnp alleles into columns +12: Draw Stacked Bar Plots for different categories and different criteria +13: Length Distribution chart +14: FASTA Width formatter +15: RNA/DNA converter +16: Draw quality score boxplot +17: Quality format converter (ASCII-Numeric) +18: Filter by quality +19: FASTQ to FASTA converter +20: Remove sequencing artifacts +21: Barcode Splitter +22: Clip adapter sequences +23: Collapse sequences +24: Draw nucleotides distribution chart +25: Compute quality statistics +26: Rename sequences +27: Reverse- Complement +28: Trim sequences +29: FunDO human genes associated with disease terms +30: HVIS visualization of genomic data with the Hilbert curve +31: Fetch Indels from 3-way alignments +32: Identify microsatellite births and deaths +33: Extract orthologous microsatellites for multiple (>2) species alignments +34: Mutate Codons with SNPs +35: Pileup-to-Interval condenses pileup format into ranges of bases +36: Filter pileup on coverage and SNPs +37: Filter SAM on bitwise flag values +38: Merge BAM Files merges BAM files together +39: Generate pileup from BAM dataset +40: SAM-to-BAM converts SAM format to BAM format +41: Convert SAM to interval +42: flagstat provides simple stats on BAM files +43: MPileup SNP and indel caller +44: rmdup remove PCR duplicates +45: Slice BAM by provided regions +46: Split paired end reads +47: T Test for Two Samples +48: Plotting tool for multiple series and graph types. The tools are now available in the repositories respectively: @@ -53,45 +57,49 @@ 3: compute_motif_frequencies_for_all_motifs 4: compute_motifs_frequency 5: ctd_batch -6: delete_overlapping_indels -7: divide_pg_snp -8: draw_stacked_barplots -9: fasta_clipping_histogram -10: fasta_formatter -11: fasta_nucleotide_changer -12: fastq_quality_boxplot -13: fastq_quality_converter -14: fastq_quality_filter -15: fastq_to_fasta -16: fastx_artifacts_filter -17: fastx_barcode_splitter -18: fastx_clipper -19: fastx_collapser -20: fastx_nucleotides_distribution -21: fastx_quality_statistics -22: fastx_renamer -23: fastx_reverse_complement -24: fastx_trimmer -25: hgv_fundo -26: hgv_hilbertvis -27: indels_3way -28: microsatellite_birthdeath -29: multispecies_orthologous_microsats -30: mutate_snp_codon -31: pileup_interval -32: pileup_parser -33: sam_bitwise_flag_filter -34: sam_merge -35: sam_pileup -36: sam_to_bam -37: sam2interval -38: samtools_flagstat -39: samtools_mpileup -40: samtools_rmdup -41: samtools_slice_bam -42: split_paired_reads -43: t_test_two_samples -44: xy_plot +6: cuffcompare +7: cuffdiff +8: cufflinks +9: cuffmerge +10: delete_overlapping_indels +11: divide_pg_snp +12: draw_stacked_barplots +13: fasta_clipping_histogram +14: fasta_formatter +15: fasta_nucleotide_changer +16: fastq_quality_boxplot +17: fastq_quality_converter +18: fastq_quality_filter +19: fastq_to_fasta +20: fastx_artifacts_filter +21: fastx_barcode_splitter +22: fastx_clipper +23: fastx_collapser +24: fastx_nucleotides_distribution +25: fastx_quality_statistics +26: fastx_renamer +27: fastx_reverse_complement +28: fastx_trimmer +29: hgv_fundo +30: hgv_hilbertvis +31: indels_3way +32: microsatellite_birthdeath +33: multispecies_orthologous_microsats +34: mutate_snp_codon +35: pileup_interval +36: pileup_parser +37: sam_bitwise_flag_filter +38: sam_merge +39: sam_pileup +40: sam_to_bam +41: sam2interval +42: samtools_flagstat +43: samtools_mpileup +44: samtools_rmdup +45: samtools_slice_bam +46: split_paired_reads +47: t_test_two_samples +48: xy_plot from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -352,6 +352,10 @@ updating_installed_repository=False, persist=True ) tool_shed_repository.metadata = metadata_dict + # Update the tool_shed_repository.tool_shed_status column in the database. + tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( trans.app, tool_shed_repository ) + if tool_shed_status_dict: + tool_shed_repository.tool_shed_status = tool_shed_status_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() if 'tool_dependencies' in metadata_dict and not reinstalling: diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -272,7 +272,11 @@ with lcd( current_dir ): action_type, action_dict = action_tup if action_type == 'make_directory': - td_common_util.make_directory( full_path=action_dict[ 'full_path' ] ) + if os.path.isabs( action_dict[ 'full_path' ] ): + full_path = action_dict[ 'full_path' ] + else: + full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) + td_common_util.make_directory( full_path=full_path ) elif action_type == 'move_directory_files': td_common_util.move_directory_files( current_dir=current_dir, source_dir=os.path.join( action_dict[ 'source_directory' ] ), diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 scripts/migrate_tools/0008_tools.xml --- a/scripts/migrate_tools/0008_tools.xml +++ b/scripts/migrate_tools/0008_tools.xml @@ -15,6 +15,18 @@ <repository owner="devteam" changeset_revision="4a32700dcaa2" name="ctd_batch" description="Galaxy wrappers for the tool CTD: analysis of chemicals, diseases, or genes"><tool id="ctdBatch_1" version="1.0.0" file="ctd.xml" /></repository> + <repository owner="devteam" changeset_revision="9a3f7a890da6" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool."> + <tool id="cuffcompare" version="0.0.5" file="cuffcompare_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="0dabb2ed6eb1" name="cuffdiff" description="Galaxy wrappers for the Cuffdiff tool."> + <tool id="cuffdiff" version="0.0.6" file="cuffdiff_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="b01956f26c36" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool."> + <tool id="cufflinks" version="0.0.6" file="cufflinks_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="fdc55fd74f78" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool."> + <tool id="cuffmerge" version="0.0.5" file="cuffmerge_wrapper.xml" /> + </repository><repository owner="devteam" changeset_revision="f16000dc644b" name="delete_overlapping_indels" description="Galaxy wrappers for the tool Delete Overlapping Indels: from a chromosome indels file"><tool id="delete_overlapping_indels" version="1.0.0" file="delete_overlapping_indels.xml" /></repository> diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 templates/admin/review_tool_migration_stages.mako --- a/templates/admin/review_tool_migration_stages.mako +++ b/templates/admin/review_tool_migration_stages.mako @@ -35,6 +35,7 @@ </p></div><table class="grid"> + <% from tool_shed.util.shed_util_common import to_html_string %> %for stage in migration_stages_dict.keys(): <% migration_command = 'sh ./scripts/migrate_tools/%04d_tools.sh' % stage @@ -54,7 +55,7 @@ <tr><td bgcolor="#FFFFCC"><div class="form-row"> - <p>${migration_info} <b>Run commands from the Galaxy installation directory!</b></p> + <p>${to_html_string(migration_info)} <b>Run commands from the Galaxy installation directory!</b></p><p> %if tool_dependencies: This migration stage includes tools that have tool dependencies that can be automatically installed. To install them, run:<br/> diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffcompare_in2.gtf --- a/test-data/cuffcompare_in2.gtf +++ /dev/null @@ -1,100 +0,0 @@ -chr1 Cufflinks transcript 3174766 3174792 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3174766 3174792 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3187402 3187428 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3187402 3187428 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3188522 3188548 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672"; -chr1 Cufflinks exon 3188522 3188548 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672"; -chr1 Cufflinks transcript 3190859 3191434 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500"; -chr1 Cufflinks exon 3190859 3191434 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500"; -chr1 Cufflinks transcript 3191513 3192077 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341"; -chr1 Cufflinks exon 3191513 3192077 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341"; -chr1 Cufflinks transcript 3189811 3190789 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804"; -chr1 Cufflinks exon 3189811 3190789 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804"; -chr1 Cufflinks transcript 3192251 3192336 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; -chr1 Cufflinks exon 3192251 3192336 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; -chr1 Cufflinks transcript 3192650 3192676 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3192650 3192676 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3194707 3194733 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3194707 3194733 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3197426 3197452 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3197426 3197452 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3200431 3200457 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3200431 3200457 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3200057 3200144 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455"; -chr1 Cufflinks exon 3200057 3200144 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455"; -chr1 Cufflinks transcript 3201161 3201187 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3201161 3201187 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3201008 3201039 1000 . . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; -chr1 Cufflinks exon 3201008 3201039 1000 . . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; -chr1 Cufflinks transcript 3201597 3201666 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429"; -chr1 Cufflinks exon 3201597 3201666 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429"; -chr1 Cufflinks transcript 3201726 3201809 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714"; -chr1 Cufflinks exon 3201726 3201809 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714"; -chr1 Cufflinks transcript 3211522 3211561 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; -chr1 Cufflinks exon 3211522 3211561 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; -chr1 Cufflinks transcript 3212718 3212801 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857"; -chr1 Cufflinks exon 3212718 3212801 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857"; -chr1 Cufflinks transcript 3213119 3213242 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226"; -chr1 Cufflinks exon 3213119 3213242 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226"; -chr1 Cufflinks transcript 3240607 3240633 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks exon 3240607 3240633 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks transcript 3242480 3242512 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545"; -chr1 Cufflinks exon 3242480 3242512 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545"; -chr1 Cufflinks transcript 3242925 3243005 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333"; -chr1 Cufflinks exon 3242925 3243005 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333"; -chr1 Cufflinks transcript 3243109 3243154 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913"; -chr1 Cufflinks exon 3243109 3243154 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913"; -chr1 Cufflinks transcript 3254080 3254106 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3254080 3254106 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3277156 3277182 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3277156 3277182 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3277914 3278390 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057"; -chr1 Cufflinks exon 3277914 3278390 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057"; -chr1 Cufflinks transcript 3280118 3280144 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks exon 3280118 3280144 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks transcript 3280499 3280525 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3280499 3280525 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3282505 3282531 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3282505 3282531 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3282651 3282677 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3282651 3282677 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3282761 3282832 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000"; -chr1 Cufflinks exon 3282761 3282832 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000"; -chr1 Cufflinks transcript 3284967 3284993 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3284967 3284993 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3290799 3290859 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492"; -chr1 Cufflinks exon 3290799 3290859 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492"; -chr1 Cufflinks transcript 3299444 3299640 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700"; -chr1 Cufflinks exon 3299444 3299640 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700"; -chr1 Cufflinks transcript 3290920 3291273 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797"; -chr1 Cufflinks exon 3290920 3291273 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797"; -chr1 Cufflinks transcript 3299692 3299733 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714"; -chr1 Cufflinks exon 3299692 3299733 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714"; -chr1 Cufflinks transcript 3307749 3307775 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3307749 3307775 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3318621 3318647 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks exon 3318621 3318647 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks transcript 3330528 3330554 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; -chr1 Cufflinks exon 3330528 3330554 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; -chr1 Cufflinks transcript 3351241 3351311 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; -chr1 Cufflinks exon 3351241 3351311 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; -chr1 Cufflinks transcript 3355908 3356119 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792"; -chr1 Cufflinks exon 3355908 3356119 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792"; -chr1 Cufflinks transcript 3356181 3356225 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000"; -chr1 Cufflinks exon 3356181 3356225 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000"; -chr1 Cufflinks transcript 3363077 3363176 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000"; -chr1 Cufflinks exon 3363077 3363176 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000"; -chr1 Cufflinks transcript 3363388 3363446 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881"; -chr1 Cufflinks exon 3363388 3363446 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881"; -chr1 Cufflinks transcript 3364872 3364919 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500"; -chr1 Cufflinks exon 3364872 3364919 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500"; -chr1 Cufflinks transcript 3367211 3367237 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3367211 3367237 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3369581 3369607 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3369581 3369607 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3375002 3375028 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3375002 3375028 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3379889 3379915 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3379889 3379915 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3386740 3386836 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402"; -chr1 Cufflinks exon 3386740 3386836 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402"; diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffcompare_in3.gtf --- a/test-data/cuffcompare_in3.gtf +++ /dev/null @@ -1,100 +0,0 @@ -chr1 mm9_refFlat stop_codon 3206103 3206105 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat CDS 3206106 3207049 0.000000 - 2 gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat exon 3204563 3207049 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat CDS 3411783 3411982 0.000000 - 1 gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat exon 3411783 3411982 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat CDS 3660633 3661429 0.000000 - 0 gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat start_codon 3661427 3661429 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat exon 3660633 3661579 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat stop_codon 4334681 4334683 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat CDS 4334684 4340172 0.000000 - 2 gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4334224 4340172 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat CDS 4341991 4342162 0.000000 - 0 gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4341991 4342162 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat CDS 4342283 4342906 0.000000 - 0 gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat start_codon 4342904 4342906 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4342283 4342918 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4350281 4350473 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat stop_codon 4481797 4481799 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat CDS 4481800 4482749 0.000000 - 2 gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4481009 4482749 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat CDS 4483181 4483487 0.000000 - 0 gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat start_codon 4483485 4483487 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4483181 4483547 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4483853 4483944 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4485217 4486023 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4486372 4486494 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat stop_codon 4766545 4766547 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4766548 4766882 0.000000 - 2 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4763279 4766882 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4767606 4767729 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4772649 4772814 0.000000 - 1 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4774032 4774186 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4774032 4774186 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4775654 4775758 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat start_codon 4775756 4775758 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat stop_codon 4764533 4764535 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4764536 4764597 0.000000 - 2 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4763279 4764597 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4767606 4767729 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4772649 4772814 0.000000 - 1 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4774032 4774186 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4774032 4774186 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4775654 4775758 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat start_codon 4775756 4775758 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4763279 4764597 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat start_codon 4797995 4797997 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4797995 4798063 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4797974 4798063 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4798536 4798567 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4798536 4798567 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4818665 4818730 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4818665 4818730 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4820349 4820396 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4820349 4820396 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4822392 4822462 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4822392 4822462 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4827082 4827155 0.000000 + 2 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4827082 4827155 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4829468 4829569 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4829468 4829569 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4831037 4831213 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4831037 4831213 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4835044 4835094 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat stop_codon 4835095 4835097 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4835044 4836816 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat start_codon 4847995 4847997 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4847995 4848057 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4847775 4848057 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4857551 4857613 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4857551 4857613 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4868108 4868213 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4868108 4868213 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4876825 4876912 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4876825 4876912 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4879538 4879683 0.000000 + 1 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4879538 4879683 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4880821 4880877 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4880821 4880877 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4881996 4882150 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4881996 4882150 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4883498 4883644 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4883498 4883644 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4885015 4885086 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4885015 4885086 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4886437 4886442 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat stop_codon 4886443 4886445 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4886437 4887987 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat start_codon 4847995 4847997 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; -chr1 mm9_refFlat CDS 4847995 4848057 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1_dup1"; -chr1 mm9_refFlat exon 4847775 4848057 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; -chr1 mm9_refFlat CDS 4857551 4857613 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1_dup1"; diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffcompare_out1.tmap --- a/test-data/cuffcompare_out1.tmap +++ /dev/null @@ -1,51 +0,0 @@ -ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 - -Xkr4 Xkr4 c CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 3634 -Xkr4 Xkr4 i CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 3634 -Xkr4 Xkr4 i CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 3634 -Xkr4 Xkr4 i CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 3634 -Xkr4 Xkr4 i CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 3634 -Xkr4 Xkr4 i CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 3634 -Xkr4 Xkr4 i CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 3634 -Xkr4 Xkr4 i CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 3634 -- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 - -- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 - -- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 - -- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 - -- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 - -- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 - -- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 - -- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 - -- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 - -- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 - -- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 - -- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 - -- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 - -- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 - -- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 - -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 3634 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 3634 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 3634 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 3634 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 3634 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 3634 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 3634 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 3634 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 3634 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 3634 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 3634 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 3634 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 3634 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 3634 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 3634 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 3634 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 3634 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 3634 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 3634 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 3634 diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffcompare_out2.refmap --- a/test-data/cuffcompare_out2.refmap +++ /dev/null @@ -1,2 +0,0 @@ -ref_gene_id ref_id class_code cuff_id_list -Xkr4 Xkr4 c CUFF.13|CUFF.13.1 diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffcompare_out3.tmap --- a/test-data/cuffcompare_out3.tmap +++ /dev/null @@ -1,51 +0,0 @@ -ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 - -- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 - -- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 - -- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 - -- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 - -- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 - -- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 - -- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 - -- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 - -- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 - -Xkr4 Xkr4 i CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 3634 -Xkr4 Xkr4 i CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 3634 -Xkr4 Xkr4 i CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 3634 -Xkr4 Xkr4 i CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 3634 -Xkr4 Xkr4 i CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 3634 -Xkr4 Xkr4 i CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 3634 -Xkr4 Xkr4 i CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 3634 -Xkr4 Xkr4 i CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 3634 -Xkr4 Xkr4 i CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 3634 -Xkr4 Xkr4 i CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 3634 -Xkr4 Xkr4 i CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 3634 -Xkr4 Xkr4 i CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 3634 -Xkr4 Xkr4 i CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 3634 -Xkr4 Xkr4 i CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 3634 -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 3634 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 3634 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 3634 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 3634 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 3634 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 3634 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 3634 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 3634 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 3634 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 3634 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 3634 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 3634 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 3634 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 3634 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 3634 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 3634 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 3634 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 3634 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 3634 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 3634 diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffcompare_out4.refmap --- a/test-data/cuffcompare_out4.refmap +++ /dev/null @@ -1,1 +0,0 @@ -ref_gene_id ref_id class_code cuff_id_list diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffcompare_out5.gtf --- a/test-data/cuffcompare_out5.gtf +++ /dev/null @@ -1,90 +0,0 @@ -chr1 Cufflinks exon 3204755 3204833 . - . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.13.1"; nearest_ref "Xkr4"; class_code "c"; tss_id "TSS1"; -chr1 Cufflinks exon 3111450 3111490 . . . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2"; -chr1 Cufflinks exon 3111546 3111576 . . . gene_id "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3"; -chr1 Cufflinks exon 3174766 3174792 . . . gene_id "XLOC_000004"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS4"; -chr1 Cufflinks exon 3187402 3187428 . . . gene_id "XLOC_000005"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS5"; -chr1 Cufflinks exon 3188522 3188548 . . . gene_id "XLOC_000006"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS6"; -chr1 Cufflinks exon 3189811 3190789 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS7"; -chr1 Cufflinks exon 3190859 3191434 . . . gene_id "XLOC_000008"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS10"; -chr1 Cufflinks exon 3191513 3192077 . . . gene_id "XLOC_000009"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS11"; -chr1 Cufflinks exon 3192251 3192336 . . . gene_id "XLOC_000010"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS13"; -chr1 Cufflinks exon 3192442 3192494 . . . gene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; tss_id "TSS14"; -chr1 Cufflinks exon 3192551 3192629 . . . gene_id "XLOC_000012"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; tss_id "TSS15"; -chr1 Cufflinks exon 3192650 3192676 . . . gene_id "XLOC_000013"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS16"; -chr1 Cufflinks exon 3192732 3192811 . . . gene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; tss_id "TSS17"; -chr1 Cufflinks exon 3192941 3193042 . . . gene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; tss_id "TSS18"; -chr1 Cufflinks exon 3194186 3194226 . . . gene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; tss_id "TSS19"; -chr1 Cufflinks exon 3194303 3194329 . . . gene_id "XLOC_000017"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; tss_id "TSS20"; -chr1 Cufflinks exon 3194707 3194733 . . . gene_id "XLOC_000018"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS21"; -chr1 Cufflinks exon 3195084 3195110 . . . gene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; tss_id "TSS22"; -chr1 Cufflinks exon 3195451 3195477 . . . gene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; tss_id "TSS23"; -chr1 Cufflinks exon 3197090 3197116 . . . gene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; tss_id "TSS24"; -chr1 Cufflinks exon 3197247 3197273 . . . gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS25"; -chr1 Cufflinks exon 3197347 3197373 . . . gene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS26"; -chr1 Cufflinks exon 3197426 3197452 . . . gene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS27"; -chr1 Cufflinks exon 3200023 3200191 . . . gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS28"; -chr1 Cufflinks exon 3200326 3200352 . . . gene_id "XLOC_000026"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29"; -chr1 Cufflinks exon 3200431 3200457 . . . gene_id "XLOC_000027"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30"; -chr1 Cufflinks exon 3201008 3201039 . . . gene_id "XLOC_000028"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31"; -chr1 Cufflinks exon 3201078 3201481 . . . gene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS32"; -chr1 Cufflinks exon 3201597 3201666 . . . gene_id "XLOC_000030"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33"; -chr1 Cufflinks exon 3201673 3201699 . . . gene_id "XLOC_000031"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34"; -chr1 Cufflinks exon 3201726 3201809 . . . gene_id "XLOC_000032"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35"; -chr1 Cufflinks exon 3211522 3211561 . . . gene_id "XLOC_000033"; transcript_id "TCONS_00000067"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS36"; -chr1 Cufflinks exon 3212214 3212292 . . . gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.15.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS37"; -chr1 Cufflinks exon 3212368 3212439 . . . gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.19.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS38"; -chr1 Cufflinks exon 3212718 3212801 . . . gene_id "XLOC_000036"; transcript_id "TCONS_00000068"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS39"; -chr1 Cufflinks exon 3213096 3213192 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.17.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40"; -chr1 Cufflinks exon 3213119 3213242 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000069"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.37.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40"; -chr1 Cufflinks exon 3240607 3240633 . . . gene_id "XLOC_000038"; transcript_id "TCONS_00000070"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.39.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS41"; -chr1 Cufflinks exon 3242480 3242512 . . . gene_id "XLOC_000039"; transcript_id "TCONS_00000071"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.41.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS42"; -chr1 Cufflinks exon 3242634 3242923 . . . gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.25.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS43"; -chr1 Cufflinks exon 3242925 3243005 . . . gene_id "XLOC_000041"; transcript_id "TCONS_00000072"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.43.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS44"; -chr1 Cufflinks exon 3243019 3243079 . . . gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.21.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS45"; -chr1 Cufflinks exon 3243109 3243154 . . . gene_id "XLOC_000043"; transcript_id "TCONS_00000073"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.45.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS46"; -chr1 Cufflinks exon 3243348 3243401 . . . gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.23.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS47"; -chr1 Cufflinks exon 3254080 3254106 . . . gene_id "XLOC_000045"; transcript_id "TCONS_00000074"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.47.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS48"; -chr1 Cufflinks exon 3256975 3257011 . . . gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.27.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS49"; -chr1 Cufflinks exon 3277156 3277182 . . . gene_id "XLOC_000047"; transcript_id "TCONS_00000075"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.49.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS50"; -chr1 Cufflinks exon 3277191 3277218 . . . gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS51"; -chr1 Cufflinks exon 3277914 3278390 . . . gene_id "XLOC_000049"; transcript_id "TCONS_00000076"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.51.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS52"; -chr1 Cufflinks exon 3280118 3280144 . . . gene_id "XLOC_000050"; transcript_id "TCONS_00000077"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.53.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS54"; -chr1 Cufflinks exon 3280499 3280525 . . . gene_id "XLOC_000051"; transcript_id "TCONS_00000078"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.55.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS55"; -chr1 Cufflinks exon 3280687 3280741 . . . gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS56"; -chr1 Cufflinks exon 3282505 3282531 . . . gene_id "XLOC_000053"; transcript_id "TCONS_00000079"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.57.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS57"; -chr1 Cufflinks exon 3282651 3282677 . . . gene_id "XLOC_000054"; transcript_id "TCONS_00000080"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.59.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS58"; -chr1 Cufflinks exon 3282761 3282832 . . . gene_id "XLOC_000055"; transcript_id "TCONS_00000081"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS59"; -chr1 Cufflinks exon 3284967 3284993 . . . gene_id "XLOC_000056"; transcript_id "TCONS_00000082"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS60"; -chr1 Cufflinks exon 3290489 3290553 . . . gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS61"; -chr1 Cufflinks exon 3290799 3290859 . . . gene_id "XLOC_000058"; transcript_id "TCONS_00000083"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS62"; -chr1 Cufflinks exon 3290920 3291273 . . . gene_id "XLOC_000059"; transcript_id "TCONS_00000084"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS63"; -chr1 Cufflinks exon 3299444 3299640 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000085"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS65"; -chr1 Cufflinks exon 3299610 3299664 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS66"; -chr1 Cufflinks exon 3299692 3299733 . . . gene_id "XLOC_000061"; transcript_id "TCONS_00000086"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS67"; -chr1 Cufflinks exon 3300052 3300078 . . . gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS68"; -chr1 Cufflinks exon 3307749 3307775 . . . gene_id "XLOC_000063"; transcript_id "TCONS_00000087"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS69"; -chr1 Cufflinks exon 3318621 3318647 . . . gene_id "XLOC_000064"; transcript_id "TCONS_00000088"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS70"; -chr1 Cufflinks exon 3319000 3319051 . . . gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS71"; -chr1 Cufflinks exon 3330528 3330554 . . . gene_id "XLOC_000066"; transcript_id "TCONS_00000089"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS72"; -chr1 Cufflinks exon 3351241 3351311 . . . gene_id "XLOC_000067"; transcript_id "TCONS_00000090"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS73"; -chr1 Cufflinks exon 3355888 3355914 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74"; -chr1 Cufflinks exon 3355908 3356119 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000091"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74"; -chr1 Cufflinks exon 3356181 3356225 . . . gene_id "XLOC_000069"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS75"; -chr1 Cufflinks exon 3363077 3363176 . . . gene_id "XLOC_000070"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS76"; -chr1 Cufflinks exon 3363215 3363278 . . . gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS77"; -chr1 Cufflinks exon 3363388 3363446 . . . gene_id "XLOC_000072"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78"; -chr1 Cufflinks exon 3363754 3363849 . . . gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS79"; -chr1 Cufflinks exon 3364872 3364919 . . . gene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80"; -chr1 Cufflinks exon 3367136 3367162 . . . gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS81"; -chr1 Cufflinks exon 3367211 3367237 . . . gene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82"; -chr1 Cufflinks exon 3367334 3367382 . . . gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS83"; -chr1 Cufflinks exon 3369581 3369607 . . . gene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84"; -chr1 Cufflinks exon 3375002 3375028 . . . gene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85"; -chr1 Cufflinks exon 3377212 3377262 . . . gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS86"; -chr1 Cufflinks exon 3379889 3379915 . . . gene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87"; -chr1 Cufflinks exon 3386740 3386836 . . . gene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88"; -chr1 Cufflinks exon 3391326 3391352 . . . gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS89"; -chr1 Cufflinks exon 3435842 3435880 . . . gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS90"; -chr1 Cufflinks exon 3447762 3447788 . . . gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS91"; -chr1 Cufflinks exon 3450907 3450965 . . . gene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS92"; -chr1 Cufflinks exon 3451052 3451109 . . . gene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS93"; diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffcompare_out6.tracking --- a/test-data/cuffcompare_out6.tracking +++ /dev/null @@ -1,100 +0,0 @@ -TCONS_00000001 XLOC_000001 Xkr4|Xkr4 c q1:CUFF.13|CUFF.13.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000002 XLOC_000002 - u q1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000003 XLOC_000003 - u q1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|- - -TCONS_00000004 XLOC_000007 - u q1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|- - -TCONS_00000005 XLOC_000007 - u q1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|- - -TCONS_00000006 XLOC_000007 - u q1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|- - -TCONS_00000007 XLOC_000009 - u q1:CUFF.35|CUFF.35.1|100|96.747183|61.420107|132.074259|6.183206|- - -TCONS_00000008 XLOC_000009 - u q1:CUFF.37|CUFF.37.1|100|104.085013|53.596365|154.573660|6.652174|- - -TCONS_00000009 XLOC_000011 - u q1:CUFF.39|CUFF.39.1|100|23.912983|0.000000|51.525317|1.528302|- - -TCONS_00000010 XLOC_000012 - u q1:CUFF.41|CUFF.41.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000011 XLOC_000014 - u q1:CUFF.43|CUFF.43.1|100|10.561567|0.000000|25.497879|0.675000|- - -TCONS_00000012 XLOC_000015 - u q1:CUFF.45|CUFF.45.1|100|20.708956|2.186303|39.231609|1.323529|- - -TCONS_00000013 XLOC_000016 - u q1:CUFF.47|CUFF.47.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000014 XLOC_000017 - u q1:CUFF.49|CUFF.49.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000015 XLOC_000019 - u q1:CUFF.51|CUFF.51.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000016 XLOC_000020 - u q1:CUFF.53|CUFF.53.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000017 XLOC_000021 - u q1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000018 XLOC_000022 - u q1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000019 XLOC_000023 - u q1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000020 XLOC_000025 - u q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|- - -TCONS_00000021 XLOC_000026 - u q1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000022 XLOC_000029 - u q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|- - -TCONS_00000023 XLOC_000031 - u q1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000024 XLOC_000034 Xkr4|Xkr4 i q1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000025 XLOC_000035 Xkr4|Xkr4 i q1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|- - -TCONS_00000026 XLOC_000037 Xkr4|Xkr4 i q1:CUFF.17|CUFF.17.1|100|8.710571|0.000000|21.029179|0.556701|- - -TCONS_00000027 XLOC_000040 Xkr4|Xkr4 i q1:CUFF.25|CUFF.25.1|100|14.567679|5.354270|23.781089|0.931034|- - -TCONS_00000028 XLOC_000042 Xkr4|Xkr4 i q1:CUFF.21|CUFF.21.1|100|13.851236|0.000000|33.439842|0.885246|- - -TCONS_00000029 XLOC_000044 Xkr4|Xkr4 i q1:CUFF.23|CUFF.23.1|100|23.470150|0.000000|50.571145|1.500000|- - -TCONS_00000030 XLOC_000046 Xkr4|Xkr4 i q1:CUFF.27|CUFF.27.1|100|34.253732|0.000000|73.806535|2.189189|- - -TCONS_00000031 XLOC_000048 Xkr4|Xkr4 i q1:CUFF.61|CUFF.61.1|100|45.263860|0.000000|97.530065|2.892857|- - -TCONS_00000032 XLOC_000049 Xkr4|Xkr4 i q1:CUFF.63|CUFF.63.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000033 XLOC_000052 Xkr4|Xkr4 i q1:CUFF.65|CUFF.65.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000034 XLOC_000057 Xkr4|Xkr4 i q1:CUFF.67|CUFF.67.1|100|12.998852|0.000000|31.382005|0.830769|- - -TCONS_00000035 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.69|CUFF.69.1|100|10.058636|0.000000|24.283695|0.642857|- - -TCONS_00000036 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.71|CUFF.71.1|100|8.621688|0.000000|20.814595|0.551020|- - -TCONS_00000037 XLOC_000060 Xkr4|Xkr4 i q1:CUFF.73|CUFF.73.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000038 XLOC_000062 Xkr4|Xkr4 i q1:CUFF.75|CUFF.75.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000039 XLOC_000065 Xkr4|Xkr4 i q1:CUFF.77|CUFF.77.1|100|16.248565|0.000000|39.227507|1.038462|- - -TCONS_00000040 XLOC_000068 Xkr4|Xkr4 i q1:CUFF.79|CUFF.79.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000041 XLOC_000071 Xkr4|Xkr4 i q1:CUFF.81|CUFF.81.1|100|13.201959|0.000000|31.872349|0.843750|- - -TCONS_00000042 XLOC_000073 Xkr4|Xkr4 i q1:CUFF.83|CUFF.83.1|100|13.201959|0.000000|28.446269|0.843750|- - -TCONS_00000043 XLOC_000075 Xkr4|Xkr4 i q1:CUFF.85|CUFF.85.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000044 XLOC_000077 Xkr4|Xkr4 i q1:CUFF.87|CUFF.87.1|100|17.243375|0.000000|41.629191|1.102041|- - -TCONS_00000045 XLOC_000080 Xkr4|Xkr4 i q1:CUFF.89|CUFF.89.1|100|16.567165|0.000000|39.996674|1.058824|- - -TCONS_00000046 XLOC_000083 Xkr4|Xkr4 i q1:CUFF.91|CUFF.91.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000047 XLOC_000084 Xkr4|Xkr4 i q1:CUFF.93|CUFF.93.1|100|21.664754|0.000000|52.303342|1.384615|- - -TCONS_00000048 XLOC_000085 Xkr4|Xkr4 i q1:CUFF.95|CUFF.95.1|100|46.940300|0.000000|101.142289|3.000000|- - -TCONS_00000049 XLOC_000086 Xkr4|Xkr4 i q1:CUFF.97|CUFF.97.1|100|21.481154|0.000000|46.285454|1.372881|- - -TCONS_00000050 XLOC_000087 Xkr4|Xkr4 i q1:CUFF.99|CUFF.99.1|100|14.567679|0.000000|35.169489|0.931034|- - -TCONS_00000051 XLOC_000004 - u - q2:CUFF.1|CUFF.1.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000052 XLOC_000005 - u - q2:CUFF.3|CUFF.3.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000053 XLOC_000006 - u - q2:CUFF.5|CUFF.5.1|100|21.226627|0.000000|59.889707|1.205672|- -TCONS_00000054 XLOC_000007 - u - q2:CUFF.11|CUFF.11.1|100|32.531777|24.582998|40.480555|1.847804|- -TCONS_00000055 XLOC_000008 - u - q2:CUFF.7|CUFF.7.1|100|29.709524|19.806349|39.612698|1.687500|- -TCONS_00000056 XLOC_000009 - u - q2:CUFF.9|CUFF.9.1|100|34.072933|23.364686|44.781179|1.935341|- -TCONS_00000057 XLOC_000010 - u - q2:CUFF.13|CUFF.13.1|100|16.582060|0.000000|35.729373|0.941860|- -TCONS_00000058 XLOC_000013 - u - q2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000059 XLOC_000018 - u - q2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000060 XLOC_000024 - u - q2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000061 XLOC_000025 - u - q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|- -TCONS_00000062 XLOC_000027 - u - q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000063 XLOC_000028 - u - q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|- -TCONS_00000064 XLOC_000029 - u - q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000065 XLOC_000030 - u - q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|- -TCONS_00000066 XLOC_000032 - u - q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|- -TCONS_00000067 XLOC_000033 Xkr4|Xkr4 i - q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|- -TCONS_00000068 XLOC_000036 Xkr4|Xkr4 i - q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|- -TCONS_00000069 XLOC_000037 Xkr4|Xkr4 i - q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|- -TCONS_00000070 XLOC_000038 Xkr4|Xkr4 i - q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000071 XLOC_000039 Xkr4|Xkr4 i - q2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|- -TCONS_00000072 XLOC_000041 Xkr4|Xkr4 i - q2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|- -TCONS_00000073 XLOC_000043 Xkr4|Xkr4 i - q2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|- -TCONS_00000074 XLOC_000045 Xkr4|Xkr4 i - q2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000075 XLOC_000047 Xkr4|Xkr4 i - q2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000076 XLOC_000049 Xkr4|Xkr4 i - q2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|- -TCONS_00000077 XLOC_000050 Xkr4|Xkr4 i - q2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000078 XLOC_000051 Xkr4|Xkr4 i - q2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000079 XLOC_000053 Xkr4|Xkr4 i - q2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000080 XLOC_000054 Xkr4|Xkr4 i - q2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000081 XLOC_000055 Xkr4|Xkr4 i - q2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|- -TCONS_00000082 XLOC_000056 Xkr4|Xkr4 i - q2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000083 XLOC_000058 Xkr4|Xkr4 i - q2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|- -TCONS_00000084 XLOC_000059 Xkr4|Xkr4 i - q2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|- -TCONS_00000085 XLOC_000060 Xkr4|Xkr4 i - q2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|- -TCONS_00000086 XLOC_000061 Xkr4|Xkr4 i - q2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|- -TCONS_00000087 XLOC_000063 Xkr4|Xkr4 i - q2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000088 XLOC_000064 Xkr4|Xkr4 i - q2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000089 XLOC_000066 Xkr4|Xkr4 i - q2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|- -TCONS_00000090 XLOC_000067 Xkr4|Xkr4 i - q2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|- -TCONS_00000091 XLOC_000068 Xkr4|Xkr4 i - q2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|- -TCONS_00000092 XLOC_000069 Xkr4|Xkr4 i - q2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|- -TCONS_00000093 XLOC_000070 Xkr4|Xkr4 i - q2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|- -TCONS_00000094 XLOC_000072 Xkr4|Xkr4 i - q2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|- -TCONS_00000095 XLOC_000074 Xkr4|Xkr4 i - q2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|- -TCONS_00000096 XLOC_000076 Xkr4|Xkr4 i - q2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000097 XLOC_000078 Xkr4|Xkr4 i - q2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000098 XLOC_000079 Xkr4|Xkr4 i - q2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000099 XLOC_000081 Xkr4|Xkr4 i - q2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000100 XLOC_000082 Xkr4|Xkr4 i - q2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|- diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffcompare_out7.txt --- a/test-data/cuffcompare_out7.txt +++ /dev/null @@ -1,33 +0,0 @@ -# Cuffcompare v2.0.2 | Command line was: -#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/002/dataset_2770.dat -R ./input1 ./input2 -# - -#= Summary for dataset: ./input1 : -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) -# (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 1 in 1 loci (1 multi-exon) -# Corresponding super-loci: 1 -#--------------------| Sn | Sp | fSn | fSp - Base level: 2.2 2.3 - - - Exon level: 0.0 0.0 0.0 0.0 - Intron level: 0.0 nan 0.0 nan -Intron chain level: 0.0 nan 0.0 nan - Transcript level: 0.0 0.0 0.0 0.0 - Locus level: 0.0 0.0 0.0 0.0 - -Matching intron chains: 0 - Matching loci: 0 - - Missed exons: 2/3 ( 66.7%) - Novel exons: 49/50 ( 98.0%) - Missed introns: 2/2 (100.0%) - Missed loci: 0/1 ( 0.0%) - Novel loci: 49/50 ( 98.0%) - -#= Summary for dataset: ./input2 : -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) -# (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 0 in 0 loci (0 multi-exon) - - Total union super-loci across all input datasets: 87 - (0 multi-transcript, ~1.1 transcripts per locus) diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffdiff_in1.sam --- a/test-data/cuffdiff_in1.sam +++ /dev/null @@ -1,400 +0,0 @@ -EAS38_8_212_338_985 0 chr1 3004981 0 35M * 0 0 CCAATGGGCCTCTATTTGCAGTGATGGGCGAGTAG hhhhhhhhhhhhhEhhhhYhhhhUhhh@Ih?BZ?e NM:i:2 -EAS38_8_8_215_414 0 chr1 3035356 0 35M * 0 0 TACCCCATAAAAGCCCCTGGCTTTCGCGCCTCGTG hhhhhhhhhhhhhhhhhhhhhhh`GI>PPIQPBOH NM:i:1 -EAS38_8_8_622_393 16 chr1 3065512 0 35M * 0 0 AAAAAAAAAAAAACAAAAAAAAAAAAAACAGCGAG hhHhhhhhhhhhhMhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_53_557_326 16 chr1 3075162 0 35M * 0 0 TAGAGAAATGGATACAGAAAGTGTGGTAATTTACA Ihehhhhh]hhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_259_911_538 0 chr1 3099409 0 35M * 0 0 TTTGGCTGGGAGACAATTAATGACTGCTTTTTTTT hhhhhhhhhhhh_hhhhhNhhP\hhaEhhHhNhhh NM:i:2 -EAS38_8_284_729_569 16 chr1 3113004 255 35M * 0 0 CTATCTGTTGCAAAGAGAACTTTCCTTGGTGTAAG EIIEKhRh@K_hahhhhhhh`ehhhhhhhhhhhhh NM:i:0 -EAS38_8_27_537_242 0 chr1 3118613 255 35M * 0 0 AGGACTCACATTCCCTTACTTTGTTTACAAAATGA hhh`hhhhhhhhhhhhhhhhhhhhhh]hhYXOhD` NM:i:0 -EAS38_8_38_947_12 0 chr1 3131368 0 35M * 0 0 TATTAGTCCCCTATCANATTTAGGATTGTTAATAA hhhhhhh_bchhhhUh;\hhhhh`EXcIVhNJZ]P NM:i:2 -EAS38_8_205_433_879 16 chr1 3136988 0 35M * 0 0 CATATCAATTGAACGGAACTAAAGTCTGTGACAGT hhhhchhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_155_191_162 16 chr1 3136999 0 35M * 0 0 AACGGAACTAAAGTCTGTGACAGTGGACATAGCTG hh_h\hhYhhhhhMhfhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_216_635_828 0 chr1 3137063 0 35M * 0 0 ATCTGGAATTATGTGATTATAATTTTCTTAGCATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_317_949_784 0 chr1 3137063 0 35M * 0 0 ATCTGGAATTATGTGATTATAATTTTCTTAGCATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhNchh NM:i:0 -EAS38_8_278_281_786 16 chr1 3137078 0 35M * 0 0 ATTATAATTTTCTTAGCATTTTCTTTGTAAAAAAA AhhhQhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_228_462_705 0 chr1 3137133 0 35M * 0 0 GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA hhhhhhhhhhhhhhhhhhh_hghhWhYh`LhhKbY NM:i:0 -EAS38_8_299_582_840 0 chr1 3137133 0 35M * 0 0 GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhWhhhhh NM:i:0 -EAS38_8_125_742_683 16 chr1 3137135 0 35M * 0 0 TGGTGTATAGTAAAAAGTAAAGAAATTCTGAGAGG GJCZSShchhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_208_212_874 0 chr1 3137137 0 35M * 0 0 GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG hhhhhhhhhhhhhhhhhhhhhhhhh[hhhhhhh`h NM:i:0 -EAS38_8_241_424_62 16 chr1 3137137 0 35M * 0 0 GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG hhhhhhhhehhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_245_195_910 16 chr1 3137137 0 35M * 0 0 GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG Bhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_234_890_706 0 chr1 3137138 0 35M * 0 0 TGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAGT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhUhh NM:i:0 -EAS38_8_317_909_810 16 chr1 3137175 0 35M * 0 0 TATTTTAGGATAATACATATATACATATGCAGTGT hhhhhhhaThhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_111_444_456 0 chr1 3137180 0 35M * 0 0 TAGGTTAATACATATATACATATGCAGTGTGTGTG hhhhhhhhhhhhhhhhhhhahhhhhhhhgehhhhH NM:i:1 -EAS38_8_134_193_731 0 chr1 3137180 0 35M * 0 0 TAGGATAATACATATATACATATGCAGTGTGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_138_869_374 0 chr1 3137180 0 35M * 0 0 TAGGATAATACATATATACATATGCAGTGTGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_36_257_907 0 chr1 3137192 0 35M * 0 0 TATATACATATGCAGTGTGTGTGCCAGTGGTGTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhNJDhS NM:i:0 -EAS38_8_50_322_852 0 chr1 3137192 0 35M * 0 0 TATATACATATGCAGTGTGTGTGCCAGTGGTGTTA hhhhhhhhhhhhhhhhhhhhhhhRcZhhhhVhShY NM:i:0 -EAS38_8_207_430_640 16 chr1 3146524 0 35M * 0 0 AAAAAACATCGGCACAACAATCAAAAAAAAAAAAA VE_AhhhhFhhhhh]hhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_289_914_684 0 chr1 3154024 255 35M * 0 0 TCACAGAAGGCTCACTTCCTTTCTGTCTGTGTCAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhdhhMGT NM:i:0 -EAS38_8_35_737_747 16 chr1 3174758 255 35M * 0 0 TTTTGGGTGAGATGGAATCTCAGAGTAGTTATTTT [hghdhMhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_75_492_572 16 chr1 3174758 255 35M * 0 0 TTTTGGGTGAGATGGAATCTCAGAGTAGTTATTTT [Vhhh^hhhhhhhhhhhdhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_187_160_172 16 chr1 3175562 255 35M * 0 0 TAGTCTGGTCTGTGGCTTCAGCGGTAGGATGGCCT BT\JAGMQVRN[QhYZGchhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_56_600_894 0 chr1 3175828 255 35M * 0 0 GAGAAAGAGGTGGGAAGGGAAAGAGAGAGAGAAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhShChDKhI NM:i:0 -EAS38_8_106_467_709 16 chr1 3181781 255 35M * 0 0 CTTTAGTACAGGTTACATTCCATACCTATAGCAAG hhhhhhhhhhh`hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_199_476_527 16 chr1 3181781 255 35M * 0 0 CTTTAGTACAGGTTACATTCCATACCTATAGCAAG E[dbhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_116_967_124 16 chr1 3187134 255 35M * 0 0 ATAGCTCTTCATCTAGGGGTGGGACTTTTGAGATT hghYhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_182_44_990 16 chr1 3187394 255 35M * 0 0 GAAATGCTCATTCTCATAGAGAAGAGATTGCCTAG EhhhaKhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_203_996_132 16 chr1 3187394 255 35M * 0 0 GAAATGATCATTCTCATAGAGAAGAGATTGCCTAG JXJ`_eFVVhhhhhchhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_318_612_118 0 chr1 3188522 255 35M * 0 0 GTATTCTTAATCTATTGTGTTTTGTTTGTTCTTTG hhhhhhhhhhhhhhhhhhShhhhIhhhWhh_hYhC NM:i:1 -EAS38_8_52_573_715 16 chr1 3188914 255 35M * 0 0 TTTGGAAGATAGTTTTCATTTCAGGACTGTCATTA hh]hDhh\hhhghhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_82_668_114 16 chr1 3189123 255 35M * 0 0 TAGATTCTGTTGAAAGCTGCTTGTGTAGGTGCTGG Jhfheh@_Nh`hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_229_732_980 16 chr1 3189293 255 35M * 0 0 ATATGTAGAAAAAGAAAGCAATTAGATGTATCATA hhhhWhhOhhhhhghhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_49_685_15 0 chr1 3189811 255 35M * 0 0 CTTTTAAAATGACCACAGTGTACTTTATTTAATTA hhhhhhhhhhhhhhhhhhhhhhhhhh]hhhPahZQ NM:i:2 -EAS38_8_228_500_937 0 chr1 3189812 255 35M * 0 0 TTTTAAAATGACCACAGTGTACTTTATTTAATGAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhLh NM:i:1 -EAS38_8_8_865_653 0 chr1 3189812 255 35M * 0 0 TTTTAAAATGACCACAGTGTACTTTATTTAATGAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_284_550_449 0 chr1 3189815 255 35M * 0 0 TGAAATGACCACAGTGTACTTTATTTAATGATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPhhhh NM:i:1 -EAS38_8_44_493_707 0 chr1 3189839 255 35M * 0 0 TTAATGATTTTTGTACTTTGTGTTGCAATAAAATA hhhhhhhhhhhhhhhhhhhhhhhhRhhhhhhhhhh NM:i:0 -EAS38_8_173_339_743 0 chr1 3189847 255 35M * 0 0 TTTTGTACTTTGTGTTGCAATAAAATAAAAAAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZhhhf NM:i:0 -EAS38_8_69_320_425 16 chr1 3189862 255 35M * 0 0 TGAAATAAAAAAAAAAAAAAATCTACAAAATTCAA _OahhShhhhAhhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_253_215_784 0 chr1 3189882 255 35M * 0 0 ATCTACAAAATTCAAATATATAAAATTTCAAGTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_254_492_492 0 chr1 3189882 255 35M * 0 0 ATCTACAAAATTCAAATATATAAAATTTCAAGTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhhhh NM:i:0 -EAS38_8_164_969_744 0 chr1 3189884 255 35M * 0 0 CTACAAAATTCAAATATATAAAATTTCAAGTTTTC hhhhhhhhhhhhhhhhhhhhhVhhWhTNchDhhgA NM:i:0 -EAS38_8_76_118_672 0 chr1 3189938 255 35M * 0 0 AGAAAAAAAATCAGATAACCGAGGAAAATTATTCA hhhhhhhhhhhhhhhhhhhhhhhh]hhhhhThhR] NM:i:0 -EAS38_8_322_903_184 16 chr1 3189967 255 35M * 0 0 TATTCATTATGAAGTACTACTTTCCACTTCATTTC O[ENehNVh`ahh]hhhhhhWhhhhhhhhhhhhhh NM:i:0 -EAS38_8_122_863_114 16 chr1 3189975 255 35M * 0 0 ATGAAGTACTACTTTCCACTTCATTTCATCACAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_328_905_544 0 chr1 3189975 255 35M * 0 0 ATGAAGTACTACTTTCCACTTCATTTCATCACAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhXhO NM:i:0 -EAS38_8_49_611_982 16 chr1 3189991 255 35M * 0 0 CACTTCATTTCATCACAAATTGTAACTTACTTAAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_149_471_590 0 chr1 3189993 255 35M * 0 0 CTTCATTTCATCACAAATTGTAACTTACTTAACTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhc NM:i:0 -EAS38_8_176_471_461 0 chr1 3189993 255 35M * 0 0 CTTCATTTCATCACAAATTGTAACTTACTTAACTG hhhhhhhhhhhhhhhhhhhhhhchhh`hhh[hhhO NM:i:0 -EAS38_8_330_91_472 16 chr1 3189999 255 35M * 0 0 TTAATCACAAATTGTAACTTACTTAACTGACCAAA hhOhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_330_964_788 16 chr1 3189999 255 35M * 0 0 TTCATCACAAATTGTAACTTACTTAACTGACCAAA aIhhhh`hhhhhhhhhhhhhBhhhhhhhchhhhhh NM:i:0 -EAS38_8_281_200_582 16 chr1 3190038 255 35M * 0 0 CTATGGTACTGCAGTATAGAAAATACTCCACACAC ONK[MhhhdhhQhhhhhhhMhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_241_125_175 16 chr1 3190056 255 35M * 0 0 GAAAATAATCCACACACTGTGCTTTGAGCTAGAGC HhhhhShIhhShhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_274_895_968 0 chr1 3190074 255 35M * 0 0 GTGCTTTGAGCTAGAGCACTTGGAGTCACTGCACA hhhhhhhhhhhhhhhhPhOhhhhPhhMTMXhLBMC NM:i:1 -EAS38_8_274_589_297 16 chr1 3190081 255 35M * 0 0 GAGCTAGAGCACTGGGAGTCACTGCCCAGGGCAGC ]W_IHUh_hh^WZDhhhhKhhh[hhhhhhhhhhhh NM:i:1 -EAS38_8_11_418_433 0 chr1 3190094 255 35M * 0 0 TGGAGTCACTGCCCAGGGCAGCAGCCTCCAACCAA hhhhhhhhhhhhhhhhhhbCchhb`PUPhJWIOGA NM:i:0 -EAS38_8_324_436_604 16 chr1 3190136 255 35M * 0 0 ACACTTACAAGTTGAATTCTAAAGGAAGGTCTGGT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_131_262_425 16 chr1 3190137 255 35M * 0 0 CACGTACAAGTTGAATTCTAAAGGAAGGTCTGGTT dVKEhhhhhhhWhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_5_661_318 16 chr1 3190137 255 35M * 0 0 CACTTACAAGTTGAATTCTAAAGGAAGGTCTGGTT F^O_ZhhhhhAhhhhhMh`hhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_109_581_805 0 chr1 3190144 255 35M * 0 0 AAGTTGAATTCTAAAGGAAGGTCTGGTTATGTGGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_279_908_963 0 chr1 3190154 255 35M * 0 0 CTAAAGGAAGGTCTGGTTATGTGGGGTTGGAATAT hhhhhhhhhhhhhhhhhhhhhhhhhhDhhhRDEhH NM:i:0 -EAS38_8_207_793_649 16 chr1 3190155 255 35M * 0 0 TAAAGGAAGGTCTGGTTATGTGGGGTTGGAATATG FThTO[ZcIHRhhShhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_249_136_550 0 chr1 3190167 255 35M * 0 0 TGGTTATGTGGGGTTGGAATATGTATATCTATATA hhhhhhhhhhhhhhhhhghhhhhhhhhhhhDhJhh NM:i:0 -EAS38_8_197_214_431 16 chr1 3190168 255 35M * 0 0 GGTTATGTGGGGTTGGAATATGTATATCTATATAT EUEU@QhJhhVgFUhhhhPhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_124_625_963 16 chr1 3190174 255 35M * 0 0 GTGGGGTTGGAATATGTATATCTATATATCTCTAT ]hdTChhhXhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_314_668_328 16 chr1 3190176 255 35M * 0 0 GGGGTTGGAATATGTATATCTATATATCTCTATAT hhhh]]hhhhOh_hhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_8_247_406 16 chr1 3190176 255 35M * 0 0 GGGGTTGGAATATGTATATCTATATATCTCTATAT fY]NUFQQhhVcRhhhhhhehhhhhhhhhhhhhhh NM:i:0 -EAS38_8_45_380_957 16 chr1 3190191 255 35M * 0 0 ATATCTATATATCTCTATATATATTTACATCAAAG hhhVhbhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_224_453_647 16 chr1 3190214 255 35M * 0 0 TTTACATCAAAGAATTTAATAACTCATTTAAATTT hKhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_120_914_892 0 chr1 3190236 255 35M * 0 0 CTCATTTAAATTTTTGTTTCAAATAAAATTCCAAA hhhhhhhhhhhhhhhhhhhhhhhhhhfhhhLWh]K NM:i:0 -EAS38_8_8_442_670 0 chr1 3190258 255 35M * 0 0 ATAAAATTCCAAATACATTTGTACAATGTTTACAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhRhhTe_\ NM:i:0 -EAS38_8_245_767_298 16 chr1 3190284 255 35M * 0 0 TGTTTACAAAGTAAGAGACAGGACTGGCAGGTTTG WOF`hhhhhhhbhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_94_374_121 16 chr1 3190284 255 35M * 0 0 TGTTTACAAAGTAAGAGACAGGACTGGCAGGTTTG Shh`hhRhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_256_414_787 0 chr1 3190333 255 35M * 0 0 CACCGTGATGTCCGGGTGATATATCTTCACGTTGC hhhhhhhhhhhhhhhhdhchhhhh`hhJRBhfhhJ NM:i:0 -EAS38_8_215_417_539 16 chr1 3190353 255 35M * 0 0 ATATCTTCACGTTGCCTGCACACACCTTATTTCTG VAHGh@XhBhhhRhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_167_839_349 0 chr1 3190379 255 35M * 0 0 TTATTTCTGAAATGGAGAGAGAAACTCAAGAATGT hhhhhhhhhhhhhhhhhhhhhdhhhhhPhhDhhCh NM:i:0 -EAS38_8_235_344_488 0 chr1 3190402 255 35M * 0 0 ACTCAAGAATGTCACCGACTATGCATCAGAATACT hhhhhhhhhhhhhhhhhLhhhhbfhGUILPJQQPL NM:i:0 -EAS38_8_287_803_220 0 chr1 3190402 255 35M * 0 0 ACTCAAGAATGTCACCGACTATGCATCAGAATACT hhhhhhhhhhhhhhhhhhhhhhhhdhgTMVEh\^N NM:i:0 -EAS38_8_23_488_181 16 chr1 3190434 255 35M * 0 0 ACTATGTACAGTTGAAGTTAGGGAGCTGAGAACCT hChhhhOhhhhgUhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_137_662_459 16 chr1 3190469 255 35M * 0 0 AGTGTTCTGTTCTCTTCTGGTTTGTCTTCATCTAC eOKeGUhIhVhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_228_762_237 16 chr1 3190469 255 35M * 0 0 AGTGGTCTGTTCTCTTCTGGTTTGTCTTCATCTAC ZhMhbWK\hgShShhhh^hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_65_836_536 16 chr1 3190469 255 35M * 0 0 AGTGTTCTGTTCTCTTCTGGTTTGTCTTCATCTAC ahYhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_100_122_849 0 chr1 3190545 255 35M * 0 0 CAAACATTGGAAAGAGGAAGGAGAAAAACACAAAA hhhhhhhhhhhhhhhhhhhhhXhhhhhhCdM[TUh NM:i:1 -EAS38_8_172_157_846 16 chr1 3190553 255 35M * 0 0 GGAAAGAGGAAGGAGAAAAGTACAAAATATTTAAG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_166_123_980 16 chr1 3190565 255 35M * 0 0 GAGAAAAGCACAAAATATTTAAGGCAAATTAAGCA FhThhhhLhhhhhhhhhhhhhhhbhhhhhhhhhhh NM:i:0 -EAS38_8_202_25_949 16 chr1 3190601 255 35M * 0 0 ATATGTATAGTCTCTTTGTGCCAGGAGGATGTGAC OKTX@[hhdGVhVhhhhMhdhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_135_382_764 0 chr1 3190604 255 35M * 0 0 TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT hhhhhhhhhhhhhhhhhhhhhhhhhOhhhhYHhhh NM:i:0 -EAS38_8_256_748_407 16 chr1 3190604 255 35M * 0 0 TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT RWEhhhhZhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_328_369_595 0 chr1 3190604 255 35M * 0 0 TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT hhhhhhhhhhhhhhhhhhhhhhhhhFahJORXhhh NM:i:0 -EAS38_8_13_985_934 16 chr1 3190609 255 35M * 0 0 AGTCTCTTTGTGCCAGGAGGATGTGACTTTCTTTT STZhQhhUhcdhhhhdSh^Zhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_13_657_254 0 chr1 3190659 255 35M * 0 0 GCTTTAAAAAATTCAAATAAAGCAAGTCTGGTGTG hhhhhhhhhhhhhhhhhhhhhhhhZhhhhhYh]h\ NM:i:0 -EAS38_8_97_368_634 0 chr1 3190659 255 35M * 0 0 GCTTTAAAAAATTCAAATAAAGCAAGTCTGGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_158_637_333 0 chr1 3190697 255 35M * 0 0 TGGGTTGCTTGTGTTGTTTTAATTTTTTTTGAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh@ZMhQ NM:i:0 -EAS38_8_7_431_889 0 chr1 3190697 255 35M * 0 0 TGGGTTGCTTGTGTTGTTTTAATTTTTTTTGAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_129_799_390 0 chr1 3190859 255 35M * 0 0 TAAAATAATGAGAGAATGGAGAACCAATGTAAGGA hhhhhhhhhhhhbhQMhhhXhJgFNJVKJLT>BI? NM:i:0 -EAS38_8_186_234_660 16 chr1 3190910 255 35M * 0 0 TCTGGAAGCAGGCTCACCAAGTATGATGGTTTCAT bb\hhhhhhhhdhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_99_392_34 16 chr1 3190940 255 35M * 0 0 TTCATACACAGAAAAACATTTGTTCTTTTGGATGC `dAhhhEUMhhhhhhhhhhThhhhhhhhhhhhhhh NM:i:1 -EAS38_8_141_299_800 0 chr1 3190964 255 35M * 0 0 CTTTTGGATGCCATTAGTTCAGCCAGTGTCAACAT hhhhhhhhhhhhhhhhhhhhhhhhahhhhhhhQh] NM:i:0 -EAS38_8_41_30_673 0 chr1 3190983 255 35M * 0 0 CAGCCAGTGTCAACATGACTAGTGGTTTCCCCAGC hhhhhhhhhhhhhhhhhhQhhhhhhJhh>SWHLEM NM:i:1 -EAS38_8_270_818_467 16 chr1 3191047 255 35M * 0 0 CTGCTTTCCAGGCTTCTCATCTATAGATAGAGAAG YADUL]DhhhhYhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_295_700_520 0 chr1 3191049 255 35M * 0 0 GCTTTCCAGGCTTCTCATCTATAGATAGAGAAGAC hhhhhhhhhhhhhhhhhhhhRhhhhhhah`IhRXG NM:i:0 -EAS38_8_326_937_869 0 chr1 3191049 255 35M * 0 0 GCTTTCCAGGCTTCTCATCTATAGATAGAGAAGAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhQMhFG? NM:i:1 -EAS38_8_156_546_203 0 chr1 3191080 255 35M * 0 0 AGACTTTTACAAGGTGTATGTATTGAATCCATTAT hhhhhhhhhhhhhhhhhhhfhhhhDhhVhhRhhPh NM:i:1 -EAS38_8_226_788_95 0 chr1 3191080 255 35M * 0 0 AGACTTTTACAAGGTGTATGTATTTAAGCCATTAT hhhhhhhhhhhhhhhhhhhhhhhhPhhSghchhhh NM:i:1 -EAS38_8_206_454_499 16 chr1 3191117 255 35M * 0 0 AAAATGACATTATTTATCATTATTAGAAATTCCAA hhhhZhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_126_432_418 0 chr1 3191141 255 35M * 0 0 AGAAATTCCAACCCTAGTTATGAAAGATTGAGGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhYhchR NM:i:0 -EAS38_8_255_473_525 0 chr1 3191143 255 35M * 0 0 AAATTCCAACCCTAGTTATGAAAGATTGAGGGAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhWhhhafh NM:i:0 -EAS38_8_293_908_459 16 chr1 3191160 255 35M * 0 0 ATGAAAGATTGAGGGAAAGTGATAAAGAACAAAAG hhehhhhhhYhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_126_512_733 0 chr1 3191163 255 35M * 0 0 AAAGATTGAGGGAAAGTGATAAAGAACAAAAGGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhN NM:i:0 -EAS38_8_132_357_350 0 chr1 3191163 255 35M * 0 0 AAAGATTGAGGGAAAGTGATAAAGAACAAAAGGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh^hL NM:i:0 -EAS38_8_225_963_686 16 chr1 3191186 255 35M * 0 0 GAACAAAAGGGAGGGATATTATTCTCTCATTTTTA UchhhhfhhhahNhahhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_91_183_721 0 chr1 3191203 255 35M * 0 0 ATTATTCTCTCATTTTTAACAGCATATTTGTCTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[ NM:i:0 -EAS38_8_91_184_720 0 chr1 3191203 255 35M * 0 0 ATTATTCTCTCATTTTTAACAGCATATTTGTCTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhX NM:i:0 -EAS38_8_37_742_366 16 chr1 3191253 255 35M * 0 0 TACTGTGTGGCTTCAAAGAAGATAGTCATCTCTGG h]hQhhB_hhRhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_164_833_223 16 chr1 3191267 255 35M * 0 0 AAAGAAGATAGTCATCTCTGGTTCTCTTACTGAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_20_3_646 16 chr1 3191299 255 35M * 0 0 AGAATAGAAAGTCTCTCCTTACTGAGAATAGGAAG hVhh_hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_305_336_434 16 chr1 3191299 255 35M * 0 0 AGAATAGAAAGTCTCTCCTTACTGAGAATAGGAAG hhhhhhhhhhhUhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_133_876_487 16 chr1 3191301 255 35M * 0 0 AATAGAAAGTCTCTCCTTACTGAGAATAGGAAGCC hhGhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_58_243_264 16 chr1 3191305 255 35M * 0 0 GAAAGTCTCTAATTACTGAGAATAGGAAGCCATCT hhhhh?UQLOIAhhhWhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_158_87_484 16 chr1 3191325 255 35M * 0 0 AATAGGAAGCCATCTTCATACCTGTCCCTCTGCAT gh@hChhhh`LhFhhghhRhhhhhghhhhhhhhhh NM:i:0 -EAS38_8_49_289_587 16 chr1 3191360 255 35M * 0 0 TTATTCTTGAGGTTACTGAGCCATCTGGCTACAGA hhh^XhKUhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_226_316_409 0 chr1 3191368 255 35M * 0 0 GAGGTTACTGAGCCATCTGGCTACAGAGAAGAAAA hhhhhhhhhhhhhhhhhhahhhah_UOhDENhC[G NM:i:0 -EAS38_8_27_871_685 16 chr1 3191375 255 35M * 0 0 CAGAGCCATCTGGCTACAGAGAAGAAAAGCAAGAG gAhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_323_782_711 16 chr1 3191375 255 35M * 0 0 CTGAGCCATCTGGCTACAGAGAAGAAAAGCAAGAG hGdhZhghhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_138_990_817 16 chr1 3191399 255 35M * 0 0 AAAAGCAAGAGTTGTTTTTTTATTTTTATTTTATT hhhhKhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_185_443_369 16 chr1 3191399 255 35M * 0 0 AAAAGCAAGAGTTGTTTTTTTATTTTTATTTTATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_16_393_343 16 chr1 3191400 255 35M * 0 0 AAAGCAAGAGTTGTTTTTTTATTTTTATTTTATTT hhhhVhhhhhI]hPJhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_50_691_313 16 chr1 3191400 255 35M * 0 0 AAAGCAAGAGTTGTTTTTTTATTTTTATTTTATTT hhhhhhhhhhhhhXhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_189_168_310 16 chr1 3191408 255 35M * 0 0 AGTTGTTTTTTTATTTTTATTTTATTTTTATTTTT hhWWhhh[hh_hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_247_520_310 16 chr1 3191408 255 35M * 0 0 AGTTGTTTTTTTATTTTTATTTTATTTTTATTTTT hhTRhhh]hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_8_620_387 0 chr1 3191411 3 35M * 0 0 TTTTTTTTTATTTTTATTTTATTTTTATTTTTTTA hhhhhhhhhhhhhhh`hhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_264_985_305 0 chr1 3191415 1 35M * 0 0 TTTTTATTTTTATTTTATTTTTATTTTTTTAATTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhOhh NM:i:1 -EAS38_8_290_750_320 16 chr1 3191505 255 35M * 0 0 CAGACAATGGCTTTAAGTGGGGCCTATATGAACTG BaFA>PbShGXfXhh_hJhh[hhhhhhhhhhhhhh NM:i:1 -EAS38_8_220_527_228 16 chr1 3191562 255 35M * 0 0 CGGTTTTGTGAAGGTAATATATCAGTAATATGGTT E[gYhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_181_540_123 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhOfhPhhEZDS NM:i:0 -EAS38_8_28_698_660 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhheRchhHhGh NM:i:0 -EAS38_8_304_298_316 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGTTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhhbchhhTchh NM:i:1 -EAS38_8_146_777_942 0 chr1 3191575 255 35M * 0 0 GTAATATATCAGTAATATGGTTGACATAAATAAGC hhhhhhhhhhhhhhhhhhhhhhhhahhhhhhhhhG NM:i:0 -EAS38_8_206_582_659 0 chr1 3191575 255 35M * 0 0 GTAATATATCAGTAATATGGTTGACATAAATAAAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhgh[hh@T NM:i:1 -EAS38_8_113_379_524 0 chr1 3191576 255 35M * 0 0 TAATATATCAGTAATATGGTTGACATAAATAAGCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhIh NM:i:0 -EAS38_8_197_772_581 16 chr1 3191611 255 35M * 0 0 GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_256_457_159 16 chr1 3191611 255 35M * 0 0 GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC hhhhhhUhhhgPhhghhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_315_836_955 0 chr1 3191675 255 35M * 0 0 TGAAAAGAATGTTAGTTGGCTGTAACCATAAAATT hhhhhhhhhhhhhhhhhhhLhhHhhhEMhghJhUW NM:i:0 -EAS38_8_255_763_380 16 chr1 3191702 255 35M * 0 0 ATAAAATGGGCAGTTGTATTTACAAATAATCACAT hhhhhhhBhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_279_818_155 0 chr1 3191716 255 35M * 0 0 TGTATTTACAAATAATCACATATATGATGCTTACA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhT^G NM:i:0 -EAS38_8_48_883_242 16 chr1 3191719 255 35M * 0 0 ATTTAAAAATAATCACATATATGATGCTTACAGAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_78_140_97 0 chr1 3191764 255 35M * 0 0 ATTTCTAAATAATCACATATGCTAAAAGCTAGTTT hhhhhhhhhhhhhhhhhhhhPhhh\ThGhhDILh] NM:i:1 -EAS38_8_322_980_805 16 chr1 3191782 255 35M * 0 0 ATGCTAAAAGCTAGGTTTTTCTAATACACTTTTAT hSYhhhhhh\hhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_319_99_291 16 chr1 3191786 255 35M * 0 0 TAAAAGCTAGGTTTTTCTAATACACTTTTACTTTC hhhhhhhdhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_64_224_620 0 chr1 3191811 255 35M * 0 0 TTTTATTTTCATGGAGGGCTCTAGAGGTTTCCACG hhhhhhhhhhhhhPhhhhhhhhhhZh]>hhCPJQJ NM:i:1 -EAS38_8_108_348_710 0 chr1 3191850 255 35M * 0 0 ATAGAAACCACTGAAAAGAGACTCAACTCTTTTTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh\ NM:i:0 -EAS38_8_231_364_552 0 chr1 3191864 255 35M * 0 0 AAAGAGACTCAACTCTTTTTCCCCCCAGCAATATT hhhhhhhhhhhhhhhhhhhhhhhhhhfhhhRhEhh NM:i:0 -EAS38_8_116_293_619 0 chr1 3191865 255 35M * 0 0 AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhhhX NM:i:0 -EAS38_8_145_345_869 0 chr1 3191865 255 35M * 0 0 AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhchhXhhh NM:i:0 -EAS38_8_275_299_203 0 chr1 3191865 255 35M * 0 0 AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA hhhhhhhhhhhhhhhhhhhhhhhhhHBhhBhXh^\ NM:i:0 -EAS38_8_14_653_187 16 chr1 3191901 255 35M * 0 0 GTTGCTCTGGGCTGCTCTATGCATATGGCATGTTG NQKhhRTYh@hNdhhWMhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_123_560_667 16 chr1 3191909 255 35M * 0 0 GTGCTGCTCTATGCATATGGCATGTTGTTGGTACC eThh]hhfhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_158_848_347 16 chr1 3191913 255 35M * 0 0 GGCTCTATGCATATGGCATGTTGTTGGTACCTGTA @U\EWWhRbhhhhbhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_259_577_716 0 chr1 3191933 255 35M * 0 0 TTGTTGGTACCTGTACCATTCTCTTCCATTGAGAA hhhhhhhhhhhhhhhRhhhhhhhhh]hhhhhKhhh NM:i:0 -EAS38_8_37_266_444 16 chr1 3191981 255 35M * 0 0 GGTGGAGGAGCTGTTCAGCTCTCTCTAACCTATTT EfQhWOhh`hhWhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_298_155_843 16 chr1 3191988 255 35M * 0 0 GAGCTGTTCAGCTCTCTCTAACCTATTTAGATTTT Lhh`hhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_171_911_326 16 chr1 3192010 255 35M * 0 0 CTATTTAGATTTTATCTTTCACTTTGTGATAGAAT [hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_213_546_978 16 chr1 3192010 255 35M * 0 0 CTATTTAGATTTTATCTTTCACTTTGTGATAGAAT afhhhhh\hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_165_431_451 0 chr1 3192012 255 35M * 0 0 ATTTAGATTTTATCTTTCACTTTGTGATAGAATCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhh]Chhhh NM:i:0 -EAS38_8_130_352_184 16 chr1 3192020 255 35M * 0 0 TTTATCTTTCACTTTGTGATAGAATCTCTCTATAG hfdhhYhhhghJhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_303_420_658 16 chr1 3192025 255 35M * 0 0 CTTTCACTTTGTGATAGAATCTCTCTATAGAATGT hKhhhUhhhhhhhhhhhhh]hhhhhhhhhhhhhhh NM:i:0 -EAS38_8_11_860_892 16 chr1 3192043 255 35M * 0 0 ATCTCTCTATAGAATGTTCTCTCCACCACCTCCTG LLhXhchhhh^@hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_166_250_850 16 chr1 3192043 255 35M * 0 0 ACCTCTCTATAGAATGTTCTCTCCACCACCTCCTG M@X?CGhhhhhLhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_41_436_855 0 chr1 3192251 255 35M * 0 0 TACCTTTTACCCACTTACTGTTCTTACATGACCTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhbAhhh NM:i:0 -EAS38_8_1_614_740 0 chr1 3192310 255 35M * 0 0 GCACTGTAGATATTTTTGAGGAGTCACATAATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_1_615_739 0 chr1 3192310 255 35M * 0 0 GCACTGTAGATATTTTTGAGGAGTCACATAATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_11_667_100 0 chr1 3192520 255 35M * 0 0 CTCCTCAAGGGAAAATTTGGAAAGTATTTCATATT hhhhhhhhhhhhhhhhhhh\hhhHhhhhhhhhhhh NM:i:0 -EAS38_8_142_397_982 16 chr1 3192642 255 35M * 0 0 CTGTTAGCACAGTTCAATGATACATTCTTATTTTA hVShThOhhhhGhhhhhhhAhFhhhhhhhhhhhhh NM:i:2 -EAS38_8_201_45_850 16 chr1 3192642 255 35M * 0 0 CTGTTAGCACAGTTCAATGGTGCATTCTTATTTTA hfMfYhhhVhh[hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_198_171_959 0 chr1 3192730 255 35M * 0 0 TAGTCATTTAGGCAAGGAAATAGACATTGTTTTGA hhhhhhhhhhhhhhhhhhhhhhhfZhhhhhhhhTR NM:i:0 -EAS38_8_300_863_946 16 chr1 3193601 255 35M * 0 0 ATTCCTTTCTTCTTTGTTGCTATCATTGAACCACA BGbhah[IhhhhhhfOhh^hhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_311_818_593 0 chr1 3193885 255 35M * 0 0 CACAGATGCACAGATTGATGATCTCTAGGAAAAAG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZ]hh NM:i:0 -EAS38_8_126_604_962 0 chr1 3194707 255 35M * 0 0 TGGATCAAACAATTTAAACAACTTTAGCTTTACAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKWh NM:i:1 -EAS38_8_95_901_210 0 chr1 3194707 255 35M * 0 0 TGGATCAAACAATTTAAACAACTTTAGCTTTACAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_145_407_869 16 chr1 3195051 255 35M * 0 0 TAGGTTGCAGTTGCTCTATGTGATGTATTTCTCTT ShP?MhHhhZhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_111_861_260 16 chr1 3196449 255 35M * 0 0 TTTTTTCCTGGAGTGCATAATGGATACATTTGATG \OhfhMhhShhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_167_257_42 16 chr1 3197418 255 35M * 0 0 AATTAAGGCATCAGTGTTCTGAACTGTGTGATAGC hhhAhhhhUhVhhhbhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_233_573_175 16 chr1 3197418 255 35M * 0 0 AATTAAGGCATAAGTGTTCTGAACTGTGTGATAGC hhDIhhhh[h_BhhVhhhdhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_305_871_204 16 chr1 3199438 255 35M * 0 0 AGTTGCTCACTTTCATGAGTAGCTTTGACTAATTA hXGMDTVdhhYhZhhPhhhhhhhhchhhhhhhhhh NM:i:0 -EAS38_8_231_724_560 0 chr1 3200057 255 35M * 0 0 TACAGCAATAACACATGGCAAATTCTTAATAATGA hhhhhhhhhhhhhhhhhhhhQhhhhhgJhShQeAA NM:i:0 -EAS38_8_203_543_728 0 chr1 3200118 255 35M * 0 0 CCACAAGGAAATCTATAGGCAAACAAAATAACCAA hhhhhhhhhhhhhhhhhhhhhhh^Xhhh_hh\@Ch NM:i:0 -EAS38_8_229_849_498 0 chr1 3200118 255 35M * 0 0 CCACAAGGAAATCTATAGGCAAACAAAATAACTAA hhhhhhhhhhhhhhhhhhhbhfhhY`hQcaK?hBV NM:i:1 -EAS38_8_119_995_590 0 chr1 3200431 255 35M * 0 0 CTTATTTCTGTGGGCACATGGCTGGTTGCCACTTC hhhhhhhhhhhhhhhhhhhhhhhhDVhEEJICIh@ NM:i:1 -EAS38_8_253_690_533 0 chr1 3200431 255 35M * 0 0 CTTATTTCTGTGGGCACATGGCTGCTTGCCCCTTC hhhhhhhhhhhhhhhhhhhhhhhhIhRHM@GQMR? NM:i:1 -EAS38_8_2_361_608 16 chr1 3200848 255 35M * 0 0 CAAATGTTGGGTAGCAGATTGGTGTCATAAGTCAA G^h^PNLLKh@hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_19_443_443 16 chr1 3201005 255 35M * 0 0 GGTCCACCTTGGTCCTGCTGTGCTGTCAGCTTCTG N\MhhAVhQYhh]hhShhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_240_860_321 0 chr1 3201008 255 35M * 0 0 CCACCTTGGTCCTGCTGTGCTGTCAGCTTTTGTCT hhhhhhhhhhhhhhhhhhehhhhSGhHhP@YI`CL NM:i:1 -EAS38_8_159_889_369 16 chr1 3201153 255 35M * 0 0 TATATAGAAATAGTCGTGGCTAATGGCAAAGATAT Nh`hPhhhhhhhhNhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_6_649_343 16 chr1 3201153 255 35M * 0 0 TATATAGAAATAGTCGTGGCTAATGGCAAAGATAT hhhhhhhhhhhhhhhhhhhZhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_159_13_859 16 chr1 3201231 255 35M * 0 0 CATTAGAAAAAATTCACAGGATTCTTGTCTAAACA hhghhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_206_389_817 0 chr1 3201597 255 35M * 0 0 CATGCATTTCTAAGTTTATCTCTGTGTAGATGCAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhZhahhh NM:i:0 -EAS38_8_8_834_910 16 chr1 3201632 255 35M * 0 0 GTAAGAGAGTCAGTCTTTCTGTCTGTCTGTTTCTG KTEPRY\hhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_193_381_989 0 chr1 3201726 255 35M * 0 0 GGCAAATCTGTAGAAATTGATATCTCTTTATGTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_218_286_583 16 chr1 3201770 255 35M * 0 0 CAGGGATCAAATTCAGGTCAAGTTTGCATCTTTTT hh[a\h\hhhh^hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_231_842_613 16 chr1 3201775 255 35M * 0 0 ATCAAGTTCAGGTCAAGTTTGCATCTTTTTTCAGT hahhhOhbhhhKhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_69_697_617 16 chr1 3201775 255 35M * 0 0 ATCAAATTCAGGTCAAGTTTGCATCTTTTTTCAGT heghhhOhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_315_783_294 16 chr1 3205321 255 35M * 0 0 CTAAAAGTAAAAACAAATCCTGAAATATGTAGAAA ERhhhhhXhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_208_943_432 16 chr1 3206163 255 35M * 0 0 CCTTGGAGGAGATGGGGAACATTCAAAAGCTAAAA bVQHbOhahhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_17_380_277 0 chr1 3209126 255 35M * 0 0 TTGGTGTGCTTATCCGACACTGTAGGTAGAAACCA hhhhhhhhhhhhhhhh]hPh\NhhJQhEKCEOJhG NM:i:1 -EAS38_8_156_409_184 16 chr1 3211514 255 35M * 0 0 CAAGAAAGATTGATGAGACACAGTTGATAGAGGGA HKhThhhhhhOhhghhhhLhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_189_963_938 0 chr1 3211535 255 35M * 0 0 AGTTGATAGAGGGATGATAAATAATCCTTTCCTTT hhhhhhhhhhhhhhhhahhh^hhdSGTTZ`>D[XR NM:i:0 -EAS38_8_194_593_290 0 chr1 3212718 255 35M * 0 0 GCTTAAGACACTTTGCATCCCTCTTTTGTAACATT hhhhhhhhhhhhhhhhhhhhhhhhhhhWhRK^Jhb NM:i:0 -EAS38_8_54_951_1001 0 chr1 3212775 255 35M * 0 0 ACTTTCCTTTTCAGGAAAAAAAATGTATATAATAT hhhhhhhhhhhhhhhhhhh[hhhhhIHhhdbaSOJ NM:i:0 -EAS38_8_55_222_593 16 chr1 3213111 255 35M * 0 0 CTCACTGCCTCCCTCTTAGGACTCTTACACTGAAA h>hPhf`ZhYhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_192_865_198 16 chr1 3213157 255 35M * 0 0 AGTCAATGCAAGAAAGCAGATGCTTCCATCTTGCT _JHhOhFhBhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_257_284_263 16 chr1 3213208 255 35M * 0 0 AAAAAAAACAAAACAAATCTCCACTTTTTGTAAAT hXhMhhhhOhhhhIhhhfhPhQhhhhhhhhhhhhh NM:i:2 -EAS38_8_14_341_452 0 chr1 3234830 255 35M * 0 0 CCTTGATGTCTTGATGGTTGAAATAGGTTACATTT hhhhhhhhhhhhhhhhhhhh`hhh^IhhhN`Lhhh NM:i:0 -EAS38_8_171_140_943 0 chr1 3239649 255 35M * 0 0 TCCCTGTTAGATTCAAATGTTACTTTATAGTTAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh^h NM:i:0 -EAS38_8_98_123_525 16 chr1 3240599 255 35M * 0 0 ACATCCCTCCCTAAATAAACCACAATCCACCCCCA hdhLDhEMhhfhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_178_873_141 16 chr1 3242478 255 35M * 0 0 TTTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT OVhhRhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_215_180_235 16 chr1 3242478 255 35M * 0 0 TGTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT hThhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_7_814_774 16 chr1 3242478 255 35M * 0 0 TTTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT Jhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_315_926_983 16 chr1 3242791 255 35M * 0 0 ACCTCCTCCTATAGCTTCTAGAGACAACAGACCTT @<BEAZIMRhHhIdhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_163_191_986 16 chr1 3242917 255 35M * 0 0 AATCATATTTTGACCTCAATTAGCCTTGGGGTTGA hhTRhSaeh\UAThhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_173_800_35 16 chr1 3242917 255 35M * 0 0 AATAATATTTTGACCTCAATTAGCCTTGGGGTTGA hh=FhRhVhOhShGhcZhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_25_295_514 0 chr1 3242979 255 35M * 0 0 GCTCTTCTGTCAAGAGTACCTGAAATTTATCTGTG hhhhhhhhhhhhhhhhhhhhhhhehhhhhhZhhhc NM:i:0 -EAS38_8_260_745_595 0 chr1 3242979 255 35M * 0 0 GCTCTTCTGTCAAGAGTACCTGAAATTTATCTGTG hhhhhhhhhhhhhhhhhhhhhhLhhhhhhhhhhfM NM:i:0 -EAS38_8_162_854_426 16 chr1 3243101 255 35M * 0 0 GAAAAAACCTGTCTTGGTCTGAGGTCTGGGCCACT >hhhhhPhhU_XhXZhhhhehhhhhhhhhhhhhhh NM:i:0 -EAS38_8_120_168_509 16 chr1 3243120 255 35M * 0 0 TGAGGTCTGGGCCACTGTTATTCAGAGTGAACAAC AZc^hCcMhhhWhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_219_315_931 16 chr1 3243676 255 35M * 0 0 TTTGTTGAAGGAGAACACAATGAGAGGTGCATATT ]OhYhhchhahhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_180_247_88 16 chr1 3244868 255 35M * 0 0 GCATACTTAAAATTAGGCTGCAATCAGTCTTCCTT _@hhhCJhhhhhhIhhhhShhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_144_513_481 0 chr1 3252847 255 35M * 0 0 AATGGCATTCAGTTAGCTTTAGTGACTGATCCCAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhBC NM:i:0 -EAS38_8_125_631_236 0 chr1 3253217 255 35M * 0 0 TGAGGCATGACCTCCTTTCACTGAATCTTAGTCTT hhhhhhhhhhhhhhhhhhhhhhhhehhhhhLChhh NM:i:1 -EAS38_8_312_169_822 16 chr1 3253312 255 35M * 0 0 AAGGCTAAAATTGCTGTTACCAGCTGCTATGCTTG [JNDIONDhWhhhhhhIhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_10_227_417 0 chr1 3253759 255 35M * 0 0 CAAATTTTAGCTCCTTTCCCAGTTTCCCTCTGGAA hYhhhhhhhhhhhhhhhh`hG_heh\V^hXhUBH? NM:i:0 -EAS38_8_144_231_566 0 chr1 3253759 255 35M * 0 0 CAAATTTTAGCTCCTTTCCCAGTTTCCCTCTGGAA hhhhhhhhhhhhhhhhhhXhghhhhROZWKbU\MM NM:i:0 -EAS38_8_208_276_857 16 chr1 3254072 255 35M * 0 0 TCAACTTCACAAGGAATTTGGAGTGACTGGCCTCC VdMOhLchXhhhh^hhhZhhhhhhh_hhhhhhhhh NM:i:0 -EAS38_8_6_640_930 16 chr1 3254072 255 35M * 0 0 TCAACTTCACAAGGAATTTGGAGTGACTGGCCTCC IHhOhJThchhhhWhhh_hhYhhhhhhhhehhhhh NM:i:0 -EAS38_8_261_856_180 0 chr1 3254263 255 35M * 0 0 GTTCCGCAACACCTGCCCTCACATTCCACTGAACT hhhhhhhhhhhhhhhhhhhhMhThh[NCKQD?DJK NM:i:1 -EAS38_8_97_169_815 0 chr1 3254597 3 35M * 0 0 ATCAGGCTACTTTCAGCAAGCACTTCTTGTCATCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhAh^hUh NM:i:1 -EAS38_8_250_270_899 0 chr1 3259536 255 35M * 0 0 CTAGATTAGCAGGTAATTTCTAAATCACACATTTA hhhhhhhhhhhhhhhhhhhhhhhhhahUJOhhYhb NM:i:0 -EAS38_8_267_436_563 0 chr1 3273793 255 35M * 0 0 TTTTTTTGTTTGTTTGTTTGTTTTTATACAACAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhh NM:i:1 -EAS38_8_244_916_490 16 chr1 3274218 255 35M * 0 0 GAGCCTAAACCAACCAACCAATGAATATACATAGG ThCYE@AhhhOhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_111_703_424 16 chr1 3274366 255 35M * 0 0 ACAGGGCACATGTTCTTCTAGCTGAGCTGCCTTGT L[gE[hhhhhghhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_224_315_306 16 chr1 3274921 255 35M * 0 0 GGAACTGTGCAAATTGTGTAACTGGAGAAAATAAT hhhh^hh_hhhhhhhhhhhhh`hhhhhhhhhhhhh NM:i:0 -EAS38_8_256_842_769 0 chr1 3277156 255 35M * 0 0 AATGATATTGGTTTGAAGTTCTTTAGCCCCATATT hhhhhhhhhhhhhhhhhhhhhhhhhhhh\hhh]hh NM:i:0 -EAS38_8_292_619_933 0 chr1 3277156 255 35M * 0 0 AATGATATTGGTTTGAAGTTCTTTAGCCTCATATT hhhhhhhhhhhhhhhhhhhhhhhhhhbOLhMhhhh NM:i:1 -EAS38_8_212_928_881 0 chr1 3277700 0 35M * 0 0 TCCTTTTCCTTTCCTTCCTTCCTTCCATCCTTCCT hhhhhhhdZghhaehhTVhhZhhhNT?h^MX]OBQ NM:i:2 -EAS38_8_223_507_484 0 chr1 3277914 255 35M * 0 0 TTCTGAAACTTGAGTACAGTGTTATTACCAATATT hhhhhhhhhhhhhhhhhhhLhhhhhhhKhLbheha NM:i:0 -EAS38_8_264_464_724 0 chr1 3277925 255 35M * 0 0 GAGTACAGTGTTATTACCAATATTCCCCCATTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhh NM:i:0 -EAS38_8_97_398_795 0 chr1 3277927 255 35M * 0 0 GTACAGTGTTATTACCAATATTCCCCCATTTTTCC hhhhhhhhhhhhhhhhhhhhhhhLhhhVhhhhh^h NM:i:0 -EAS38_8_271_224_790 16 chr1 3277983 255 35M * 0 0 AGTGATGTCCTAACATGCTTGCTCTCTCATAACCA FhhQ`hhhhhhhhhhhhhhhhhghhhhhhhhhhhh NM:i:0 -EAS38_8_249_919_47 16 chr1 3277988 255 35M * 0 0 TGTCCTAACATGCTTGCTCTCTCATAACCAGACTT K=DFHUhLXhaJSbfLPfhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_264_398_810 16 chr1 3278029 255 35M * 0 0 AGTTTTGTTAGGTTTGCTGGTCTTTTAAAAGGTCT ZghhHhhhhTh[hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_202_252_118 16 chr1 3278057 255 35M * 0 0 AAGGTCTAGATTTTTGTTTCATTATTTTTTTTCTG hhhTDhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_195_472_45 0 chr1 3278134 255 35M * 0 0 CTTTTATTATATTCTTCCTCTTCGTTATTTTGAAT hhhhhhhhhhhhhhhhhhhhhhhPhhh]hhhWENh NM:i:1 -EAS38_8_200_268_981 0 chr1 3278134 255 35M * 0 0 CTTTTATTATATTCTTCCTCTTCGTTAGTTTGAAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheh NM:i:0 -EAS38_8_87_755_875 16 chr1 3278180 255 35M * 0 0 TTCTCTTAAGTATATGTTCTTATTAACTATTTTTT hhhUhhhhhThhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_184_481_627 16 chr1 3278254 255 35M * 0 0 GAGGCATTTTAGTGTTATGAACTCCCCTTGGCACT NH?=BNI[BT^YdUZ[hKJhhhPhhhhhhhhhhhh NM:i:0 -EAS38_8_241_955_483 16 chr1 3278295 255 35M * 0 0 GACACAGATAGGTTTTTATGTGCTATACTTACATT DbHYMhVhhhVhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_24_420_629 0 chr1 3278309 255 35M * 0 0 TTTATGTGCTATACTTACATTCAGTTCAATGTAAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhfhhhhhh NM:i:0 -EAS38_8_307_620_12 16 chr1 3278356 255 35M * 0 0 TTAGACTTCATTTTCTTCTTCTTTTTGGTTGTGAG IOhKhhJdLhhhJhIeTVZhhhhhhhfWhhhhhhh NM:i:0 -EAS38_8_55_835_895 0 chr1 3278373 255 35M * 0 0 CTTCTTTTTGGTTGTGAGCCTAGCCTTCAACGGTT hhhhhhhhhhhhhhhhhhWWhhhMTIhPTHIhc>D NM:i:1 -EAS38_8_230_275_815 16 chr1 3278376 0 35M * 0 0 TTTTTTGTTTGTGAGCCTAGCCTTCAACGGCTGAG \_NF]RQGZhWPOXPhhhahhhhhhhMhhXhhhhh NM:i:2 -EAS38_8_24_167_957 16 chr1 3278397 255 35M * 0 0 CTTCAACGTCTGAGCCATCTCTCCAGCCCTCTTCT VFA`N?hQ@hhLhehhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_253_546_769 0 chr1 3278576 255 35M * 0 0 TTCCCACTCTCTGGGGCCTCAAGTCTCTCAAATTA hhhhhhhhhhhhhhhhhhhhKRZhhhhh`KMhRTM NM:i:2 -EAS38_8_283_280_992 0 chr1 3278576 255 35M * 0 0 TTCCCACTCTCTGGGGCCTCAAGTCTCTCAAATGT hhhhhhhhhhhhhhhhhhhYhhhFHcBQJHUNK?C NM:i:0 -EAS38_8_4_499_790 0 chr1 3278607 255 35M * 0 0 ATGTTAGGCACATCTCCCACTGATTCCAGACCAGG hhhhhhhhhhhhhhhhe[hhhhUhcVOP`I?LTXH NM:i:0 -EAS38_8_166_353_693 0 chr1 3278725 255 35M * 0 0 GGTTAGTTGAGATTGCTGGTCTTTCTATGGGTTGC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhhhFS NM:i:0 -EAS38_8_227_305_410 16 chr1 3278920 255 35M * 0 0 TCAGACCTCTGCTGATCACCTGCATAGTTGGAGAT KJhH@NRIA_B`hhhhhhhhThhhhhhhhhhhhhh NM:i:1 -EAS38_8_151_783_299 16 chr1 3279317 255 35M * 0 0 CTTTTTTGTTCTATAGATATCAATTATTTACCCAC BTS^WdIUehQhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_130_64_600 0 chr1 3280118 255 35M * 0 0 GGTTTCGAGAAAATGTTTTGAAGTGTTTATGCGCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhchKOhSh NM:i:0 -EAS38_8_204_14_612 0 chr1 3280118 255 35M * 0 0 GGTTTCGAGAAAATGTTTTGAAGTGTTTATTCGCT hhhhhhhhhhhhhhhhhhhhfhhhhhhhhhBQhL\ NM:i:1 -EAS38_8_242_889_996 0 chr1 3280118 255 35M * 0 0 GGTTTCGAGAAAATGTTTTGAAGTGTTTATGCGCT hhhhhhhhhhhhhhhhhhhhh^hVhaahgeh@Z?N NM:i:0 -EAS38_8_82_262_363 0 chr1 3280320 255 35M * 0 0 AACATATTTTAAATTCCTCTCAGATTAAGAGAATT hhhhhhhhhhhhehhhhhhhh^hWhKhShWD@hhB NM:i:2 -EAS38_8_111_150_178 0 chr1 3282505 255 35M * 0 0 AGATACATAGAAAAGCTACTTGACTTTAGGTCAAC hhhhhhhhhhhhhhhhhhhhhUfhhhhhQOhh\Sh NM:i:0 -EAS38_8_260_477_698 0 chr1 3282505 255 35M * 0 0 AGATACATAGAAAAGCTACTTGACTTTAGGTCAAC hhhhhhhhhhhhhhhhhhhhhhhhhhhXhhhh`hM NM:i:0 -EAS38_8_187_894_354 16 chr1 3282753 255 35M * 0 0 CTGCACTTGTTTAGAGAAGTGCTGTCTACATGAAG dhNhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_219_350_890 0 chr1 3282806 255 35M * 0 0 TTTTGGAACTTAGGCAAGAATGTTCTTTGGCTCCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPVh NM:i:0 -EAS38_8_185_258_316 16 chr1 3282902 255 35M * 0 0 TGAGAGCTAAATGTAAAGCTCAGTAATGCCAGCTC IJhhhhh^hhhhMhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_5_912_317 16 chr1 3284777 255 35M * 0 0 CTCTCGCTCTCTCTCTCTCTCCCCTCACTCCTTTC BPWFbChNSRhFhShehOh_hhhhhhhhhhhhhhh NM:i:1 -EAS38_8_119_362_614 0 chr1 3284967 255 35M * 0 0 TGTACCCTGAGATCAAGTACTTATTGCTTTCACTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_276_838_443 0 chr1 3284967 255 35M * 0 0 TGTACCCTGAGATCAAGTACTTATTGCTTTCACTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhahhhh NM:i:0 -EAS38_8_74_720_526 0 chr1 3286259 255 35M * 0 0 CAAATTGTAGAAAATTTGCATGTGTACTGAACACA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhL NM:i:0 -EAS38_8_273_582_300 16 chr1 3289456 255 35M * 0 0 TCTTCAGTTCTTTGTTAAATATATCATCTGGGTCT HhYchhhQhRhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_232_852_815 0 chr1 3290417 255 35M * 0 0 TTTTTTTTTTTAACTTTCATATGTAGTAGTTATTT hhhhhhhhhhhhh^hhhKhhhhhhhGV^hh[MHhh NM:i:2 -EAS38_8_121_748_181 0 chr1 3290799 255 35M * 0 0 ACCACACCCTGCTGCTCCATATTTCTTATCTTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhh\Bhhhhhh NM:i:1 -EAS38_8_36_138_632 0 chr1 3290826 255 35M * 0 0 AGCTTTTTTTTTTTAACAGCTACTGGGTGGTTTGC hhhhhhhhhhhhhhhhhhhhhOhhbhCXHZLI\BF NM:i:1 -EAS38_8_141_369_534 0 chr1 3290833 255 35M * 0 0 TTTTTTTAACAGCTACTGGGTGGTCTGCATAGCTT hhhhhhhhhhhhhhhhhhhhhhhhhhhfPRLdhhS NM:i:0 -EAS38_8_84_402_647 0 chr1 3290833 255 35M * 0 0 TTTTTTTAACAGCTACTGGGTGGTCTGCCTAGCTT hhhhhhhhhhhhhhhhhhhhhhhhhhVhBhThahe NM:i:1 -EAS38_8_169_576_313 16 chr1 3290912 255 35M * 0 0 ATGCTTCTTTCCACAGTTGAGTGGAATTGTAGGGG hPhRWPJhVLhhhhhh[hhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_279_571_717 16 chr1 3290912 255 35M * 0 0 ATGCTTCTTTCCACAGTTGAGTGGAATTGTAGGGG he\hhYhaOYhhThhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_234_793_825 16 chr1 3290951 255 35M * 0 0 AAAAGACATTTCTGAGTTCTAGCACTCTCAGGTCT hhhhRhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_217_210_636 16 chr1 3290952 255 35M * 0 0 AANGACATTTCTGAGTTCTAGCACTCTCAGGTCTG hh;PYhhWXhh^hhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_168_998_377 0 chr1 3290961 255 35M * 0 0 TCTGAGTTCTAGCACTCTCAGGTCTGGCTTTGACA hhhhhhWhhhhhhhhhhhhTe\YThhOIWJaC@A? NM:i:0 -EAS38_8_179_44_982 16 chr1 3290986 255 35M * 0 0 GCCTTTGACATTAGCTTCCTGACAGGCTGGCAGGT ?@[_GhH[hhhhhEhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_210_147_536 0 chr1 3291026 255 35M * 0 0 TCCTGAAGGTCAGGACTGTGCAAAACTGTCAGGCA hhhhhhhhhhhhhhhhhhhhhhQg`hh^hbGYYPH NM:i:0 -EAS38_8_228_906_499 0 chr1 3291047 255 35M * 0 0 AAAACTGTCAGGCAGCTATTTCAGGAGTGCCTTTT hhhhhhhhhhhhhThhh_hhhhUThYZPVED[@C@ NM:i:2 -EAS38_8_223_934_468 16 chr1 3291092 255 35M * 0 0 GCCCTGGATGATTTTTGAATGGGAATAATCCCTAT RXhf\Phh`hhhhhVhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_27_794_86 16 chr1 3291130 255 35M * 0 0 TCCATATAGGCTCATATATTTAAACACCTAGTCAT X@FSSZhhhADhShhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_205_713_101 16 chr1 3291163 255 35M * 0 0 ATTGTTGGTGGCACTGTCTGTAAGGATCACGAACC CEJLUB`WcgZ]hLhheHahhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_269_175_878 16 chr1 3291192 255 35M * 0 0 CAAACCCATTAGAAGGTAACAACATGCTAAAAAAA eChhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_127_466_820 0 chr1 3291247 255 35M * 0 0 GTGAGGGCTTGTGTTCTCTCTGCTTCCTCTGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhV_hTeSWhhh NM:i:0 -EAS38_8_29_659_107 0 chr1 3291649 255 35M * 0 0 TCCTGAGTTGGGAGGACAGATGAGAAGGGCTTTTT hhhhhhhhhhhhhhhXhhhShhh`PFVhALNChJd NM:i:2 -EAS38_8_210_520_140 16 chr1 3299511 255 35M * 0 0 GAAATAAAGAAAATTCTAATCTACAGGCTGACCAT VhhLDhhhhhhhhVLHShhPhfhhhhhhhhhhhhh NM:i:2 -EAS38_8_45_100_198 0 chr1 3299523 255 35M * 0 0 ATTCTAATCTACAGGCTGACCATACTGTATTTCAC hhhhhhhhhhhhhhhhhhhhhhhZhhIh^hhhhHh NM:i:0 -EAS38_8_145_894_137 0 chr1 3299538 255 35M * 0 0 CTGACCATACTGTATTTCACTAATATAATGGTGTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhRChhhU NM:i:0 -EAS38_8_231_634_172 16 chr1 3299568 255 35M * 0 0 GTGACAGTGATGCCAGAGAGCTCTAGCTGTGGCTG MHS?]hVChhPhHVhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_68_279_670 16 chr1 3299606 255 35M * 0 0 TGAATACTGGGTAGAAAATAAAAAAATTTACGGAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_157_544_34 16 chr1 3299684 255 35M * 0 0 TCATAAGATCGGGTAGTTAGTAAACCCTGCCTAGA ?MhFhhHMRZGSdhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_317_518_457 0 chr1 3299798 255 35M * 0 0 GATTTCTGTCTACTAGATCAAAACCTGATAACATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhMhh NM:i:0 -EAS38_8_87_383_194 16 chr1 3300173 255 35M * 0 0 AAACTACAAAATTGTGGATGTTTGGCTGTTCTTTT hhhSZhhhhhhKhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_220_990_452 16 chr1 3300259 255 35M * 0 0 TGCACCATCTTAGGAGTGAGGGAGGCAGCTGAGTG NHPUJ]hhSPa`ChhhYhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_168_713_356 0 chr1 3307749 255 35M * 0 0 GGTTAACCCGAAGCCAAACTTTTCTTTGTAATTTC hhhhhhhhhhhhhhhhhRhhhhhhhHhRhhIhhhJ NM:i:1 -EAS38_8_222_724_349 0 chr1 3307749 255 35M * 0 0 GGTTAACCCGAAGCCAAACTTTTCTGTGTAATTTC hhhhhhhhhhahhhh`eGhhhhhhhJhPhNKhhhQ NM:i:0 -EAS38_8_223_971_288 16 chr1 3310176 255 35M * 0 0 AATAATCATCACCTGAATGTCATGATCTAAAGGCT hhChhAhh\Ghhh[hhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_288_770_517 0 chr1 3310786 255 35M * 0 0 AGGTTTTGAGTTTTTGATCCAGAGGCTATGTTTAT hhhhhhhhhhhhhhhhgh\h]hQgQH\FS`HRJEW NM:i:0 -EAS38_8_310_958_947 16 chr1 3311201 255 35M * 0 0 CAATTTTTGATCATTCATCTTGTTTTCTTAACAAT hP\hJhh_Hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_140_291_179 16 chr1 3313701 255 35M * 0 0 ACCGCTGCCTTCCTTTCTTCTCTCCTTCCTTTCTT PW`@dP@hYhKhhhhchh]hZhahhhhhhhhhhhh NM:i:2 -EAS38_8_113_205_724 16 chr1 3318613 255 35M * 0 0 ACCTGGAAGAATTTCATAAAAATTCCCTTCCCAGC HhedLQhhbhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_236_727_634 16 chr1 3318613 255 35M * 0 0 ACCTGGAAGAATTTCATAAAAATTCCCTTCCCAGC Sd]QXehhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_21_827_590 0 chr1 3319045 255 35M * 0 0 TACAAACCAAGAGAAAAATCTGAAAATGAAAAATT hhhhhhhhhhhhhhhhhhhhhh_hhhhhhghhhhh NM:i:0 -EAS38_8_204_62_686 0 chr1 3321977 255 35M * 0 0 AAGCTGGCAATGTTTGGGATATAAACAAGCAAACA hhhhhhhhhhhhhhhhhhhhhhhhhhhahhhh[Yh NM:i:0 -EAS38_8_86_854_652 16 chr1 3324385 255 35M * 0 0 GCAGTGGCTGAGTGATATAACACAGGGATGCAGGT hhhhhhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_192_343_954 0 chr1 3329232 255 35M * 0 0 CTGCCCTTTTTCTCCCTGCCTATTCATTATAGTTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhU NM:i:0 -EAS38_8_6_774_928 0 chr1 3330010 255 35M * 0 0 GCACTGTAGCCAGGAGTGACACACAGCAAGGATGC hhhhhhhhhhhhhhhhhhhhhhhN`hUhhhhT`h? NM:i:0 -EAS38_8_256_461_804 16 chr1 3330063 1 23M11637N12M * 0 0 TTTGTTTGTTTGTTTGTTTGTTTGTTTTGACAGGG dhh@ZhhRhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 XS:A:+ NS:i:2 -EAS38_8_288_334_735 0 chr1 3330212 0 35M * 0 0 TTATAGCTATAAAAAGTAACATTCTTTGATTGGTC hhQhhhhhKhhQ`hhNKaXAXUaGQQVLOWKRFC> NM:i:1 -EAS38_8_11_615_231 0 chr1 3330440 255 35M * 0 0 ATTGGTTACAAAAAAGTTAGCTTTAACTTTGTAAC hhhhhhhhhhhhhhhhhhhhhhhhIhhhhTLhehR NM:i:1 -EAS38_8_284_883_215 0 chr1 3330528 255 35M * 0 0 ACTAGGCCTCTAGAGTACTTCTAAATTGAGATATT hhhhhhhhhhhhhhhhhhhhhhYhhhhIWEKh`hh NM:i:0 -EAS38_8_30_530_423 16 chr1 3330584 255 35M * 0 0 AGTAGACTTATAGAGATAAGCATTAAAATTTGTAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_202_722_286 16 chr1 3330653 255 35M * 0 0 ACTTTGTAACGTTAAAGTGATGTTTCTGGTATTGA NB[KZhhcYhhhdhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_214_253_466 16 chr1 3330653 255 35M * 0 0 ACTTGGTAACGTTAAAGTGATGTTTCTGGTATTGA hSN[DRShhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_4_564_326 16 chr1 3330653 255 35M * 0 0 ACTTTGTAACGTTAAAGTGATGTTTCTGGTATTGA ZXSVTYQhehh\hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_142_357_440 16 chr1 3330660 255 35M * 0 0 AACGTTAAAGTGATGTTTCTGGTATTGATCTTTAA hhhhhdhhhhhhhhhhh_hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_317_782_44 16 chr1 3330660 255 35M * 0 0 AACGTTAAAGTGATGTTTCTGGTATTGATCTTTAA hhFHbhhhhhhbhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_137_536_758 16 chr1 3330697 255 35M * 0 0 TAATAAATTGTTTAAAATTGGGTTTTGCTAACCAA `hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_129_924_268 16 chr1 3330838 255 35M * 0 0 CAATTCACCTATATATTGTAATTAGGATAATTACA BhhhDhhCZhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_48_834_938 0 chr1 3331062 255 35M * 0 0 GTTGTTCTAAATAAAGATTAAATTCAGAATTTATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_154_283_922 0 chr1 3331674 255 35M * 0 0 TTAACTAGTAAAGAACAAAAGGCTTTGCAGAAAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh_hhX NM:i:0 -EAS38_8_215_43_278 0 chr1 3331674 255 35M * 0 0 TTAACTAGTAAAGAACAAAAGGCTTTGCAGAAATA hhhhhhhhhhhhhhhhhhh\hhhhhhKhhVONhB@ NM:i:1 -EAS38_8_227_874_535 16 chr1 3341199 255 35M * 0 0 AGACCAAGATGATGGGAACATCTTCTCCACCCCAT =>?NBTPFLEDVHOaEhhhh\hghhYhhhhhhhhh NM:i:2 -EAS38_8_255_514_861 0 chr1 3341232 255 35M * 0 0 ATCAGAATTCCCAAGTCCCTGGGTCTTCAAGTCTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhY^h_RhH NM:i:0 -EAS38_8_135_67_741 16 chr1 3341341 255 35M * 0 0 AACTCAGCTGTTGTATGCTGCCTGGTTGGTGACTC @FHPQGOXhYO[Whhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_230_743_701 16 chr1 3341490 255 35M * 0 0 GCTTCTGTCCATTTGTTGGGTATGAGTATCTGCAT NhLahhUKhhhhhcWhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_212_374_788 0 chr1 3341507 255 35M * 0 0 GGGTATGAGTATCTGCATCTTACTCTTTCAGCTGC hhhhhhhhhhhhhhhhghhhhhhhhhhhh\hHhh[ NM:i:0 -EAS38_8_250_863_818 0 chr1 3341507 255 35M * 0 0 GGGTATGAGTATCTGCATCTTACTCTTTCAGGTGC hhhhhhhhhhhhfhh[Ph]hh]\^N`XhLQE>LGD NM:i:1 -EAS38_8_48_225_977 0 chr1 3341551 255 35M * 0 0 TTCTCAGAAGGTAGTTATGCTAGGCTCCTGTCTGC hhhhhhhhhhhhhhhhhhhhhhhhOhSYh\MF]hI NM:i:0 -EAS38_8_83_343_929 16 chr1 3341762 255 35M * 0 0 TCCCCTATTTCTCTACTGAAGGAGGACTCTACCAC TRhhhhhhhbhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_96_862_886 16 chr1 3341818 255 35M * 0 0 CCCCATGATTGTTTTCTTCTCCCTCCCATGTTGAA hhhh^hJhhhhhhhhhbhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_134_781_817 0 chr1 3342105 255 35M * 0 0 ACTCTTTAATAGAGTCTCCTGAAGAGGTAAAAATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_155_230_356 16 chr1 3342124 255 35M * 0 0 TGAAGAGGTAAAAATTTTAATTTTGACAGTCCAAT ]hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_179_463_472 16 chr1 3347662 255 35M * 0 0 TACCCTTGCGTCAAGGTGTGTTTTCTTACTCAAAT OG?[DIQhbAhdhLhhhhRhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_4_219_976 16 chr1 3347662 255 35M * 0 0 TATCCTTGCCTCAAGGTGTGTTTTCTTACTCAAAT hhhhhhhchhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_79_243_815 16 chr1 3349048 0 35M * 0 0 AAAAAGAGAAACCCTGTCTCAGAAAGAAAAAAAAA ]WhAhHh_hhhhhhehhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_133_197_589 0 chr1 3349165 255 35M * 0 0 CACCAGTTCTCCTGTGCATCCTCAGGAGAAATCAT hhhhhhhhhhhhhhhhhhhhhhhhhhUhKSPhUJh NM:i:0 -EAS38_8_188_649_421 0 chr1 3351241 255 35M * 0 0 GTAGATGGACAAACATCTCCCTCACGCATTCTCAG hhhhhhhhhhhhhhhhhhhhhhhhhhhhahhhbP> NM:i:0 -EAS38_8_268_213_808 0 chr1 3355908 255 35M * 0 0 ATCTAACTAAGTAAACTATGTTATAGGAAAGAAAT hhhhhhhhhhhhhhhhhhhh^hhhhhhhhhhZhhZ NM:i:0 -EAS38_8_11_161_707 0 chr1 3355956 255 35M * 0 0 TTTGTCACATGATCAGCATAGTAGATGATGTGTCT hhhhhhhhhhhhhhhhhhhhhhhhhhhPhhhhhHh NM:i:0 -EAS38_8_291_670_580 16 chr1 3356011 255 35M * 0 0 GAAGCAGTTAAAATTGTGTGTGTGTGGTTCTGGAT hV_OXh[VIhXNhP^hhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_44_851_834 16 chr1 3356011 255 35M * 0 0 GAAGCAGTTAAAATTGTGTGTGTGTGTTTCTGGAT ECD@MDGhJXDSAChdhPh]hUhbhhEhhhhhHhh NM:i:1 -EAS38_8_105_754_762 0 chr1 3356093 255 35M * 0 0 TATAGATGTAGTTTATCTCCTAATCCCACCCTTCC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_219_312_881 16 chr1 3356191 255 35M * 0 0 TTTAATTACTTTCCCATCAAAGGCCCATTGAGCAG XZNhNLhHhhZhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_299_450_385 0 chr1 3356483 255 35M * 0 0 ATTCTGGTGGGCTTTCGAGTGTTTCAGTTTCATCT hhhhhhhhhhhhhhhhhVhhhhhhhhhhhhhhhAh NM:i:1 -EAS38_8_52_623_649 0 chr1 3356578 255 35M * 0 0 GGAGCATATGTGAGTAAGCAAATGATGTTCTTGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhh]hEUNE NM:i:1 -EAS38_8_117_306_426 16 chr1 3359531 255 35M * 0 0 TCAGAGTGTCCACCTCATTCCTCTGGGTCAGTCTT @EN_DgWhhhh_hhhhhhdhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_120_120_744 16 chr1 3361583 255 35M * 0 0 CAAAGACAAGTAGGATAATGCTGAAAGCCCAAGCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_307_422_12 0 chr1 3362018 255 35M * 0 0 CTGAAAAATTACAGTGTTCTTGTACTGGACACTAC hhhhhhhhhhhhhhhdhSahhKDYGhECFJF@TI? NM:i:2 -EAS38_8_101_691_200 0 chr1 3363077 255 35M * 0 0 CTTTTTTCCATTTTAATGTTTGCATGCAAATCTTA hhhhhhhhhhhhhhhhhXhNhh`hhhhhMhhChhI NM:i:2 -EAS38_8_205_648_802 0 chr1 3363077 255 35M * 0 0 CTTTTTTCCATTTTAATGTGTGCATGCAAATGTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZ NM:i:0 -EAS38_8_265_441_688 0 chr1 3363150 255 35M * 0 0 CAGGAATCAATCTCAACCACTTTTCATCTTACTCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhOhhch NM:i:0 -EAS38_8_53_996_162 0 chr1 3363150 255 35M * 0 0 CAGGAATCAATCTCAACCACTTTTCATCTTACTCA hhhhUhh_hYhUhc^LEHALV^]]MIVE_MMB[MO NM:i:0 -EAS38_8_28_805_359 0 chr1 3363388 255 35M * 0 0 CCAACACCTTATTATCACTTATTTTTGTCATTCTA hhhhhhhhhhhhhhhhhhhhhhhhhhIhhhh@hhZ NM:i:1 -EAS38_8_229_300_432 16 chr1 3363412 255 35M * 0 0 TTGTGATGCTATATATGTGTGCATTAACCACTGCC RObh>QWGShUahhhhBUhNhPhhhhhhhhhhhhh NM:i:2 -EAS38_8_247_121_676 16 chr1 3363412 255 35M * 0 0 TTGTCATGCTATATATTTGTGCATTAACCACTGCC QQMhgLRNfhh[hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_180_822_42 16 chr1 3363658 255 35M * 0 0 GAGTAACTGCTGCATGTTAATCTATGTCATCCCTA MXE@dhhIP__Xhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_83_317_544 0 chr1 3364348 255 35M * 0 0 GCATTTCTGAGCCTGGGTGATCTTACTTTATATTC hhhhhhhhhhhhhhhhhhhhhhhhchhhhhhhhhb NM:i:0 -EAS38_8_194_299_688 16 chr1 3364585 255 35M * 0 0 AAGGATGTTATAATTGAATCATATGGAAGTTCTTT ^hh_h_hhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_42_578_279 0 chr1 3364694 255 35M * 0 0 AAGATGTATTTTTATTTGTTTACTGTATAATTTCC hhhhhhhhhhhhhhhhhhhhhhhhChhhh_hhCP\ NM:i:2 -EAS38_8_309_762_904 16 chr1 3364864 255 35M * 0 0 AAAAGGACATCTGAATTACCTACTTGTTTTTATCA hhhhhFhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_236_498_116 16 chr1 3364885 255 35M * 0 0 ACTTGTTTTTATCAGGTTGGTCTGTAAGCATATCT LI_hhQhhMahh\hhbhFhhh\hhhhhhhhhhhhh NM:i:0 -EAS38_8_184_968_83 0 chr1 3365051 255 35M * 0 0 TAATTGCCAGGAGTTCATTGTTTTCCATATTGTCT hhhhhhhhhhhhhhhhfhhhhhhhh]EhVhhHhUh NM:i:0 -EAS38_8_194_34_599 16 chr1 3367203 255 35M * 0 0 ATTGTGGATATAAGTGGAGAAAGAGCAAGAAAAAA hhHhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_73_896_111 16 chr1 3367203 255 35M * 0 0 ATTGTGGATATAAGTGGAGAAAGAGCAAGAAAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_115_579_578 16 chr1 3369573 255 35M * 0 0 TCAGAGCATTTGGATTTTGGTCTTTAGATTAAGGT ^hhhhhhhhXhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_260_546_322 16 chr1 3369573 255 35M * 0 0 TCAGAGCATTGGGATTTTGGTCTTTAGATTAAGGT >>NELH=IJ@@@QIMBDDKOS\KJfhhh[Phhhhh NM:i:1 -EAS38_8_168_10_541 16 chr1 3375680 255 35M * 0 0 CCGTGCAGACATTCTGATGTTGGGTAATATCAAAT LT>IKNhhhWhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_316_251_752 0 chr1 3377312 255 35M * 0 0 TCACAATATTGTCTATACTTCTAAACATCCTCAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhh NM:i:0 -EAS38_8_127_130_231 0 chr1 3379889 255 35M * 0 0 AATAAATTTCTCTTGTTTGCAAGCTATCTACTCTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhbhhhhe NM:i:1 -EAS38_8_262_614_438 0 chr1 3379889 255 35M * 0 0 AATAAATTTCTCTTGTTTGCAAGCTATCTACTCTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhA NM:i:1 -EAS38_8_152_675_620 0 chr1 3379983 255 35M * 0 0 ATCACACTTCAATTTTCATTTTCCAGCAAAAGCTT hhhhhhhhhhhhhhhhhhhhhhhhhhhghZhhhhh NM:i:2 -EAS38_8_315_641_621 16 chr1 3380977 255 35M * 0 0 CATTTATTCTATGTCAATTTATCTTTTGAGTATAA hhhhhhahhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_223_839_518 16 chr1 3381656 255 35M * 0 0 GTCCTTTTTCTAGTGTCGTGTTTAAGCTCCCGTGA PVLMUG`YLSVhaNhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_189_893_589 16 chr1 3382043 255 35M * 0 0 GCAGAGCCTCTGTGTCATTGCCTGGCAGGTAGGAG =L`KeShhhhdhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_228_882_739 0 chr1 3383793 255 35M * 0 0 TGGTGAGTATTGGAACGACTAAATCAGTGTATTAA hhhhhhhhhhhhhhh]hhfhhhh]^]hehbghNHO NM:i:0 -EAS38_8_290_281_824 16 chr1 3386732 255 35M * 0 0 GTAGAAAACTGGATTTTTTTTTTTTGGTGATATAG `GUEhEhhhd\hhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffdiff_in2.sam --- a/test-data/cuffdiff_in2.sam +++ /dev/null @@ -1,400 +0,0 @@ -EAS38_1_126_860_867 16 chr1 3009675 0 35M * 0 0 ATAGTCCCTTACTGCTTTTAGTATTCTATCTTTAT WFGAeC\gVShhhLh`hhPbPhhhhhhhhhhhhhh NM:i:2 -EAS38_1_125_842_97 0 chr1 3023056 0 35M * 0 0 ATCTTCTTCAATTTGTTTCTTCAGAGACTTTAATT hhhhhhhhhhhhhhhhhhhhhhhJhhNhhh_KINh NM:i:2 -EAS38_1_261_52_728 16 chr1 3035247 0 35M * 0 0 AATCCCCCACCCCACAGGAACAAAGTCCTGATGCA @???GIH@C?HXINLQJ=VVhhgTFHfhYhhJLhb NM:i:2 -EAS38_1_71_500_217 16 chr1 3081731 0 35M * 0 0 AGGAGATAAATAACTAATAAAAAATGAAAAAAAAA h?DhLhFhfhKhRFhhhShhhhhhThhhhhhhhhh NM:i:2 -EAS38_1_2_666_566 0 chr1 3111450 255 35M * 0 0 CCACTCACAAGACAAGACCAGGATCCTGGAGAGAT hhhhhhhhhhhhhhNh^Yh]d]GRNVYURK^JU>I NM:i:0 -EAS38_1_220_990_991 0 chr1 3111546 255 35M * 0 0 AAAAGCTGAGAGTCAGCATGAATCAAGAGATAGAA hhchhMabNhP_>BKXQSNKDRD?@@TBJJ=GL@G NM:i:1 -EAS38_1_133_518_728 0 chr1 3111550 255 35M * 0 0 GCTGAGAGTCAGCATGAATCCAGAGATAGAAAAAG hhhhhhhhhhhhhhhhhhhOhQhhhNL^ZT[PLNN NM:i:0 -EAS38_1_219_471_934 0 chr1 3117684 255 35M * 0 0 TGTCCTTTGGCTTACAGAAGTTTTATAATTTTATG hhhhhhhhhhhhhhhhhhhhhhhhRhhehhhh]hH NM:i:0 -EAS38_1_180_265_430 16 chr1 3131249 0 35M * 0 0 TGATCAGCCCTTTGGCATTCCTCAGTTGAGAATTC GICHVhhCY`\TYhhhh[fdhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_155_516_677 0 chr1 3137065 0 35M * 0 0 CTGGAATTATGTGATTATAATTTTCTTATCATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhh`Dhhhhhh NM:i:1 -EAS38_1_156_788_924 0 chr1 3137065 0 35M * 0 0 CTGGAATTATGTGATTATAATTTTCTTAGCATTTT hhhhhhhhhhhhhhhhhhhhhhhhbhhhh]Shhhh NM:i:0 -EAS38_1_219_907_956 0 chr1 3137065 0 35M * 0 0 CTGGAATTATGTGATTATAATTTTCTTAGCATTTT hhhhhhhhhhh\hhhhhhhhRhhh^hhg`h\hhhh NM:i:0 -EAS38_1_224_924_816 0 chr1 3137074 0 35M * 0 0 TGTGATTATAATTTTNTTAGCATTTTCTTCGTAAA hhhhhhhhhhhhhhh;hhhhh`hhhhhhhXhhhg] NM:i:2 -EAS38_1_128_932_926 16 chr1 3137133 0 35M * 0 0 GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA XYV[Lhfhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_146_271_903 16 chr1 3137133 0 35M * 0 0 TTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA HVhT[`hhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_127_823_362 0 chr1 3137183 0 35M * 0 0 GATAATACATATATACATATGCAGTGTGTGTGCCA hhhhhhhhhhhhhhhhhhhhhhhXhhhhhhhNU[H NM:i:0 -EAS38_1_282_34_255 16 chr1 3137183 0 35M * 0 0 GATAATACATATATAAATATGCAGTGTGTGTGCCA KhNhhLhQh\h`hJhCh`h^hLhhdhhhhhhhheh NM:i:1 -EAS38_1_215_971_567 0 chr1 3137204 0 35M * 0 0 CAGTGTGTGTGCCAGTGGTGTTAACAATACTAATA hhhhh[hhhhhhhhh\hSQeLYcVFKGAKH]XD^H NM:i:1 -EAS38_1_143_6_639 16 chr1 3137450 0 35M * 0 0 ATGTTCCCACACGGTCTATCTCCCTGACAAATCCC RH?>EJUcHhhILIhFhhYShb`hhhhhhhhchhh NM:i:2 -EAS38_1_132_603_749 0 chr1 3154107 255 35M * 0 0 TATATTTGGAAAAAAAAAGAAAGGAGTGTAGAGTC hhhhhhhhhhhhhhhhhhhhhhhhhhehhhhPhSS NM:i:0 -EAS38_1_238_595_598 0 chr1 3178632 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_238_595_598 0 chr1 3178639 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_238_595_598 0 chr1 3178646 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_238_595_598 0 chr1 3178653 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_118_1000_212 0 chr1 3179061 0 35M * 0 0 ATGTGATTTTAAATCATAGTCTTGCTTTTCCATTG hhhhhhhhhhhhghhhEMDPKhhLNh[hhMPNETJ NM:i:2 -EAS38_1_311_90_296 16 chr1 3179539 255 35M * 0 0 ACATAGGAAATGGAAGAGTACTTTATTATTATTAT bEhIhhhhTCNhhhhhhhVhRQhhhhhhhhhhhhh NM:i:1 -EAS38_1_221_489_194 16 chr1 3183282 3 35M * 0 0 ACTGACAGAAAAGAGACAGAGGTAGGACTTCTAGG >>FL[@RL@^WSRYUP@`UZeSLhhRQbOGWThhh NM:i:2 -EAS38_1_221_489_194 16 chr1 3183945 3 35M * 0 0 ACTGACAGAAAAGAGACAGAGGTAGGACTTCTAGG >>FL[@RL@^WSRYUP@`UZeSLhhRQbOGWThhh NM:i:2 -EAS38_1_205_642_159 16 chr1 3186543 255 35M * 0 0 CACATGCCTTTTTCATTTTTTCCAAGTGCCATCTG KhUhSHT]VS]_hFhhMhDbheHhhhhhhhhhhhh NM:i:0 -EAS38_1_26_282_635 16 chr1 3188051 255 35M * 0 0 TTCTGATCCTCAGGATCTGGAGTTACAGATGGTTG ECaSghKhh]ZhhhhdhVhhhh]hhhhhhhhhhhh NM:i:0 -EAS38_1_221_487_440 16 chr1 3188179 255 35M * 0 0 TTACTAAATTTTGTAATACTACTTAGTCTGGAAAA Oge[WhhhTKRShhhhbhhYhhchhh]hhhhhhhh NM:i:0 -EAS38_1_7_602_714 16 chr1 3188938 255 35M * 0 0 GACTGTCATTACATTATTTTAGTAGTTGTATTTTC A\h^SLhhChQhhhhhhhhUhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_239_803_441 16 chr1 3189316 255 35M * 0 0 AGATGTATCATAGCTCAGAAAGTACATTTGTAAGA hhhVhWhRJhYhh^Wbhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_318_649_84 16 chr1 3189316 255 35M * 0 0 AGATGTATCATAGCTCAGAAAGTACATTTGTAAGA hhh\hhhhKhhhhKMhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_178_556_269 0 chr1 3189808 255 35M * 0 0 CTTTTTTTAAAATGACCACAGTGTACTTTATTTAA hhhhhhhhhhhhhhhhhhhhLhhhXhhhhZhhhhX NM:i:2 -EAS38_1_184_810_767 16 chr1 3189830 255 35M * 0 0 GTACTTTATTTAATGATTTTTGTACTTTGTGTTGC dhah]hhhhhhhhhchh_hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_307_56_994 16 chr1 3189841 255 35M * 0 0 AATGATTTTTGTACTTTGTGTTGCAATAAAATAAA hh[Shhhhhh`hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_1_924_497 16 chr1 3189853 255 35M * 0 0 ACTTTGTGTTGAAATAAAATAAAAAAAAAATCTAC SNT[Za]ahh]Lhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_95_808_182 0 chr1 3189880 255 35M * 0 0 AAATCTACAAAATTCAAATATATAAAATTTCAAGT hhhhhhhhhhhhhhhehhhhhhhhhMhhhhh\h^h NM:i:0 -EAS38_1_43_924_188 0 chr1 3189887 255 35M * 0 0 CAAAATTCAAATATATAAAATTTCAAGTTTTCTTT hhhhhhhhh^Xhhhh?hh[RhhhhOMDhhhhhhhh NM:i:0 -EAS38_1_11_826_352 16 chr1 3189890 255 35M * 0 0 AATTCAAATATATAAAATTTCACGTTTTCTTTGTT hhIQAhhhShchchhhhUNU[hChhehhhhbhAhh NM:i:2 -EAS38_1_131_730_378 16 chr1 3189892 255 35M * 0 0 TTCAAATATATAAAATTTCAAGTTTTCTTTCTTTT HIhhhhhhhhhhhhhhhZhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_317_700_555 16 chr1 3189893 255 35M * 0 0 ACAAATATATAAAAGTTCAAGTTTTCTTTCTTTTA ?hhhhhh[hThhhhHhYhEhhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_46_519_952 0 chr1 3189903 255 35M * 0 0 AAAATTTCAAGTTTTNTTTCTTTTAAAGTTTTACA hhhhhhhhhhhhhhh;hhhhhhhhhhhhhhhhhPf NM:i:1 -EAS38_1_26_849_836 0 chr1 3189906 255 35M * 0 0 ATTTCAAGTTTTCTTTCTTTTAAAGTTTTACAAGA hhhhhhhhhhhhhhhhhhhhhdhhhhhhhhhhNXU NM:i:0 -EAS38_1_271_964_726 0 chr1 3189906 255 35M * 0 0 ATTTCAAGTTTTCTTACTTTTAAAGTTTTACAAGA hhhhhhhhhhhhhhhCXhhhhhhhHhhhhhhVhhh NM:i:1 -EAS38_1_305_225_753 16 chr1 3189909 255 35M * 0 0 TCAAGTTTTCTTTCTTTTAAAGTTTTACAAGAAAA Zhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_231_735 16 chr1 3189912 255 35M * 0 0 AGTTTTCTTTCTTTTAAAGTTTTACAAGAAAAAAA hhVhhhhhh_hhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_55_110 0 chr1 3189915 255 35M * 0 0 TTTCTTTCTTTTAAATTTTTACAATAAAAAAAATC hhhhhhhhhhhhUPh\hhhhdhLRcCLTRW@FMhh NM:i:2 -EAS38_1_230_130_609 16 chr1 3189915 255 35M * 0 0 TTTCTTTCTTTTAAAGTTTTACAAGAAAAAAAATC TDMO]K^FLYWWhhhh[S^Rhhhh^hhhhhhhhhh NM:i:0 -EAS38_1_203_262_383 16 chr1 3189917 255 35M * 0 0 TCTTTCTTTTAAAGTTTTACAAGAAAAAAAATCAG ]hJh[ahhhPhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_23_872_103 0 chr1 3189918 255 35M * 0 0 CTTTCTTTTAAATTTTTACAATAAAAAAAATCAGA hhhhhhhhhb_[Dhhhhhh[XAT[hUfKFhhVTM> NM:i:2 -EAS38_1_74_546_492 0 chr1 3189937 255 35M * 0 0 AAGAAAAAAAATCAGATAACCGAGGAAAATTCTTC hhhhhhhhhhhhhhh`h]hhhhThaRPOOhhBhhX NM:i:1 -EAS38_1_177_466_463 0 chr1 3189943 255 35M * 0 0 AAAAATCAGATAACCGAGGAAAATTATTCATTATG hhhhhhhhhhhhhhhhOhMSIIhhhdhh\hhhfhB NM:i:0 -EAS38_1_326_846_82 0 chr1 3189943 255 35M * 0 0 AAAAATCAGATAACCGAGGAAAATTATTCATTATT hhhhhhhhhhhhhhhh]hJdRdhhhZhhhYhbhhG NM:i:1 -EAS38_1_235_891_810 0 chr1 3189957 255 35M * 0 0 CGAGGAAAATTATTCATTATGAAGTACTACTTTCC hhhhhhhhhhhhhhhhhhhhhhhhh_HhOJhhPWI NM:i:0 -EAS38_1_73_865_289 16 chr1 3189961 255 35M * 0 0 GAAAATTATTCATTATGAAGTACTACTTTCCACTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_201_984_898 0 chr1 3189963 255 35M * 0 0 AAATTATTCATTATGAAGTACTACTTTCCACTTCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_37_723_474 16 chr1 3189968 255 35M * 0 0 ATTCATTATGAAGTACTACTTTCCACTTCATTTCA hHEJhFThZhhhhXhUShhhhhhhhhXhhhhhhhh NM:i:0 -EAS38_1_183_791_724 0 chr1 3189973 255 35M * 0 0 TTATGAAGTACTACTTTCCACTTCAGTTCATCACA hhhhhhhhhhhhhhhhhafhhhhdWBhhPYhHPh[ NM:i:1 -EAS38_1_69_87_770 16 chr1 3189978 255 35M * 0 0 AAGTACTACTTTCCACTTCATTTCATCACAAATTG hhJhghhhhhhghhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_54_211_781 16 chr1 3189984 255 35M * 0 0 TACTTTCCACTTCATTTCATCACAAATTGTAACTT hghhhLhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_203_766_573 16 chr1 3189985 255 35M * 0 0 ACTTTCCACTTCATTTCATCACAAATTGTAACTTA SQPbUhhZhhhhhhhWhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_195_866_158 0 chr1 3189991 255 35M * 0 0 CACTTCATTTCAACACAAATTGTAACTTACTTAAC hhhhhhRhhhhh@hchHOThhRh[F`hhPShbNSI NM:i:1 -EAS38_1_122_739_820 16 chr1 3190001 255 35M * 0 0 CATCACAAATTGTAACATACTTAACTGACCAAAAA hhXhfYhhhhSORhhhAghhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_144_950_152 16 chr1 3190008 255 35M * 0 0 AATTGTAACTTACTTAACTGAACAAAAAAACTATG hhIIc_hhI[\hHghhhYhhhHhhhhhhhhhhhhh NM:i:1 -EAS38_1_168_613_587 0 chr1 3190008 255 35M * 0 0 AATTGTAACTTACTTAACTGACCAAAAAAACTATG hhhhhhhhhhhhhhhhhhhhgh`SNhfhhRahZf\ NM:i:0 -EAS38_1_134_699_616 16 chr1 3190013 255 35M * 0 0 TAACTTACTTAACTGACCAAAAAAACTATGGTACT hhhQhMhhehhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_777_789 0 chr1 3190014 255 35M * 0 0 AACTTACTTAACTGACCAAAAAAACTATGGTACTG hhhhhhhhhhhhhhhWfh\`hHhhShgYhXGZIQU NM:i:0 -EAS38_1_66_446_787 0 chr1 3190014 255 35M * 0 0 AACTTACTTAACTGACCAAAAAAACTATGGTACTG hhhhhhhhhhhhhhhhhhhhhhh]dhhhhdghShh NM:i:0 -EAS38_1_179_978_676 16 chr1 3190032 255 35M * 0 0 AAAAAACTATGGTACTGCAGTATAGCAAATACTCC hhhhhghWhZhFhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_308_776_503 16 chr1 3190032 255 35M * 0 0 AAAAAACTATGGTACTGCAGTATAGCAAATACTCC hhhhhh^?hRhThhhghbhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_172_693_734 16 chr1 3190040 255 35M * 0 0 ATGGTACTGCAGTATAGCANATACTCCACACACTG hLD?UFaLLhaJhhhh[hh;hhhhhhhhhhhhhhh NM:i:1 -EAS38_1_239_423_396 16 chr1 3190040 255 35M * 0 0 AGGGTACTGAAGTATAGCAAATACTCCACACACTG _AH?>LADTCZh^h]hhDhhhZhhehhhhhhhhhh NM:i:2 -EAS38_1_284_912_582 16 chr1 3190042 255 35M * 0 0 GGTACTGCAGTATAGCAAATACTCCACACACTGTG LhhhhhhhhhhhhhhWhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_209_687_576 0 chr1 3190073 255 35M * 0 0 TGTGCTTTGAGCTAGAGCACTTGGAGTCACTGCCC hhhhhhhhhhhhhhhdhhZdhhYhPMhRPIeMWGP NM:i:0 -EAS38_1_185_490_551 16 chr1 3190085 255 35M * 0 0 TAGAGCACTTGGAGTCACTGCCCAGGGCAGCAGCC FJDFJGJJODb\`hJQ_hNghhhhhhhh`hhhhhh NM:i:0 -EAS38_1_65_838_419 0 chr1 3190102 255 35M * 0 0 CTGCCCAGGGCAGCAGCCTCCAACCAAGAAAGACA hhhhhhhhhhh]_hKhhchceBdGaOCG@?BGIIP NM:i:0 -EAS38_1_323_255_975 0 chr1 3190107 255 35M * 0 0 CAGGGCAGCAGCCTCCAACCAAGAAAGACACACTT hhhhhhhh\hhUShNYh]@Uh\hMXMaJ?YRRBFH NM:i:0 -EAS38_1_296_538_461 0 chr1 3190126 255 35M * 0 0 CAAGAAATACACACTTACAAGTTGAATTCTAAAGG hhhhhhhhhhhhhhhhhh]hhhhh\hhhhhMhbhh NM:i:1 -EAS38_1_132_195_514 16 chr1 3190129 255 35M * 0 0 GAAAGACACACTTACAAGTTGAATTCTAAAGGAAG chbhhhShFhhYhhghhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_155_895_725 16 chr1 3190140 255 35M * 0 0 TTTCAAGTTGAATTCTAAAGGAAGGTCTGGTTATG VhO[ghWSchhh_hZhhhhhhhhhXhhhhhhhhhh NM:i:1 -EAS38_1_193_609_633 16 chr1 3190140 255 35M * 0 0 TTACAAGTTGAATTCTAAAGGAAGGTCTGGTTATG Q`hbhhh[hhhhShhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_135_816_228 16 chr1 3190142 255 35M * 0 0 AAAAGTTGAATTCTAAAGGAAGGTCTGGTTATGTG fC_]SH_VhhIABLhhhhfhhhWfZhhhhhhhhhh NM:i:1 -EAS38_1_145_593_539 0 chr1 3190150 255 35M * 0 0 AATTCTAAAGGAAGGTCTGGTTATGTGGGGTTGTA hhhhhhhhhhhhhhhhhhhhhhhhQh`ShhhhhAH NM:i:1 -EAS38_1_121_577_810 16 chr1 3190177 255 35M * 0 0 GGGTTGGAGTATGTATATCTATATATCTCTATATA KJM]OSdhbXhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_194_207_828 0 chr1 3190207 255 35M * 0 0 ATATATATTTACATCAAAGAATTTAATAACTCATT hhhhhhhhhhhhhhhhhhhhhhhhchhTh_h_`hh NM:i:0 -EAS38_1_113_803_974 0 chr1 3190221 255 35M * 0 0 CAAAGAATTTAATAACTCATTTAAATTTTTGTTTC hhhhhhhhhhhhhhhchQhhhhhgOhh_hhh_hhL NM:i:0 -EAS38_1_160_812_510 16 chr1 3190244 255 35M * 0 0 AATTTTTGTTTCAAATAAAATTCCAAATACACTTG hhWOhG]h^hhQhhhhhhhhh_\hhhhhhhhBhhh NM:i:1 -EAS38_1_40_88_508 16 chr1 3190249 255 35M * 0 0 TTGTTTCAAATAAAATTCCAAATACATTTGTACAA QhhgVhdhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_84_935_631 16 chr1 3190249 255 35M * 0 0 TTGTTTCAAATAAAATTCCAAATACATTTGTACAA ^]hJhZWhhhhhhhhhUhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_36_762_603 0 chr1 3190263 255 35M * 0 0 ATTCCAAATACATTTGTACAATGTTTACAAAGTAA hhhhhhhhhhhhhhhhhhhhhh^hhhhahX\]_hb NM:i:0 -EAS38_1_16_788_728 16 chr1 3190265 255 35M * 0 0 TCCAAATACATTTGTACAATGTTTACAAAGTAAGA @hEhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_172_782_398 16 chr1 3190269 255 35M * 0 0 AATACATTTGTACAATGTTNACAAAGTAAGAGACA hhZhhhaZhhWhhhhhheh;hThhhhehhhhhhhh NM:i:1 -EAS38_1_319_78_862 16 chr1 3190274 255 35M * 0 0 ATTTGTACAATGTTTACAAAGTAAGAGACAGGACT dLhZM_ehdhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_27_817_428 16 chr1 3190276 255 35M * 0 0 TTGTAAAATGTTTACAAAGTAAGAGACAGGACTGG VPhchChh_ghfhhEhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_188_256_713 0 chr1 3190325 255 35M * 0 0 AGGCCAGGCACCGTGATGTCCGGGTGATATATCTT hhhhhhhhhhhhhhhKhhaMhUhhNgA_E[GhM[G NM:i:0 -EAS38_1_315_859_502 16 chr1 3190329 255 35M * 0 0 CAGGAACCGTGATGTCCGGGTGATATATCTTCACG BNSIKHNI\SK]VdXZR`Uhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_152_381_800 16 chr1 3190355 255 35M * 0 0 ATCTTCACGTTGCCTGCACACACCTTATTTCTGAA ZVhQIhhhhhhXhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_282_558_872 0 chr1 3190364 255 35M * 0 0 TTGTCTGCACACACCTTATTTCTGAAATGGAGAGA hhh=hhhhhhhhh_hhhhhhhYhh`hhhhhQhhhC NM:i:1 -EAS38_1_215_759_830 0 chr1 3190407 255 35M * 0 0 AGAATGTCACCGACTATGCATCAGAATACTATGTA hhhhhhhhhhhhhhhhhhh_hh[hUWhhbh^hhXc NM:i:0 -EAS38_1_277_471_798 16 chr1 3190412 255 35M * 0 0 GTCACCGACTATGCATCAGAATACTATGTACAGTT KJYK\eYhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_279_405_802 16 chr1 3190418 255 35M * 0 0 GACTATGCATCAGAATACTATGTACAGTTGAAGTT Chhhhhhhhhhhhhhhhhhhhhhhhh`hhhhhhhh NM:i:0 -EAS38_1_75_573_457 16 chr1 3190428 255 35M * 0 0 CAGAATACTATGTACAGTTGAAGTTAGGGAGCTGA Zhdhh_dhYhRh\hhhhUKhhhhhUhhhhhhhhhh NM:i:0 -EAS38_1_238_427_419 16 chr1 3190444 255 35M * 0 0 GTTGAAGTTAGGGAGCTGAGAACCTAGTGGTCTGT XKEQdhhNKZhhhhhhdhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_24_788_817 0 chr1 3190444 255 35M * 0 0 GTTGAAGTTAGGGAGCTGAGAACCTAGTGGGCTGT hhhhhhhhhhhhhQhHhhUeK_AGXKhNfe>=ITO NM:i:1 -EAS38_1_307_22_417 16 chr1 3190449 255 35M * 0 0 AGTTAGGGAGCTGAGAACCTAGTGGTCTGTTCTCT KU@DX`XWbV@JhghhTETVhh^hTWh_hh[hhhh NM:i:0 -EAS38_1_104_731_910 0 chr1 3190455 255 35M * 0 0 GGAGCTGAGAACCTAGTGGTCTGTTCTCTTCTGGT hhhhhhhhhhhJYhhhhhhZOhhhhBhF\hFhhaO NM:i:0 -EAS38_1_189_367_978 16 chr1 3190466 255 35M * 0 0 CCTAGTGTTCTGTTCTCTTCTGGTTTGTCTTCATC HhCMIbQEShcKTYhhh\hhhYPhhhhhhhhhhhh NM:i:1 -EAS38_1_288_697_269 0 chr1 3190470 255 35M * 0 0 GTGGTCTGTTCTCTTCTTGTTTGTCTTCATCTACC hhhhhhhhhhhhhhhhhBChhhDhhhhhQhhhI?c NM:i:1 -EAS38_1_239_232_371 16 chr1 3190490 255 35M * 0 0 GTGTCTTAATCTACCAGCTATTACTCCTCTTTTGC DKK?ADHAhKCIhVhhhB_hchhhbhhZhhhhhhh NM:i:2 -EAS38_1_17_329_620 16 chr1 3190509 255 35M * 0 0 ATTACTCCTCTTTTGCTCAGAGATAAATTTAAAAT h^E_hMhchhhThVhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_145_66_863 0 chr1 3190520 255 35M * 0 0 TTTGCTCAGAGATAAATTTAAAATACAAACATTGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhc NM:i:0 -EAS38_1_318_476_736 0 chr1 3190562 255 35M * 0 0 AAGGAGAAAAGCACAAAATATTTAAGGCAAATTAA hhhhhhhhhhhhhhhhhhhhhhhhfhh^hF\hhhH NM:i:0 -EAS38_1_91_887_139 16 chr1 3190577 255 35M * 0 0 AAATATTTAAGGCAAATTAAGCAAATATGTACAGT hhhhhK^ThhZhThhh\hhhhZhhhhhhhhhhhhh NM:i:0 -EAS38_1_42_628_869 16 chr1 3190582 255 35M * 0 0 TTTAAGGCAAATTAAGCAAATATGTACAGTCTCTT EYEhhBDYhhh^hhhLhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_266_296_122 16 chr1 3190587 255 35M * 0 0 GGAAAATTAAGAAAATATGTACAGTCTCTTTGTGC hUJhhh@ehhhFhhhShIhehhhh`h\hhbhhhhh NM:i:2 -EAS38_1_296_47_651 0 chr1 3190588 255 35M * 0 0 GCAAATTAAGCAAATATGTACAGTCTCTTTTTTCC hhhhhhhhhhhhhhhhhhhhh[hhhhhhhhDhIRE NM:i:2 -EAS38_1_298_622_554 16 chr1 3190612 255 35M * 0 0 CTCTGTGTGCCAGGAGGATGTGACTTTCTTTTTAA QXfIBXhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_55_346_335 16 chr1 3190613 255 35M * 0 0 TCGGTGTGCCAGGAGGATGTGACTTTCTTTTTAAA KABCGhGh@hhhhhhhhhh^hhhhhhhhhhhhhhh NM:i:2 -EAS38_1_144_104_681 16 chr1 3190646 255 35M * 0 0 AATCCCAAACCATGCTTTAAAAAATTCAAATAAAG hhVhJThhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_307_505_905 0 chr1 3190650 255 35M * 0 0 CCAAACCATGCTTTAAAAAATTCAAATAAAGCAAG hhhhhhhhhhhhhhhhhhhhhhhhShhhh_h\`hh NM:i:0 -EAS38_1_4_468_915 0 chr1 3190667 255 35M * 0 0 AAATTCAAATAAAGCAAGTCTGGTGTGAGTTGGGT hhhhhhhhhhhhhhhhhhhhhhhahfhJhhhhhha NM:i:0 -EAS38_1_177_100_872 0 chr1 3190682 255 35M * 0 0 AAGTCTGGTGTGAGTTGGGTTGCTTGTGTTGTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhThhhhh NM:i:0 -EAS38_1_201_448_983 0 chr1 3190733 255 35M * 0 0 TGTTTTGCACAAAATAACCATTTGGAATTTGCAGT hhhhhhhahhhhhhhhhZMhhhhhhNhhhhXGXhH NM:i:0 -EAS38_1_205_905_511 16 chr1 3190740 255 35M * 0 0 AACAAAATAACCATTTGGAATTTGCAGTGGAATAA hhFhhhhahhhhhhahhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_22_834_621 0 chr1 3190741 255 35M * 0 0 ACAAAATAACCATTTGGAATTTGCAGTGGAATAAT hhhhhhhhhhhhhhhhhYhhhhhh]h]h[NVhI`h NM:i:0 -EAS38_1_297_847_594 16 chr1 3190753 255 35M * 0 0 TTTGGAATTTGCAGTGGAATAATTTGTTAATTGTG `KYZ\hX^dhYhhhhbhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_105_929_305 16 chr1 3190768 255 35M * 0 0 GGAATAATTTGTTAATTGAGAAGTGTATGGTTTTG hhhhhhhQ]hhhhhh_hhEhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_323_29_609 0 chr1 3190771 255 35M * 0 0 ATAATTTGTTAATTGTGAAGTGTATGGTTTTGTAT hhhhhhhhhhhhhhhhhhhOhhhhhhhhhhh@hGh NM:i:0 -EAS38_1_174_674_495 0 chr1 3190781 255 35M * 0 0 AATTGTGAAGTGTATGGTTTTGTATTTTTAAACCA hhhhhhhhhhhhhhhhhhhhhFhhhhhhLUPaeSG NM:i:1 -EAS38_1_156_965_73 16 chr1 3190814 255 35M * 0 0 CAAAAAACAGTAGCTGAGGTAGTTAAATGTGAAAC DhhhCghNhhhhhRhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_264_136_776 0 chr1 3190842 255 35M * 0 0 GTGAAACTTACACAACTTAAAATAATGAGAGAATG hhhhhhhhhh`hbhhYhhbh_eh_hhbM\O]IVYR NM:i:0 -EAS38_1_269_103_855 16 chr1 3190853 255 35M * 0 0 ACAACTTAAAATAATGAGAGAATGGAGAACCAATG ShhhhhXhhhhchhLhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_133_823_893 0 chr1 3190856 255 35M * 0 0 GCTTAAAATAATGAGAGAATGGAGAAACAATGTAA hhhhhhhhhhhhhhhbhhVhhhahQZ@KZhSUKgH NM:i:2 -EAS38_1_316_626_26 0 chr1 3190872 255 35M * 0 0 GAATGGAGAACCAATGTAAGGAGCCCAGACTCTTG hhhhhhhhhh]hhhhh^hXNhhXLcGGFEMVIL\A NM:i:0 -EAS38_1_14_936_623 0 chr1 3190882 255 35M * 0 0 CCAATGTAAGGAGCCCAGACTCTTGCCATCTGGGA hhhhhhhhdhhhhYTbFhTWehhNJdKDJVREM?E NM:i:1 -EAS38_1_112_85_814 16 chr1 3190885 255 35M * 0 0 ATGTAAGGAACCCAGACTCTTGCCATCTGGAAGCA dBCDhhRNh?RhWhWhhWhZh[hhhhhhhhhhhhh NM:i:1 -EAS38_1_153_136_402 16 chr1 3190885 255 35M * 0 0 ATGTAAGGAGCCCAGACTCTTGCCATCTGGAAGCA QUhWhhh[hTahhhhQhhUhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_267_293_629 16 chr1 3190891 255 35M * 0 0 GGAGCCCAGACTCTTGCCATCTGGAAGCAGGCTCA Zg]YhEhhhhfd`hZhJhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_60_948_719 16 chr1 3190944 255 35M * 0 0 TACCCAGAAAAACATTTGTTCTTTTGGATGCCATT BAHQQhFehhhRhUPKJVf\hh^bWh_hhhhhhhh NM:i:0 -EAS38_1_279_273_497 0 chr1 3190975 255 35M * 0 0 CATTAGTTCAGCCAGTGTCAACATGACTAGTGGTT hhhhhhhhhhhhhhhZYhhhhahhh`Uh`ELGVVg NM:i:0 -EAS38_1_35_405_941 16 chr1 3190979 255 35M * 0 0 AGTTCAGCCAGTGTCAACATGACTAGTGGTTTCCC E??>bfB^hhOIT_hhhhhhUWhhhhh^hhhhhhh NM:i:0 -EAS38_1_307_828_462 16 chr1 3190995 255 35M * 0 0 ACATGACTAGTGGTTTCCCAAGCACTTGCTTGGAA hRhhhhh^hhhhhhhhGfhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_118_418_323 16 chr1 3191023 255 35M * 0 0 CGTGGAAGCAAAGATAAAGAAAGTCTGCTTTCCAG IS@dWhh]NhhhHhbhhhhhhhhZhchhhhghhhh NM:i:2 -EAS38_1_144_10_603 0 chr1 3191023 255 35M * 0 0 CTTGGAAGCAAATATAAAGAAAGTCTGCTTTCCAG hhhhhhhhhhZhhhhhhdhWhhhhhhh^hhhDhKU NM:i:0 -EAS38_1_219_965_773 16 chr1 3191038 255 35M * 0 0 AAAGAAAGTCTGCTTTCCACGCTTCTCATCTATAG hhhIhhh[ehXQhhhahhhJhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_56_375_762 16 chr1 3191134 255 35M * 0 0 CATTATTAGAAATTCCAACCCTAGTTATGAAAGAT hh_VhKZhMhhhSXbhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_148_601_688 16 chr1 3191142 255 35M * 0 0 GAAATTCCAACCCTAGTTATGAAAGATTGAGGGGA hhhhhTdhhhhhhhhhhhhhhhhhhhhhhhhhh>h NM:i:1 -EAS38_1_236_489_757 0 chr1 3191149 255 35M * 0 0 CAACCCTAGTTATGAAAGATTGAGGGAAAGTGATA hhhhhhhhhhhhhhhhhhThhhbhhhSKhhXhTh_ NM:i:0 -EAS38_1_144_552_470 0 chr1 3191153 255 35M * 0 0 CCTAGTTATGAAAGATTGAGGGAAAGTGATAAAGA hhhhhhhhhhhhhhehhhh`h\IPThhhThGKUML NM:i:0 -EAS38_1_288_225_365 16 chr1 3191173 255 35M * 0 0 GGAAAGTGATAAAGAACAAAAGGGAGGGATATTAT hhhhhh\hh`hhhhhhMhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_33_904_669 0 chr1 3191192 255 35M * 0 0 AAGGGAGGGATATTATTCTCTCATTTTTAACAGCA hhhhhhhhhhhhhhhhhhhhhhghhhhhhhhYKJH NM:i:0 -EAS38_1_123_430_125 16 chr1 3191220 255 35M * 0 0 AACAGCATATTTGTCTTAGCTTTAAATCCAGAGTA hhDh`Ch`h[UTh[RhehhcThhhhhhhhhhhhhh NM:i:0 -EAS38_1_179_676_404 16 chr1 3191241 255 35M * 0 0 TTAAATCCAGAGTACTGTTTGGCTTCAAAGAAGAT QhhhhLZUhhhhfhhbhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_120_22_725 0 chr1 3191250 255 35M * 0 0 GAGTACTGTTTGGCTTCAAAGAAGATAGTCATCTC hhhhhhhhhhhhhhhhfhhhhahhhhdhhhZhNhX NM:i:0 -EAS38_1_223_373_449 0 chr1 3191268 255 35M * 0 0 AAGAAGATAGTCATCACTGGTTCTCTTACTGAGAA hhhhhhhhhhhhhhhDhhhhZhhhhhh^hh[NFCQ NM:i:1 -EAS38_1_112_183_986 0 chr1 3191269 255 35M * 0 0 AGAAGATAGTCATCTCTGGTTCTCTTACTGAGAAT hhhhhhhhhhhhhhhfhhhehhhfhhX\hhVhbKg NM:i:0 -EAS38_1_172_99_819 16 chr1 3191287 255 35M * 0 0 GTTCTCTTACTGAGAATAGNAAGTCTCTCCTTACT U\VhOhhhhhhhhhhhhhh;hhhhhhhhhhhhhhh NM:i:1 -EAS38_1_210_930_591 16 chr1 3191287 255 35M * 0 0 GTTCTCTTACTGAGAATAGAAAGTCTCTCCTTACT LWK^Khh^ShNhhhhhhhhhhhhXhhhhhhhhhhh NM:i:0 -EAS38_1_100_778_539 16 chr1 3191290 255 35M * 0 0 CTCTTACTGAGAATAGAAAGTCTCTCCTTACTGAG hhfhhhThhhhhhhhhhhhh^hhhhhhhhhhhhhh NM:i:0 -EAS38_1_25_830_623 16 chr1 3191298 255 35M * 0 0 GAGAATAGAAAGTCTCTCCTTACTGAGAATAGGAA YhRhhLhhhhhh`h\hhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_304_473_442 0 chr1 3191304 255 35M * 0 0 AGAAAGTCTCTCCTTACTGAGAATAGGAAGCCATC `hhhThehhhhh\hhXYhgJ`ILQLDNBIAAM=HD NM:i:0 -EAS38_1_205_508_718 16 chr1 3191307 255 35M * 0 0 AAGTCTCTCCTTACTGAGAATAGGAAGCCATCTTC hhRBOThbhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_293_376_615 16 chr1 3191307 255 35M * 0 0 AAGTCTCTCCTTACTGAGAATAGGAAGCCATCTTC hhh@hFhOhhghhh[hh`hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_182_907_727 16 chr1 3191326 255 35M * 0 0 ATAGGAAGCNATCTTCATACCTGTCCCTCTGCATT hM^FJg`Mh;hhhhfhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_222_741_776 0 chr1 3191358 255 35M * 0 0 ATTTATTCTTGAGGTTACTGAGCCATCTGGCTACA hhhhhhhhhhhhhhChhYhTehDVghIhh][ZF?K NM:i:0 -EAS38_1_88_323_543 16 chr1 3191374 255 35M * 0 0 ACTGAGCCATCTGGCTACAGAGAAGAAAAGCAAGA X\Ghhe^JhNaXhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_66_197_743 16 chr1 3191383 255 35M * 0 0 TCTGGCTACAGAGAAGAAAAGCAAGAGTTGTTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_173_864_740 16 chr1 3191391 255 35M * 0 0 CAGAGAAGAAAAGCAAGAGTTGTTTTTTTATTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_124_858_171 16 chr1 3191398 255 35M * 0 0 GAAAAGCAAGAGTTGTTTTTTTATTTTTATTTTAT chhhhU\hhhhcOchhObh]hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_126_138_418 16 chr1 3191410 255 35M * 0 0 TTGTGTTTTTATTTTTATTTTATTTTTATTTTTTT U`hhBfhZZhhh`Yhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_221_397_462 0 chr1 3191429 255 35M * 0 0 TTTTTTTTATTTTTTTAAGTAGAAGCAAGATTCTC hhhhhhhhZhhhhhhhhVFhbKMSWhRG]?hhQh[ NM:i:1 -EAS38_1_216_901_971 0 chr1 3191444 255 35M * 0 0 TAAGTAGAAGCAAGATTCTCATTAAGGCTAACTAT hhhhhhhhhhhhhhhhhahZZhbhabfQ[MKFWGU NM:i:0 -EAS38_1_282_128_662 0 chr1 3191445 255 35M * 0 0 AAGTAGAAGCAAGATTCTCATTAAGGCTAACTATG hhhhhhhchhhhh]hhhhhVhhZhhhZhZ@MbMaL NM:i:0 -EAS38_1_77_686_871 0 chr1 3191446 255 35M * 0 0 AGTAGAAGCAAGATTCTCATTAAGGCTAATTATGT hhhhhhhhhhhhhhhdhhhhhhhhh^hh]@hhh`B NM:i:2 -EAS38_1_95_356_853 0 chr1 3191446 255 35M * 0 0 AGTAGAAGCAAGATTCTCATTAAGGCTAACTATGC hhhhhhhhhhhhhhhhhhhhhhPhhfh\HJGUhLN NM:i:0 -EAS38_1_315_80_525 0 chr1 3191449 255 35M * 0 0 AGATGCAAGATTCTCATTAAGGCTAACTATGCTAT hhhhhhhhhhhhhhhehhhR\Khh]]gh[hZ_hJh NM:i:1 -EAS38_1_211_797_532 0 chr1 3191471 255 35M * 0 0 CTAACTATGCTATTCTCCACTGCGCCCCATTGATC hhhhhhhhhhhhhhhhhhhhhfcIhLh[HhgUUhK NM:i:0 -EAS38_1_326_311_799 0 chr1 3191471 255 35M * 0 0 CTAACTATGCTATTCTCCACTGCGCCCCATTGATC hhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhVhG NM:i:0 -EAS38_1_107_806_891 16 chr1 3191478 255 35M * 0 0 TCCTATTCTCCACTGCGCCCCATTGATCAGACAAT LBfP^MWhAhh_hh^hZhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_121_349_512 0 chr1 3191489 255 35M * 0 0 ACTGCGCCCCATTGATCAGACAATGGCTTTAAGTG hhhhhhhhhhhhhhhhhhhhhBhhhhhhhhOOJeT NM:i:0 -EAS38_1_219_430_836 16 chr1 3191498 255 35M * 0 0 CATTGATCAGACAATGGCTTTAAGTGGGGCCTAAA c_WRRdUhhN[hhhdaWhOhhhghhhhhhhhhhhh NM:i:0 -EAS38_1_98_807_431 16 chr1 3191517 255 35M * 0 0 TTAAGTGGGGCCTAAATGAACTGTTGGACATCAGG PQg^SGhO[eOKhhhh`hhhYahhXhhhhhhhhhh NM:i:0 -EAS38_1_155_241_829 16 chr1 3191535 255 35M * 0 0 AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG ]QbLHKRRThhhWhhh[hdghhhhhhhhhhhhhhh NM:i:0 -EAS38_1_223_732_501 0 chr1 3191535 255 35M * 0 0 AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG hhhhhhhhhYhahh\EQghh\hPMJd_hSX[XhgE NM:i:0 -EAS38_1_320_444_109 16 chr1 3191535 255 35M * 0 0 AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG hbHUhhGhhhRhhhhhWZhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_103_761_542 0 chr1 3191537 255 35M * 0 0 CTGTTGGACATCAGGTTCATGAAAACGGTTTTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_245_218_950 0 chr1 3191539 255 35M * 0 0 GTTGGACATCAGGTTCATGAAAACGGTTTTGTGCA hhhhhhhhhchhhhhhhhhhhhhKhhhhhh_\R>f NM:i:1 -EAS38_1_54_654_789 0 chr1 3191548 255 35M * 0 0 CAGGTTCATGAAAACGGTTTTGTGAAGGTAATATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhLhChhh^ NM:i:0 -EAS38_1_242_532_556 0 chr1 3191553 255 35M * 0 0 TCATGAAAACGGTTTTGTGAAGGTAATATATCAGT hhhhhh]hhhhhhhhhZhTfchhO[LhUhXTCJJP NM:i:0 -EAS38_1_37_578_493 16 chr1 3191563 255 35M * 0 0 GGTTTGGTGAAGGTAATATATCAGTAATATGGTTG THOCeDUEhhZQgchhhhhhJhhhhhhhhhhhhhh NM:i:1 -EAS38_1_151_713_632 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhhh`hhhSThh NM:i:0 -EAS38_1_152_680_718 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhh^g\hhbhhh^ NM:i:0 -EAS38_1_152_24_706 0 chr1 3191573 255 35M * 0 0 AGGTAATATATCAGTAATATGGTTGACATAAATAA hhhhhhhhhhhhhhhhhhhhhhhhhOehhhWhhhW NM:i:0 -EAS38_1_330_686_422 16 chr1 3191575 255 35M * 0 0 GTAATATATCAGTAATATGGTTGACATAAATAAGC GLhhdhbhGJhh_hhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_275_44_659 0 chr1 3191579 255 35M * 0 0 TATATCAGTAATATGGTTGACATAAATAAGCTGGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhTcg NM:i:0 -EAS38_1_324_589_894 0 chr1 3191579 255 35M * 0 0 TATATCAGTAATATGGTTGACATAAATAAGATGGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhXhhhh NM:i:1 -EAS38_1_121_763_313 0 chr1 3191589 255 35M * 0 0 ATATGGTTGACATAAATAAGCTGGGAAATAGTTCT hhhhhhhhhhhhhhhhhhhhhhchhWFhhTChhfh NM:i:0 -EAS38_1_130_668_987 16 chr1 3191610 255 35M * 0 0 TGGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTT UT>Khbhbhhh[hhhhZhhfhhhhhhhhhhhhhBh NM:i:0 -EAS38_1_80_262_758 16 chr1 3191611 255 35M * 0 0 GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC PYdhhhMhh\HhhVhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_272_104_967 0 chr1 3191614 255 35M * 0 0 AAATAGTTCTTTTAGAAAGTAGAAGATTTTTCTCT hhhhhhhhhhhhhhhGhhhhhhhehXhhhhhZhZh NM:i:1 -EAS38_1_142_144_587 16 chr1 3191617 255 35M * 0 0 TAGTTCTTTTAGGAAGTAGAAGATTTTTCTCTTTG bhhhHPhNhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_282_509_344 16 chr1 3191618 255 35M * 0 0 AGTTCTTTTAGGAAGTAGAAGATTTTTCTCTTTGT hh^YdVSKWhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_3_797_743 0 chr1 3191619 255 35M * 0 0 GTTCTTTTAGGAAGCAGAAGATTTTTCTCTTTTTG hhhhhhhhhhhhhhAhhhhhXhhhhhhhfhhhHhb NM:i:2 -EAS38_1_311_266_241 16 chr1 3191633 255 35M * 0 0 TAGAAGATTTTTCTCTTTGTGTCTGTGTCTTTCAT LhhhhhhXGFHH_HhhhThhhdhhhhhhhhhhhhh NM:i:0 -EAS38_1_282_320_153 16 chr1 3191635 255 35M * 0 0 GAAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTT OQ\\PEA[JHNGRQJhhhhXNhhWhVhhUfhhhhh NM:i:0 -EAS38_1_74_839_687 16 chr1 3191635 255 35M * 0 0 GAAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTT MhhWhS[hhGhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_119_931_54 16 chr1 3191636 255 35M * 0 0 AAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTTG QJ?JRKXIZaOhYYdbhhhhbhhhfhhhhhhhhhh NM:i:0 -EAS38_1_171_559_793 16 chr1 3191638 255 35M * 0 0 GATTTTTCTCTTTGTGTCTGTGTCTTTCATTTGCC U_NhR[ZhhhRhWhhhhhh>hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_9_831_797 0 chr1 3191643 255 35M * 0 0 TTCTCTTTGTGTCTGTGTCTTTCATTTGCCTTTGT hhhhhhhhhhhhhhhhhhGhhhGChhhH>Kd?hEA NM:i:2 -EAS38_1_112_463_853 0 chr1 3191663 255 35M * 0 0 TTCATTTGCCTATGAAAAGAATGTTAGTTGGCTGT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhah^h NM:i:0 -EAS38_1_200_507_523 16 chr1 3191673 255 35M * 0 0 TATGAAAAGAATGTTAGTTGGCTGTAACCATAAAA @hW^hhhhehhKgXh\hh^hhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_307_105_716 0 chr1 3191676 255 35M * 0 0 GAAAAGAATGTTAGTTGGCTGTAACCATAAAATTG hhhhhhhhhhhhhhhhhhhhhhUh[_Hh]aQdhhZ NM:i:0 -EAS38_1_81_670_875 16 chr1 3191698 255 35M * 0 0 AACCATAAAATTGGCAGTTGTATTTACAAATAATC hehhhhhhhhhhhZhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_285_30_406 0 chr1 3191712 255 35M * 0 0 CAGTTGTATTTACAAATAATCACATATATTATGCT h_hhhhh_hhh]hQQShILhhYhQhIhHhCIh@U_ NM:i:1 -EAS38_1_45_791_522 16 chr1 3191716 255 35M * 0 0 TGTATTTACAAATAATCACATATATGATGCTTACA hh`hhXhhhhhhhhhfhhhHhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_43_819_567 16 chr1 3191719 255 35M * 0 0 ATTTACAAATAATCACATATATGATGCTTACAGAA hhQhhChhhhhhhhhhhhh@hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_26_772_717 0 chr1 3191761 255 35M * 0 0 CTCATTTCTAAATAATCACATATGCTAAAAGCTAG hhhhhhhhhhhhhhhhhhhhhZhhYhWfahSIhHS NM:i:0 -EAS38_1_130_865_419 0 chr1 3191766 255 35M * 0 0 TTCTAAATAATCACATATGCTAAAAGCTAGGTTTT hhhhhhhhhhhhhhhhhhhhh\`hhOhhELh_hhh NM:i:0 -EAS38_1_327_933_866 0 chr1 3191766 255 35M * 0 0 TTCTAAATAATCACATATGCTAAAAGCTAGGTTTT hhhhhhhhhhhhhhhhhhhhhhh]chYhPhLYhhh NM:i:0 -EAS38_1_126_547_811 16 chr1 3191773 255 35M * 0 0 TAATCACATATGCTAAAAGCTAGGTTTTTCTAATA hhhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_277_668_994 16 chr1 3191773 255 35M * 0 0 TAATCACATATGCTAAAAGCTAGGTTTTTCTAATA _hhJhhhhhhh]hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_181_734_387 16 chr1 3191780 255 35M * 0 0 ATATGCTAAAAGCTAGGTTTTTCTAATACACTTTT hNhNTARh`hhhIOhhhXeRMhLahhhhhhhhhhh NM:i:0 -EAS38_1_174_224_835 16 chr1 3191785 255 35M * 0 0 CTAAAAGCTAGGTTTTTCTAATACACTTTTACTTT hhhhhhhhhhdghhhhhhhhhhhhhhhhhhh>hhh NM:i:1 -EAS38_1_192_253_159 16 chr1 3191794 255 35M * 0 0 AGGTTTTTATAATACACTTTTATTTTCATGGAGGG hhc\PLNGAfhhhhhh[hZ[_hh[ahhhYhhhhhh NM:i:1 -EAS38_1_184_325_530 16 chr1 3191800 255 35M * 0 0 TTCTAATACACTTTTATTTTCATGGAGGGCTCTAG hGV[hhWhhhhhXh^hghhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_250_311_830 16 chr1 3191810 255 35M * 0 0 CTTTTATTTTCATGGAGGGCTCTAGAGGATTCCAC YLGJTUPJNNXgKQR_VKThhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_275_852_575 16 chr1 3191813 255 35M * 0 0 TTATTTTCATGGAGGGCTCTAGAGGATTCCACGTG JVeYM[E`hJSLV]SQVRChhhhhhhhhhhShhhh NM:i:0 -EAS38_1_77_390_526 0 chr1 3191818 255 35M * 0 0 TTCATGGAGGGCTCTAGAGGATTCCCCGTGGCATA hhhhhhhhhhhhhhhThNhhOhhOQA_^TEV=^EG NM:i:2 -EAS38_1_299_893_564 16 chr1 3191846 255 35M * 0 0 TGGAATAGAAACCACTGAAAAGAGACTCAACTCTT @aVhhKhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_294_440_933 16 chr1 3191865 255 35M * 0 0 TAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA O^EV?MhDhhUh\hYKVTKhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_278_780_674 16 chr1 3191873 255 35M * 0 0 CAACTCTTTTTCCCCCCAGCAATATTATGTTGCTC hhVWchcZHXMhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_86_970_279 0 chr1 3191876 255 35M * 0 0 CTCTTTTTCCCCCCAGCAATATTATGTTGCTCTGT hhhhhhhhhhhhhhPhheHhfhhehOhhEOhUhAF NM:i:0 -EAS38_1_148_146_536 0 chr1 3191881 255 35M * 0 0 TCTCCCCCCAGCAATATTATGTTGCTCTGTGCTGC hDhhhhhhh]hhhdhhhhhhhhhEhhhh\hEhhHG NM:i:1 -EAS38_1_224_888_484 16 chr1 3191884 255 35M * 0 0 CACCCCAGCAATATTATGTTGCTCTGTGCTGCTCT P?KJEARLNW`TdVWhF^OThhMgQ\hhhhfhhhh NM:i:1 -EAS38_1_223_648_752 0 chr1 3191887 255 35M * 0 0 CCCAGCAATATTATGCTGCTCTGTGCTGCTCTATG h_hhhhhhhhhhhhh=hhhhYhhOVghhB\AhWhM NM:i:1 -EAS38_1_300_220_617 0 chr1 3191891 255 35M * 0 0 GCAATATTATGTTGCTCTGTGCTGCTCTATGCATA hhdhhhhhhhhhhhhhhhhhh\hhhhZhhhhPKhL NM:i:0 -EAS38_1_63_467_696 16 chr1 3191897 255 35M * 0 0 TTATGTTGCTCTGTGCTGCTCTATGCATATGGCAT FHh^h]Fhe?hfhhchhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_24_141_869 0 chr1 3191905 255 35M * 0 0 CTCTGTGCTGCTCTATGCATATGGCATGTTGTTGG hhhhhhh^hhUhUhhhhYhhfhh_BPcfh`RXOLS NM:i:0 -EAS38_1_184_494_683 16 chr1 3191911 255 35M * 0 0 GCTGCTCTATGCATATGGCATGTTGTTGGTACCTG =Qab\ahVhchahhh]hhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_263_460_363 16 chr1 3191919 255 35M * 0 0 ATGCATATGGCATGTTGTTGGTACCTGTACCATTC h?UIhJhWhhOhghhKhDhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_80_670_426 16 chr1 3191919 255 35M * 0 0 ATGCATATGGCATGTTGTTGGTACCTGTACCATTC cPgPhNh\hhhh[hhhhUahhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_118_725_870 0 chr1 3191927 255 35M * 0 0 GGCATGTTGTTGGTACCTGTACCATTCTCTTCCAT hhhhhhhhhhhhhhhcghhhhRSQhhUhHhhGKLh NM:i:0 -EAS38_1_88_806_693 16 chr1 3191952 255 35M * 0 0 TCTCTTCCATTGAGAATTCTAAGCCATTATGTGGA fhhhhahhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_160_191_877 16 chr1 3191955 255 35M * 0 0 CTTCCATTGAGAATTCTAAGCCATTATGTGGAGGA hhXhhh\hhhhhhehhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_300_179_943 16 chr1 3191975 255 35M * 0 0 CCATTATGTGGAGGAGCTGTTCAGCTCTCTCTAAC h^IRPXZNMBIMZL[Ehh[hdhhQhchhhhhhhhh NM:i:0 -EAS38_1_208_195_556 0 chr1 3191986 255 35M * 0 0 AGGAGCTGTTCAGCTCTCTCTAACCTATTTAGATT hhhhhhhhhhhdhhhhhhhhhPhehhMhhhTH?bh NM:i:0 -EAS38_1_16_568_852 0 chr1 3191993 255 35M * 0 0 GTTCAGCTCTCTCTAACCTATTTAGATTTTATCTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhLhMhh NM:i:0 -EAS38_1_290_6_992 16 chr1 3192030 255 35M * 0 0 ACTTTGTGATAGAATCTCTCTATAGAATGTTCTCT F_UhhHhLhbeKhhhh^hhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_300_29_772 16 chr1 3192030 255 35M * 0 0 TCTTTGTGATAGAATCTCTCTATAGAATGTTCTCT Ahh`Vhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_109_466_314 0 chr1 3192031 255 35M * 0 0 CTTTGTGATAGAATCTCTCTATAGAATGTTCTCTC hhhhhhhhhhhfhhhhhhhhKhhGLXhRhhPhLhS NM:i:0 -EAS38_1_112_657_773 0 chr1 3192037 255 35M * 0 0 GATAGAATCTCTCTATAGAATGTTCTCTCCACCCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh]BG NM:i:2 -EAS38_1_137_971_213 16 chr1 3192048 255 35M * 0 0 TATATAGAATGTTCTCTCAACCACCTCCTGCTAGT C@BHTcZhaFFRSB\hVT@Oehhhhhhhhhhhhhh NM:i:2 -EAS38_1_185_636_515 16 chr1 3192048 255 35M * 0 0 TCTATAGAATGATCTCTCAACCACCTCCTGCTAGT F@J\Jd]Q\ABBAcA[Mhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_44_970_650 0 chr1 3192058 255 35M * 0 0 GTTCTCTCCACCACCCCCTGCTAGTCATACCAAAC hhhhhhhhhhhhhhThMhhhac\h[e_WRGfUIMH NM:i:1 -EAS38_1_92_965_745 0 chr1 3192064 255 35M * 0 0 TCCACCACCTCCTGCTAGTCATACCAAACCCACCC hhhhhhhhhhhhhhhhhhhhhhhJh_hhPIV_X?G NM:i:0 -EAS38_1_261_922_44 0 chr1 3192119 255 35M * 0 0 ACTTCAGTTTTTCTTTATAAAACTTAATCAAAACC hhhh_hhfhhhhhhEh_hTTY]hh@aJhOFMTOLM NM:i:2 -EAS38_1_123_430_987 16 chr1 3192133 255 35M * 0 0 GTATAAAACTGAATCAAAACCGATGTTTATTTTTA GZhdhhh]hhdhhdhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_234_381_448 0 chr1 3192142 255 35M * 0 0 TGAATCAAAACCGATGTTTATTTTTATGATAAAAA hhBhhh]hhhhhhhhhhhhFhhhhhThB_hQ]O@Y NM:i:0 -EAS38_1_46_449_600 0 chr1 3192148 255 35M * 0 0 AAAACCGATGTTTATNTTTATGATAAAAAGGATAT hhhhhhhahhhhhhh;hhhhhhfhThNh^OGWh]h NM:i:1 -EAS38_1_239_737_373 0 chr1 3192153 255 35M * 0 0 CGATGTTTATTTTTATTATAAAAAGGATATACTTT hhhhhhhhhhhhhhdhK[hhhRW\JMPhbhNhhhh NM:i:1 -EAS38_1_24_496_314 0 chr1 3192169 255 35M * 0 0 GATAAAAAGGATATACTTTTGTATTTTGTTGTAGA hhhhhhhhhhhhhhhhhhhhDhLhhhhHM[O]EA? NM:i:2 -EAS38_1_150_229_75 16 chr1 3192202 255 35M * 0 0 GAAAAAATATTGGTTTAAGAAGGAGATAAAAAGTC hhhhhhhJhA]hhSPARhhhhhhhhhbhhhhhhhh NM:i:1 -EAS38_1_170_110_874 16 chr1 3192248 255 35M * 0 0 AATTACCTTTTACCCACTTACTGTTCTTACATGAC hhhhXhh]hQhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_142_857_213 0 chr1 3192280 255 35M * 0 0 GACCTGACTATCCTAACAAACTCTATTCTAGCACT hhhhhhhhhhhhhhh\hQh_hhhhYhhhhRB]Wbh NM:i:0 -EAS38_1_7_223_584 0 chr1 3192314 255 35M * 0 0 TGTAGATATTTTTGAGGAGTCACATACTTTTCTAT hhhhhhhhhhhhhghhK^YhhhhJhhDhhhhhhMh NM:i:1 -EAS38_1_95_195_644 16 chr1 3192330 255 35M * 0 0 GAGTCACATAATTTTCTATGCTACAGTCATGCTTC hhhbPhZhhhhOhh`hhhYhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_219_903_777 0 chr1 3192346 255 35M * 0 0 TATGCTACAGTCATGATTCAGAAAGTCTAATGTCG hhhhhhhhhhhhhhhBhhhhhhhhhghh\hhhhJ[ NM:i:1 -EAS38_1_108_439_554 16 chr1 3192349 255 35M * 0 0 GCTACAGTCATGCTTCAGAAAGTCTAATGTCGTGA aThhhhhehhdhhXhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_239_516_540 0 chr1 3192442 255 35M * 0 0 TAATTTTAGAGAATCAGAGGAGATTATATTGTGTG hhhhhhhhhhhhhhhhhhhhNhLhhThhhheOfhW NM:i:1 -EAS38_1_196_124_875 16 chr1 3192460 255 35M * 0 0 GGAGATTATATTGGGTGTCAATACTGTAAGTATTC ?N[Mhh_hWhXh[LVhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_222_834_314 16 chr1 3192460 255 35M * 0 0 GGAGATTAGATTGGGTGTCGATACTGTAAGTATTC WDXGRJOR?hCMfKhR]OAIhPXZRh^hhhhhhSh NM:i:2 -EAS38_1_230_638_588 0 chr1 3192551 255 35M * 0 0 TATTTGAAGAGTATGGAATTTATTTTGTAAATGAA hhhhhhhhhhhhhhhhhhhhhWhhhhhh\`hhhG` NM:i:0 -EAS38_1_264_255_706 0 chr1 3192603 255 35M * 0 0 AGTACTGAATGGAGCCACATCATTCACATATTTCC hhhhhhhhhhhhhhhhhhhhhghhbhhdhfhhhdP NM:i:0 -EAS38_1_105_766_448 16 chr1 3192724 255 35M * 0 0 TTAGTTTAGTCATTTAGGCAAGGAAATAGACATTG Ghhhhhhhhhhhghhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_281_8_752 0 chr1 3192785 255 35M * 0 0 GCTCAGGTTGTTTTTCCTACCATCTCTCCACATTT hhhEhhhhhhhhhhhN\hh@MOhHU>WDGHW?WTd NM:i:1 -EAS38_1_273_517_672 16 chr1 3192933 255 35M * 0 0 ATAATATGGAGATGAATCAGCTCAAGAGTTCTGAG hhhhghCfdhhhhhhhhhhhhahhhhhhhhhhhhh NM:i:0 -EAS38_1_194_915_453 16 chr1 3192959 255 35M * 0 0 AGTCCTGAGCAGAAACACCATTCCACATTCTTCTG hbIGI_hhhOhhhhhfV\hhhdhhhhhhQhhhhhh NM:i:1 -EAS38_1_270_767_516 16 chr1 3193008 255 35M * 0 0 TGTTAGAAATGGTATAAAATCCCAGTTAAACCATT ThUchhhhhfhJhhhhhhhDOhchhhhhhhhhhhh NM:i:1 -EAS38_1_311_398_506 16 chr1 3193008 255 35M * 0 0 TGTTAGAAATGGTATAAAAACCCAGTTAAACCATT OWRbhhhhhUhZhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_77_151_681 16 chr1 3193008 255 35M * 0 0 TGTTAGAAATGGTATAAAAACCCAGTTAAACCATT WCP`hhhhhRhO\hhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_41_603 16 chr1 3193471 255 35M * 0 0 CACATTCCTTATAACACACTGTGAGGTAGGTGAAG ^bZV`R]hh_hOhhh`hhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_124_634_862 16 chr1 3193821 255 35M * 0 0 TTTCTGGGTATGATTGCTGTTAGCCTTTCTGTTTT h^HhhhDBhhhhhhhdhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_101_162_624 0 chr1 3194186 255 35M * 0 0 TTGCACTGTGTTTAGAAATCCCTCAAAAGGTTTGC hhhhhhhhhhhhhhhhhhhhhhhhW[hPfeUhhVY NM:i:0 -EAS38_1_235_609_726 0 chr1 3194200 255 35M * 0 0 GACATCCCTCAAAAGGTTTGCATAGCCAAATGCCT QJH]I]TaV[_X^\QIERLJHEG?H>JFFD@BCC? NM:i:1 -EAS38_1_162_13_894 16 chr1 3194295 255 35M * 0 0 GGGAATTGTTCACACAATTTGTGTGTTTTTCTGTC ?HCMeVTN?Sh[hRhhhhZhbhhhhhhhhhhhhhh NM:i:2 -EAS38_1_201_123_722 0 chr1 3194814 255 35M * 0 0 AACCATTATGTAAAGTATACTTTATAAATGTTTAA hhhhhhhhhhhhhhhhhhhhhhhhh]hhhhhhh\M NM:i:0 -EAS38_1_251_938_580 16 chr1 3195076 255 35M * 0 0 TATTTATCTTTGTACAACAAAGAGACTCTTAGCAG dYGWNFSQhWVPhhGhh`hhhehhhhhhhhhhhhh NM:i:1 -EAS38_1_8_777_292 16 chr1 3195076 255 35M * 0 0 TATTTATCTTTGTACAAAAAAGAGACTCTTAGCAG JQFAH@BLJGRNEhQhhDhhhfhhhh]]hhhhhhh NM:i:2 -EAS38_1_212_466_584 0 chr1 3195258 255 35M * 0 0 GCTATCCCAAAACCATATGTGCTGCTTGTATGAAC hhhhhhhhhghhhhfhhhh]hZhhhhhbhfhOD>M NM:i:1 -EAS38_1_137_805_954 0 chr1 3195451 255 35M * 0 0 GGAAAAGTCAGAACTTTGGGGTGATCAAACGTCTA hhhhhhhhhhhhhhhhhhhhhghhhCPhPIhMJYD NM:i:1 -EAS38_1_63_741_75 0 chr1 3195451 255 35M * 0 0 GGAAAAGTCAGAACTTTTGTGTGATCAACCGTCTA hhhhhhhhhhhVhhhhhFEJFhOHhSVRG@N_D_Q NM:i:2 -EAS38_1_146_999_561 16 chr1 3197082 255 35M * 0 0 GGAATCCATTGGCTGATCTTTTAAGAAGTAGTTCT SahhhRhhhXh\hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_295_1_556 16 chr1 3197082 255 35M * 0 0 GGAATCCATTGGCTGATCTTTTAAGAAGTAGTTCT bdhhMFhhgehhhhhhbIhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_133_696_323 16 chr1 3197239 255 35M * 0 0 CCTGCAATGAACCAACTGCTCCTTTCCCATTAATT ??FCJ??@DSCECKJ]JbhLXbXh\hUhhh^hhhf NM:i:2 -EAS38_1_184_992_275 0 chr1 3197347 255 35M * 0 0 GATTAATTAACTGCAATTCATCTCCAGTAAAATTT hhhhhhhhhhhhhhhShhhhhhhhh^`WILU_hhh NM:i:0 -EAS38_1_261_311_801 16 chr1 3197969 255 35M * 0 0 ATAAAAATTGAACAAAAAAAAGAAATGGGTTTCTT hchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_199_494_378 16 chr1 3198110 255 35M * 0 0 GCCATGCCAGAATGCTAGGACAATAGTTAAATTAA ?Dhh\hKPhhhhUhZhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_186_296_431 16 chr1 3199201 255 35M * 0 0 GTTAGCACTTTGTCACATATTCCACTGCTTTTAAA S>MhSKKDFJVhGHhPh]hdWhhhhhhhhhhhhhh NM:i:0 -EAS38_1_32_939_527 0 chr1 3199927 255 35M * 0 0 TTTCCCTAGTTTAGCTGTGATGCCTTTGACAAGCT hhhhhhhhhhhhhhhhhhhhhhghhhhVFYNVGYh NM:i:0 -EAS38_1_174_562_297 0 chr1 3200023 255 35M * 0 0 AAGGGAGATAGATCCCAGAGGTAAGGATCTTCAAG hbhRL^hCXHWNdNTMIH?IJG?DDE?C>KFH@B? NM:i:2 -EAS38_1_80_292_639 0 chr1 3200090 255 35M * 0 0 GATACTCTTAACTGATATGGGAATCAAGCCACACG hhhhhhhhhhhhhhhhhhhYcEhhh^d^TOhh]K? NM:i:1 -EAS38_1_146_971_305 16 chr1 3200157 255 35M * 0 0 ACGTTCAGCTTAGATTGTTTCTGAGTTTGTGTCCT RMOUAJ[YRHYh\hZhhhW[hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_103_633_813 16 chr1 3200318 255 35M * 0 0 TATAATATAATAAGGATCTAACATGTTGCTTTCTC YghhhNhUhh^hhThh]hhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_268_250_819 16 chr1 3200318 255 35M * 0 0 TATAATATAATAAGGATCTAACATGTTGCTTTCTC hhhhhVhhhhhhhgVhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_195_376_807 16 chr1 3200796 255 35M * 0 0 TCAGGGAGGGGGACTAAAGTGAGGTCACCTATTCC Ihe[Ihh]XahhhhhhhhhhhhFhhhhhhhhhhhh NM:i:1 -EAS38_1_92_137_414 0 chr1 3200902 0 35M * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTCTCTATTTTCC hhhhhhhhhhhhhhhhhhhhhhdhCA@hJ@IK@AE NM:i:2 -EAS38_1_142_636_259 0 chr1 3200903 0 35M * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTCCTATTTTCTA hhhhhhhhhhhhhhhhhhhhhhM?EM@>FLICF@@ NM:i:2 -EAS38_1_72_206_749 0 chr1 3200905 0 35M * 0 0 TTTTTTTTTTTTTTTTTTTTTTGATACTTTCCAAA hhhhhhhhhhhhhhhhhhhhhhBAN@UOE@YEE=@ NM:i:2 -EAS38_1_111_883_143 16 chr1 3201070 255 35M * 0 0 AAAGACAGTTGGAACTATTTTTAAAAGGCGCTTTA hhhhhQhhH`hchhfhhh\ghhhhhhhhhhhhhhh NM:i:0 -EAS38_1_255_841_137 0 chr1 3201133 255 35M * 0 0 CAGGCATCTCATCCAAGCTTTATATATAAATAGTC hhhhh\hhhhdhahDPDhhhhKhSh`LFPEePCYI NM:i:1 -EAS38_1_25_534_590 0 chr1 3201133 255 35M * 0 0 CAGGCATCTCATCCAAGCTTTATATAGAAATAGTC hhhhhUhhhhhh`hVYhYhchMgO^LWKGJHFDNE NM:i:0 -EAS38_1_11_826_739 0 chr1 3201151 255 35M * 0 0 CTAATATAGAAATAGTCGTGGCTAATGGCAAAGAT hhBhhhhhhhhhhhhhhhLhhR]`]TY^@DNPQ@D NM:i:2 -EAS38_1_200_667_750 0 chr1 3201166 255 35M * 0 0 TCGTGGCTAATGGCAAAGATATGTGATGAATGCAA hhhhhhhhhhhhhLRhIhbQ]fZYULURBNRG?EP NM:i:0 -EAS38_1_148_510_997 0 chr1 3201180 255 35M * 0 0 AAAGATATGTGATGAATGCAAGGGAGCATATATTT hhhhhhhhhhhehhhhhhZhMhhZD`FOXSV_SPZ NM:i:0 -EAS38_1_221_65_299 16 chr1 3201185 255 35M * 0 0 TATGTGATGAATGAAAGGGAGAATATATTTAGTCT BhG[Egh]hhhLhAhhhhhhhPhbhUhTWMhhSVh NM:i:2 -EAS38_1_149_164_972 0 chr1 3201186 255 35M * 0 0 ATGTGATGAATGCAAGGGAGGATATATTTAGTGTA hhhhhhhhhhhhNhhhhhdhCWh_MhhWOVhVBhU NM:i:2 -EAS38_1_269_935_919 16 chr1 3201203 255 35M * 0 0 AAACATATATTTAGTCTAGAAAGTAGTTCATTAGA FWQhh[hbhhbhhQXhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_289_238_636 0 chr1 3201226 255 35M * 0 0 TAGTTCATTAGAAAAAATTCACAGGATTCTTGTCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_125_517_695 16 chr1 3201271 255 35M * 0 0 TCAGAATTTGTTTCCACTCAGTAGCATCCAATGCA hJhHhhhWPehh\hhhhhchhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_22_489_754 16 chr1 3201281 255 35M * 0 0 TTTCCACTCGGTAGCATCCAATGCATTTGAAAGTG VNChUNhM\fDhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_122_450_662 16 chr1 3201346 255 35M * 0 0 TACACGTTTTCCTTGACTTAAGCCACGTGTTCAAT \PhJh`h[hKhhhhh`hhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_157_676_368 16 chr1 3201388 255 35M * 0 0 GAAGTAACATAAACTATTCAATTAGGCCACTTACA ghhYehhhhThhhhhh[Yhhh]hhhhhhhhhhhhh NM:i:0 -EAS38_1_4_358_468 16 chr1 3201390 255 35M * 0 0 AGTAAAAGAAACTATTCAATTAGGCCACTTACAAG hNDhhAhBhhhhWhMKdhhKbhhhhhhhhhhhhhh NM:i:2 -EAS38_1_15_825_658 16 chr1 3201447 255 35M * 0 0 AGTTCAGTCAAATCATGGAGCAAGGAATTCCATGT ]BZOJhZ`hhhhhhhhhhhhhhh]hhhhhhhhhhh NM:i:0 -EAS38_1_222_809_300 0 chr1 3201569 255 35M * 0 0 CAAAAAGTCATGGAAGTTTAAATTATCCCATGCAT hhhhh]hhhhhhS\c>hhhYhPhhhhhhhUhPhWh NM:i:1 -EAS38_1_116_429_381 16 chr1 3201665 255 35M * 0 0 TGTGTGTTTATTGAGAGTATGTGAGAAGATACCTG PhhhLhhchhh`hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_156_372_572 16 chr1 3201665 255 35M * 0 0 TGTGTGTTTATTGAGAGTATGTGAGAAGATACCTG hhhhhhhEhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_79_182_652 16 chr1 3201849 255 35M * 0 0 TACAAAAAGCTATCATATAACAATCCATCTATCAT IAYhhhhhbhXhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_186_626_713 16 chr1 3202147 255 35M * 0 0 CATTTATCAATCAATCTAATCTAACTTATCTATCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_16_258_505 16 chr1 3203603 255 35M * 0 0 TTCCAGCTGGGAGGGTGAGTCTTCAGAGTTCATCA ?AIDSAPEhhhhhhhhhhhhhhfhhhhhhhhhhhh NM:i:1 -EAS38_1_197_118_218 16 chr1 3204368 255 35M * 0 0 GGTGAGGTAGGCTGATGGATTTGTAGACTGGATTC VPGgUMhAXhh@GchGdhhOXLhfhhfhhhhhhhh NM:i:1 -EAS38_1_141_404_857 0 chr1 3204755 255 35M * 0 0 TTTTTAATGGCATACACATTGCATCTGTATGCTCT hhhhhhhhhhhhhhhhhhhhhhhh_hdhhhhIhEh NM:i:0 -EAS38_1_125_490_276 16 chr1 3204799 255 35M * 0 0 AATTGTGACCCAAAGTCTCTAGTAGACACATCATT h\]@VFQ@QPAhhhhGhhI_hhhhhhhhhhhhhhh NM:i:1 -EAS38_1_171_771_691 16 chr1 3205563 255 35M * 0 0 TATGGGTATTTTGCCTGCATATATGTCTATGCACC ]hOhKfhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_284_911_331 0 chr1 3210849 255 35M * 0 0 CTCTGTATTCTCTTCTTCTATTCACATCTCTACAA hhhhhhhhhhhhhhhhhhhbhhhhhbhhhhhFhhG NM:i:0 -EAS38_1_101_808_273 0 chr1 3212214 255 35M * 0 0 AGATGGTTGGTTGTAGTTTGACCCTTGAAGTTTAT hhhhhhhhhhhhhh^XhhhhJ]hhhhHLHR\hhKh NM:i:0 -EAS38_1_161_452_506 16 chr1 3212258 255 35M * 0 0 CCGGAGTTCCCGGTGTGTTGCTACTGGCATGGTGG HJ>@_ZEEc]R[hWhfhhThhhhh]hhhhhhhhhh NM:i:2 -EAS38_1_246_740_824 0 chr1 3212368 255 35M * 0 0 TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTG hhhhhhhhhhhhhh]hh[OhhhhhhOZZhMh_`Lh NM:i:0 -EAS38_1_328_863_236 0 chr1 3212368 255 35M * 0 0 TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTG hhhhhhhhhhhfhhhh[hhRIhahh`ghh[hhhhW NM:i:0 -EAS38_1_71_507_507 0 chr1 3212368 255 35M * 0 0 TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTT hhhhhhhhhhhhhhhhhhhg]LQhhhOhhShhHc? NM:i:1 -EAS38_1_156_360_657 0 chr1 3212393 255 35M * 0 0 AACTATTGTGAGTCTAGAGCTTCTCCAAATGCCTC hhhhhhhhhhhhhhhhhhhhhhXhVhChhhhhdbh NM:i:0 -EAS38_1_327_554_773 0 chr1 3212413 255 35M * 0 0 TTCTCCAAATGCCTCTTGTTACAAACATGCATATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_316_581_646 0 chr1 3213096 255 35M * 0 0 TTTTAATCTTATCTCCTCACTGCCTCCCTCTTAGG hhhhhhhhhhhhhhhhhgdhh_dRhhG^hfhYKJF NM:i:0 -EAS38_1_90_952_487 16 chr1 3214147 255 35M * 0 0 TCCCTGGATGAAGGAGGTTCAATTGGATTGAATTA DCQNQXOaeUhhUThcNhh`hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_191_680_14 0 chr1 3225128 255 35M * 0 0 ATATTTTCCAACAGGTAAGAAGTATGCAAGCTCCA hhMhhhhhhchhhJJUIhEOPPDHhE[T@@IDD?A NM:i:1 -EAS38_1_138_982_940 0 chr1 3233636 0 35M * 0 0 TACCTCTCGCCATCTGTCAATCTCTGGAGTCAGTT hJhhhhh^hahYhhhhJBhhhLhJhhVaXJAB_BL NM:i:2 -EAS38_1_158_9_677 16 chr1 3242626 255 35M * 0 0 AAAATAAATAAGAGAGAGGAGCCTTACTGTGCTTG hhhhPhhh^hhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_253_923_934 16 chr1 3242672 255 35M * 0 0 AACATTGTCTTTCTGCCAGGTTTCTGTGGAGCATA CIOHFhHOhO@LhTLhhhhKhh[hhhhhchXhhhh NM:i:1 -EAS38_1_5_178_743 16 chr1 3242672 255 35M * 0 0 AACATTTTCTGTCTGCCAGGTTTCTGTGGAGCATA QEDJM@C?]OOKhKRh^fUOR^Nhchehhhhhhhh NM:i:1 -EAS38_1_198_267_632 0 chr1 3242722 255 35M * 0 0 CGACACACCCCTTCTGCATACTGGCCTGTCACTGA hhhhhhhhhhhhhhhhhhhhhhhhhQhJT?ISHLA NM:i:2 -EAS38_1_19_755_678 0 chr1 3242782 255 35M * 0 0 GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACA hhhhhhhhhhVRhUZghFgEhYhLQROfI?OCIGE NM:i:0 -EAS38_1_243_907_786 0 chr1 3242782 255 35M * 0 0 GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACC hhhhhVhhNhhhhUahhWhJWhZOKhO\MPTGN?> NM:i:1 -EAS38_1_278_440_897 0 chr1 3242782 255 35M * 0 0 GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACA hhhhhhhhhhhhhehh_YhhhhhDhhDhNMEXANO NM:i:0 -EAS38_1_173_938_288 0 chr1 3242827 255 35M * 0 0 GCACTGGGCCTTTCTTCTGTGTCTGAGCTATTTCA hhhhhhhhhhhhhhhhhhhhhINhg?e\hVhhHhC NM:i:1 -EAS38_1_157_930_237 16 chr1 3242836 255 35M * 0 0 CTTTCTTCTGTGTCTGAGCTATTGCATTATATCTT PMUNNFZYHhFaVhUhhh^Shhhhhhhhhhhhhhh NM:i:0 -EAS38_1_266_172_602 16 chr1 3242889 255 35M * 0 0 TTCTAATCACTGATGCATTAATTAAAAGAATCATA XJLLBhchhNehhhhYhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_149_88_885 0 chr1 3243019 255 35M * 0 0 TTCTCTATATTCCTAGAGTTGTGTGGAAACTAATA hhhhhhhhhhhhhhhhhhhhhhhhhadLhObALgf NM:i:1 -EAS38_1_62_896_441 16 chr1 3243045 255 35M * 0 0 AAAATCATATGATACCATTTATGCTTGCCAGAACG hh_CZJh[hhhhhhhhhhXhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_12_294_576 16 chr1 3243367 255 35M * 0 0 AGAATAATAAATTATCCTATAAGCTGGGCTTGATG _hhhQhhahhhNNhDh[\hNhhhhWhhhhdhh>hh NM:i:1 -EAS38_1_2_533_514 16 chr1 3243367 255 35M * 0 0 AGAATAATAAATGATCCTATAAGCGGGGCTTGGTG hahhPh\ChZhhXhPhBNRZKhhh\hhhhhhhhhh NM:i:2 -EAS38_1_305_285_786 16 chr1 3243648 255 35M * 0 0 CAAAATATTGTTAGATTTGTTTGAGAGATTTGTTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_67_916_874 0 chr1 3243986 255 35M * 0 0 GATTATAATACCCTCGTTGAGATTTGTTTGTTATT hhhhhhhhhhhhhhhhhhh\hZhhhhhhhh^hfhh NM:i:0 -EAS38_1_123_564_954 16 chr1 3254091 255 35M * 0 0 GGAGTGACTGGCCTCCCCTCTTCTTTATAAAGCGT CDM?P<Mh@=FhhThhhhhhhdhhhhhhhhhhhhh NM:i:0 -EAS38_1_55_599_652 16 chr1 3254559 3 35M * 0 0 GTGTCAAGCTCTTGCAGAGCCTCTCAGGAGACAGC @AC=EhKFhAZMGW^Zhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_143_932_612 16 chr1 3256967 255 35M * 0 0 CCTAGAGACAAGGGCTGAAGCAGGCCAGTTATTTT JEEKSVIQNMSdN_h[dhhhhhehhhhhhhhhhhh NM:i:0 -EAS38_1_212_69_386 16 chr1 3256977 255 35M * 0 0 AGGGCTGAAGCAGGCCAGTTATTTTAGGAGAGCAG ROJUGJhhhhCUh]RJhhhhhh[hhhhhhhhhhhh NM:i:0 -EAS38_1_256_785_413 16 chr1 3256977 255 35M * 0 0 AGGGATGAAGCAGGCCAGTTATTTTAGGAGAGCAG U`MUAAebhaM[WbHHhhNhhfhh`hhhhhhhhhh NM:i:1 -EAS38_1_105_481_788 16 chr1 3268974 255 35M * 0 0 GCCCGAAAAAATCTGCTTTATATTGGCCACATACG DhGaahhhhhhhhhchhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_16_282_422 16 chr1 3273908 255 35M * 0 0 CAAATGGGACACCATTGTCTACATTTATGGTAAGT AOBNCFVEVCWFM_PCdOFGhRhXLahhhhehhhh NM:i:2 -EAS38_1_283_187_798 0 chr1 3274213 255 35M * 0 0 TTAGTGAGCCTGAACCAACCAACCAATGAATATAC hhhhhhhhhhhhhhVhhhPhhhLhhXhhZOhhhhY NM:i:0 -EAS38_1_329_178_196 0 chr1 3274786 255 35M * 0 0 GGAAGGCAGATCAGTATAGGTTACCAATAAAATTG hhhhhhhdhhhhhhhchh_@ERhhhEhhCgUWhha NM:i:1 -EAS38_1_300_318_77 16 chr1 3276576 255 35M * 0 0 GAAGAAGAAATATAAGCAGTCCAAGCAGGTTTCAG hhhhMhhhhhhhZKhhghhhARhhhhhhhhhhhhh NM:i:2 -EAS38_1_118_479_935 0 chr1 3276843 255 35M * 0 0 TTTTATCCTCTAGCATGTCAGTCAGGTACAGGGAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh?O NM:i:0 -EAS38_1_41_971_61 0 chr1 3277038 255 35M * 0 0 TGATAAAACAAAAATGTAGACCTTTTAACAGACCC hhhhh\`Z^NhV[]hO[ODJJHW`TbIE?GDBDE> NM:i:2 -EAS38_1_183_306_813 16 chr1 3277183 255 35M * 0 0 CCCATATTATCTTGGAGGTAGGATGATAGTGGTTT ehhhhhdhVNhZhhhhh[hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_288_251_841 16 chr1 3277184 255 35M * 0 0 CCATATTATCTTGGAGGTAGGATGATAGTGGTTTC U[h^hNhh]hehhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_40_672_870 16 chr1 3277184 255 35M * 0 0 CCATATTATCTTGGAGGTAGGATGATAGTGGTTTC Uhh]hMhhNhhgQ[h_Nhh_fhhhhhhhhhhhhhh NM:i:0 -EAS38_1_325_652_299 0 chr1 3278086 255 35M * 0 0 TTTCTGTTTTAAATTAATTACCTTTATTCCATGTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPhh NM:i:0 -EAS38_1_188_971_708 16 chr1 3278146 255 35M * 0 0 TCTTCCTCTTCGTTAGTTTGAATTTATTTCGTTCT P_QOhhWhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_295_186_302 16 chr1 3278229 255 35M * 0 0 CTTGTTGAGTGTTCTGCATGGAATAGAGGCATTTT CDG@ENd`[KQF@J?TEOBXYXaR\`V`hRhLhPh NM:i:1 -EAS38_1_314_975_553 16 chr1 3279235 255 35M * 0 0 ATTTGATAGGGACAGAATAAAAAGTGATAATTCTG hNJaVhahQDLhhhhhhRhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_220_655_831 16 chr1 3279355 255 35M * 0 0 AGAAAATACTTGCTTATTGCTGGAACACGTGACAT hShchXMRhK]Rhahhhhhhh^QhhhShhhhhhhh NM:i:0 -EAS38_1_267_333_743 16 chr1 3280494 255 35M * 0 0 CGTGATGCATCACCAGGGTATCCATGTATAGACTA FQNFhGVHhPfehVehKhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_165_158_507 16 chr1 3280679 255 35M * 0 0 GGGAACGTTATTTGGTGTCTATTGTGATTATTTCC hhbU`ZhhhhdX`hhYhhNhhhghhhhhhhhhchh NM:i:0 -EAS38_1_218_851_888 16 chr1 3280707 255 35M * 0 0 TATTTCCTAAATGCCCCTCNGTTTTTGTATGTTCT MPDILT_PI[`OLhc]hCh;hhh\VhKhhhdhhhh NM:i:1 -EAS38_1_144_853_896 16 chr1 3282690 255 35M * 0 0 GTATCACAAAGGCTCTTTTAACTCAAGAGTTTCTG MhhhhhhhhhXhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_232_504_623 0 chr1 3290489 255 35M * 0 0 TCCCTACATCTCTCCATGTTACTGTAAATGATAGT hhhhhhhhhhhhhhhhhhhhhhhh\Oee_PK`OV@ NM:i:1 -EAS38_1_238_304_582 0 chr1 3290527 255 35M * 0 0 TCATTCTTATTTAGCACTGAAATAATAACCGCCTA hhhhhhhhhhhhhMhhhhhhK]hRehha\DCGWhK NM:i:0 -EAS38_1_125_161_809 0 chr1 3290844 255 35M * 0 0 GCTACTGGGTGGTCTGCATAGCTTAGTGATACACT hh`bhhhhSYhhTE[QH@RFT>RJEVDCFLMCCBI NM:i:0 -EAS38_1_155_358_888 16 chr1 3290932 255 35M * 0 0 GTGGAATTGTAGGGGTGAAAAAAGACATTTCTGAG ghhRhhhhfhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_157_904_203 0 chr1 3291089 255 35M * 0 0 ACAGCCCTGGATGATTTTTGAATGGGAATAATCCC hhhhhhhhhhLhh]hhhhhM^hhNI_@hhQ^hUMW NM:i:0 -EAS38_1_180_814_759 16 chr1 3291152 255 35M * 0 0 AACACCTAGTCATTGTTGGTGGCACTGTCTGTAAG NNWAgXVhhVh_RYhhSeYJh_hhhhhhhhhhhhh NM:i:0 -EAS38_1_170_391_724 16 chr1 3291373 255 35M * 0 0 AAGTAAACCCTTTCTCCTGTAAGTTTCCTTTGGTC _hhWhgQhhhUbchhhhhhhhhhhhhhhhhhhXhh NM:i:0 -EAS38_1_315_950_278 16 chr1 3291611 255 35M * 0 0 TCCATGCCCAGTTTCAGGTGGGAAAACAACTAAGT QAchLb^ChhhhhYhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_330_167_763 16 chr1 3299360 255 35M * 0 0 AAAAATCTTTTTTCTTCTTCTTTCTTTCTTTCTAT hhhhhhhhLh__hhhhhhhhhhhhhhhhhhhhh=h NM:i:1 -EAS38_1_7_984_851 16 chr1 3299360 255 35M * 0 0 AAAAATCTTTTTTCTTCTTNTTTCTTTCTTTCTTT NLPMNN`LEdULNhVhhhh;Phhhhhhhhhhhhhh NM:i:1 -EAS38_1_133_814_850 0 chr1 3299443 1 35M * 0 0 TTTGAGACAGGGTTTCTTTATATAGCCATGGTTGG hhhhhhhhhhhhEhhChhhhhhhhhOTUhhf?SSG NM:i:2 -EAS38_1_303_411_338 16 chr1 3299602 255 35M * 0 0 GAGATGAATACTGGGTAGAAAATAAAAAAATTTAC ThYhFHhhI_JXh_XhhhhhhhYhhhhhhhhhhhh NM:i:0 diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffdiff_out1.txt --- a/test-data/cuffdiff_out1.txt +++ /dev/null @@ -1,91 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -TCONS_00000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000011 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000014 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000015 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000016 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000017 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000018 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000019 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no -TCONS_00000021 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no -TCONS_00000023 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000024 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000025 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TCONS_00000026 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 3.99739e+06 1.82908e+06 -1.12794 0.781831 0.434314 1 no -TCONS_00000027 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no -TCONS_00000028 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000029 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000030 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000031 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000033 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000034 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000037 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000038 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000039 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000040 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000041 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000042 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000043 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000044 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000045 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000046 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000047 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000048 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000049 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000050 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000051 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000052 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000053 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no -TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no -TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no -TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no -TCONS_00000058 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000059 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000060 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000062 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000063 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000065 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TCONS_00000066 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.150149 no -TCONS_00000067 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000068 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no -TCONS_00000069 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 1.36901e+06 0 0 0 1 1 no -TCONS_00000070 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000071 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000072 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000073 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000074 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000075 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000076 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no -TCONS_00000077 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000078 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000079 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000080 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000081 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000082 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000083 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000084 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no -TCONS_00000085 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no -TCONS_00000086 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000087 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000088 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000089 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000090 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000091 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no -TCONS_00000092 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000093 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no -TCONS_00000094 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TCONS_00000095 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000096 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000097 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000098 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000099 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000100 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffdiff_out10.txt --- a/test-data/cuffdiff_out10.txt +++ /dev/null @@ -1,88 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant -XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 LOWDATA 0 0 0 0 0 1 no diff -r a5764a397a989eb30e890d974c04f877ff169b0b -r 1d49fb745d2f59eb3846feb87569a49d4f5fd241 test-data/cuffdiff_out11.txt --- a/test-data/cuffdiff_out11.txt +++ /dev/null @@ -1,1 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Remove sam_fa_indices.loc.sample from tool-data. Update migration xml to the correct revisions of cufflinks repositories.
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/313da0e75a88/ Changeset: 313da0e75a88 User: Dave Bouvier Date: 2013-10-01 21:49:08 Summary: Remove sam_fa_indices.loc.sample from tool-data. Update migration xml to the correct revisions of cufflinks repositories. Affected #: 3 files diff -r 5aef59e6841170aa6e21794d78f709b17738595e -r 313da0e75a88883610cc878bb291b3f9f2d81a9b scripts/migrate_tools/0008_tools.xml --- a/scripts/migrate_tools/0008_tools.xml +++ b/scripts/migrate_tools/0008_tools.xml @@ -15,16 +15,16 @@ <repository owner="devteam" changeset_revision="4a32700dcaa2" name="ctd_batch" description="Galaxy wrappers for the tool CTD: analysis of chemicals, diseases, or genes"><tool id="ctdBatch_1" version="1.0.0" file="ctd.xml" /></repository> - <repository owner="devteam" changeset_revision="9d35cf35634e" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool."> + <repository owner="devteam" changeset_revision="9a3f7a890da6" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool."><tool id="cuffcompare" version="0.0.5" file="cuffcompare_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="0dabb2ed6eb1" name="cuffdiff" description="Galaxy wrappers for the Cuffdiff tool."><tool id="cuffdiff" version="0.0.6" file="cuffdiff_wrapper.xml" /></repository> - <repository owner="devteam" changeset_revision="b50aacc8ae49" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool."> + <repository owner="devteam" changeset_revision="b01956f26c36" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool."><tool id="cufflinks" version="0.0.6" file="cufflinks_wrapper.xml" /></repository> - <repository owner="devteam" changeset_revision="dbbd37e013aa" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool."> + <repository owner="devteam" changeset_revision="fdc55fd74f78" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool."><tool id="cuffmerge" version="0.0.5" file="cuffmerge_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="f16000dc644b" name="delete_overlapping_indels" description="Galaxy wrappers for the tool Delete Overlapping Indels: from a chromosome indels file"> diff -r 5aef59e6841170aa6e21794d78f709b17738595e -r 313da0e75a88883610cc878bb291b3f9f2d81a9b tool-data/sam_fa_indices.loc.sample --- a/tool-data/sam_fa_indices.loc.sample +++ /dev/null @@ -1,28 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Samtools indexed sequences data files. You will need -#to create these data files and then create a sam_fa_indices.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The sam_fa_indices.loc -#file has this format (white space characters are TAB characters): -# -#index <seq><location> -# -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/sam/, -#then the sam_fa_indices.loc entry would look like this: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -# -#and your /depot/data2/galaxy/sam/ directory -#would contain hg18.fa and hg18.fa.fai files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai -# -#Your sam_fa_indices.loc file should include an entry per line for -#each index set you have stored. The file in the path does actually -#exist, but it should never be directly used. Instead, the name serves -#as a prefix for the index file. For example: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -#index hg19 /depot/data2/galaxy/sam/hg19.fa diff -r 5aef59e6841170aa6e21794d78f709b17738595e -r 313da0e75a88883610cc878bb291b3f9f2d81a9b tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -55,11 +55,6 @@ <columns>value, name, path</columns><file path="tool-data/perm_color_index.loc" /></table> -  - <table name="sam_fa_indexes" comment_char="#"> - <columns>line_type, value, path</columns> - <file path="tool-data/sam_fa_indices.loc" /> - </table><table name="picard_indexes" comment_char="#"><columns>value, dbkey, name, path</columns> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: (1) enhance the 'Manage installed tool shed repositories' grid to mark repositories that contain exported workflows, (2) Set the tool_shed_status column value when installing a new repository or reinstalling an uninstalled repository, (3) On the 'Manage installed tool shed repositories' gird, display installed repositories ordered by tool_shed, name, owner, ctx_rev.
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5aef59e68411/ Changeset: 5aef59e68411 User: greg Date: 2013-10-01 20:31:40 Summary: (1) enhance the 'Manage installed tool shed repositories' grid to mark repositories that contain exported workflows, (2) Set the tool_shed_status column value when installing a new repository or reinstalling an uninstalled repository, (3) On the 'Manage installed tool shed repositories' gird, display installed repositories ordered by tool_shed, name, owner, ctx_rev. Affected #: 2 files diff -r da46b521540df29f936aa51cd03e75068eff1204 -r 5aef59e6841170aa6e21794d78f709b17738595e lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -15,6 +15,13 @@ deprecated_tip_str = '' return '<img src="/static/images/icon_error_sml.gif" %s/>' % deprecated_tip_str +def generate_includes_workflows_img_str( include_mouse_over=False ): + if include_mouse_over: + deprecated_tip_str = 'class="icon-button" title="This repository contains exported workflows"' + else: + deprecated_tip_str = '' + return '<img src="/static/images/fugue/gear.png" %s/>' % deprecated_tip_str + def generate_latest_revision_img_str( include_mouse_over=False ): if include_mouse_over: latest_revision_tip_str = 'class="icon-button" title="This is the latest installable revision of this repository"' @@ -60,6 +67,8 @@ tool_shed_status_str += generate_revision_updates_img_str( include_mouse_over=True ) if tool_shed_repository.upgrade_available: tool_shed_status_str += generate_revision_upgrades_img_str( include_mouse_over=True ) + if tool_shed_repository.includes_workflows: + tool_shed_status_str += generate_includes_workflows_img_str( include_mouse_over=True ) else: tool_shed_status_str = generate_unknown_img_str( include_mouse_over=True ) return tool_shed_status_str @@ -211,7 +220,11 @@ use_paging = False def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ) + return trans.sa_session.query( self.model_class ) \ + .order_by( self.model_class.table.c.tool_shed, + self.model_class.table.c.name, + self.model_class.table.c.owner, + self.model_class.table.c.ctx_rev ) @property def legend( self ): @@ -219,6 +232,7 @@ legend_str += '%s  A newer installable revision is available for this repository<br/>' % generate_revision_upgrades_img_str() legend_str += '%s  This is the latest installable revision of this repository<br/>' % generate_latest_revision_img_str() legend_str += '%s  This repository is deprecated in the Tool Shed<br/>' % generate_deprecated_repository_img_str() + legend_str += '%s  This repository contains exported workflows<br/>' % generate_includes_workflows_img_str() legend_str += '%s  Unable to get information from the Tool Shed<br/>' % generate_unknown_img_str() return legend_str diff -r da46b521540df29f936aa51cd03e75068eff1204 -r 5aef59e6841170aa6e21794d78f709b17738595e lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -352,6 +352,10 @@ updating_installed_repository=False, persist=True ) tool_shed_repository.metadata = metadata_dict + # Update the tool_shed_repository.tool_shed_status column in the database. + tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( trans.app, tool_shed_repository ) + if tool_shed_status_dict: + tool_shed_repository.tool_shed_status = tool_shed_status_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() if 'tool_dependencies' in metadata_dict and not reinstalling: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5019491835c7/ Changeset: 5019491835c7 User: Dave Bouvier Date: 2013-10-01 19:54:57 Summary: Migrate cuffcompare, cuffdiff, cufflinks, and cuffmerge from the distribution to the tool shed. Update the 'Review migration stages' layout. Affected #: 38 files diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py --- a/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py +++ b/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py @@ -6,45 +6,49 @@ 3: Compute Motif Frequencies For All Motifs motif by motif 4: Compute Motif Frequencies in indel flanking regions 5: CTD analysis of chemicals, diseases, or genes -6: Delete Overlapping Indels from a chromosome indels file -7: Separate pgSnp alleles into columns -8: Draw Stacked Bar Plots for different categories and different criteria -9: Length Distribution chart -10: FASTA Width formatter -11: RNA/DNA converter -12: Draw quality score boxplot -13: Quality format converter (ASCII-Numeric) -14: Filter by quality -15: FASTQ to FASTA converter -16: Remove sequencing artifacts -17: Barcode Splitter -18: Clip adapter sequences -19: Collapse sequences -20: Draw nucleotides distribution chart -21: Compute quality statistics -22: Rename sequences -23: Reverse- Complement -24: Trim sequences -25: FunDO human genes associated with disease terms -26: HVIS visualization of genomic data with the Hilbert curve -27: Fetch Indels from 3-way alignments -28: Identify microsatellite births and deaths -29: Extract orthologous microsatellites for multiple (>2) species alignments -30: Mutate Codons with SNPs -31: Pileup-to-Interval condenses pileup format into ranges of bases -32: Filter pileup on coverage and SNPs -33: Filter SAM on bitwise flag values -34: Merge BAM Files merges BAM files together -35: Generate pileup from BAM dataset -36: SAM-to-BAM converts SAM format to BAM format -37: Convert SAM to interval -38: flagstat provides simple stats on BAM files -39: MPileup SNP and indel caller -40: rmdup remove PCR duplicates -41: Slice BAM by provided regions -42: Split paired end reads -43: T Test for Two Samples -44: Plotting tool for multiple series and graph types. +6: Cuffcompare +7: Cuffdiff +8: Cufflinks +9: Cuffmerge +10: Delete Overlapping Indels from a chromosome indels file +11: Separate pgSnp alleles into columns +12: Draw Stacked Bar Plots for different categories and different criteria +13: Length Distribution chart +14: FASTA Width formatter +15: RNA/DNA converter +16: Draw quality score boxplot +17: Quality format converter (ASCII-Numeric) +18: Filter by quality +19: FASTQ to FASTA converter +20: Remove sequencing artifacts +21: Barcode Splitter +22: Clip adapter sequences +23: Collapse sequences +24: Draw nucleotides distribution chart +25: Compute quality statistics +26: Rename sequences +27: Reverse- Complement +28: Trim sequences +29: FunDO human genes associated with disease terms +30: HVIS visualization of genomic data with the Hilbert curve +31: Fetch Indels from 3-way alignments +32: Identify microsatellite births and deaths +33: Extract orthologous microsatellites for multiple (>2) species alignments +34: Mutate Codons with SNPs +35: Pileup-to-Interval condenses pileup format into ranges of bases +36: Filter pileup on coverage and SNPs +37: Filter SAM on bitwise flag values +38: Merge BAM Files merges BAM files together +39: Generate pileup from BAM dataset +40: SAM-to-BAM converts SAM format to BAM format +41: Convert SAM to interval +42: flagstat provides simple stats on BAM files +43: MPileup SNP and indel caller +44: rmdup remove PCR duplicates +45: Slice BAM by provided regions +46: Split paired end reads +47: T Test for Two Samples +48: Plotting tool for multiple series and graph types. The tools are now available in the repositories respectively: @@ -53,45 +57,49 @@ 3: compute_motif_frequencies_for_all_motifs 4: compute_motifs_frequency 5: ctd_batch -6: delete_overlapping_indels -7: divide_pg_snp -8: draw_stacked_barplots -9: fasta_clipping_histogram -10: fasta_formatter -11: fasta_nucleotide_changer -12: fastq_quality_boxplot -13: fastq_quality_converter -14: fastq_quality_filter -15: fastq_to_fasta -16: fastx_artifacts_filter -17: fastx_barcode_splitter -18: fastx_clipper -19: fastx_collapser -20: fastx_nucleotides_distribution -21: fastx_quality_statistics -22: fastx_renamer -23: fastx_reverse_complement -24: fastx_trimmer -25: hgv_fundo -26: hgv_hilbertvis -27: indels_3way -28: microsatellite_birthdeath -29: multispecies_orthologous_microsats -30: mutate_snp_codon -31: pileup_interval -32: pileup_parser -33: sam_bitwise_flag_filter -34: sam_merge -35: sam_pileup -36: sam_to_bam -37: sam2interval -38: samtools_flagstat -39: samtools_mpileup -40: samtools_rmdup -41: samtools_slice_bam -42: split_paired_reads -43: t_test_two_samples -44: xy_plot +6: cuffcompare +7: cuffdiff +8: cufflinks +9: cuffmerge +10: delete_overlapping_indels +11: divide_pg_snp +12: draw_stacked_barplots +13: fasta_clipping_histogram +14: fasta_formatter +15: fasta_nucleotide_changer +16: fastq_quality_boxplot +17: fastq_quality_converter +18: fastq_quality_filter +19: fastq_to_fasta +20: fastx_artifacts_filter +21: fastx_barcode_splitter +22: fastx_clipper +23: fastx_collapser +24: fastx_nucleotides_distribution +25: fastx_quality_statistics +26: fastx_renamer +27: fastx_reverse_complement +28: fastx_trimmer +29: hgv_fundo +30: hgv_hilbertvis +31: indels_3way +32: microsatellite_birthdeath +33: multispecies_orthologous_microsats +34: mutate_snp_codon +35: pileup_interval +36: pileup_parser +37: sam_bitwise_flag_filter +38: sam_merge +39: sam_pileup +40: sam_to_bam +41: sam2interval +42: samtools_flagstat +43: samtools_mpileup +44: samtools_rmdup +45: samtools_slice_bam +46: split_paired_reads +47: t_test_two_samples +48: xy_plot from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 scripts/migrate_tools/0008_tools.xml --- a/scripts/migrate_tools/0008_tools.xml +++ b/scripts/migrate_tools/0008_tools.xml @@ -15,6 +15,18 @@ <repository owner="devteam" changeset_revision="4a32700dcaa2" name="ctd_batch" description="Galaxy wrappers for the tool CTD: analysis of chemicals, diseases, or genes"><tool id="ctdBatch_1" version="1.0.0" file="ctd.xml" /></repository> + <repository owner="devteam" changeset_revision="9d35cf35634e" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool."> + <tool id="cuffcompare" version="0.0.5" file="cuffcompare_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="0dabb2ed6eb1" name="cuffdiff" description="Galaxy wrappers for the Cuffdiff tool."> + <tool id="cuffdiff" version="0.0.6" file="cuffdiff_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="b50aacc8ae49" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool."> + <tool id="cufflinks" version="0.0.6" file="cufflinks_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="dbbd37e013aa" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool."> + <tool id="cuffmerge" version="0.0.5" file="cuffmerge_wrapper.xml" /> + </repository><repository owner="devteam" changeset_revision="f16000dc644b" name="delete_overlapping_indels" description="Galaxy wrappers for the tool Delete Overlapping Indels: from a chromosome indels file"><tool id="delete_overlapping_indels" version="1.0.0" file="delete_overlapping_indels.xml" /></repository> diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 templates/admin/review_tool_migration_stages.mako --- a/templates/admin/review_tool_migration_stages.mako +++ b/templates/admin/review_tool_migration_stages.mako @@ -35,6 +35,7 @@ </p></div><table class="grid"> + <% from tool_shed.util.shed_util_common import to_html_string %> %for stage in migration_stages_dict.keys(): <% migration_command = 'sh ./scripts/migrate_tools/%04d_tools.sh' % stage @@ -54,7 +55,7 @@ <tr><td bgcolor="#FFFFCC"><div class="form-row"> - <p>${migration_info} <b>Run commands from the Galaxy installation directory!</b></p> + <p>${to_html_string(migration_info)} <b>Run commands from the Galaxy installation directory!</b></p><p> %if tool_dependencies: This migration stage includes tools that have tool dependencies that can be automatically installed. To install them, run:<br/> diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_in2.gtf --- a/test-data/cuffcompare_in2.gtf +++ /dev/null @@ -1,100 +0,0 @@ -chr1 Cufflinks transcript 3174766 3174792 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3174766 3174792 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3187402 3187428 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3187402 3187428 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3188522 3188548 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672"; -chr1 Cufflinks exon 3188522 3188548 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672"; -chr1 Cufflinks transcript 3190859 3191434 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500"; -chr1 Cufflinks exon 3190859 3191434 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500"; -chr1 Cufflinks transcript 3191513 3192077 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341"; -chr1 Cufflinks exon 3191513 3192077 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341"; -chr1 Cufflinks transcript 3189811 3190789 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804"; -chr1 Cufflinks exon 3189811 3190789 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804"; -chr1 Cufflinks transcript 3192251 3192336 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; -chr1 Cufflinks exon 3192251 3192336 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; -chr1 Cufflinks transcript 3192650 3192676 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3192650 3192676 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3194707 3194733 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3194707 3194733 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3197426 3197452 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3197426 3197452 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3200431 3200457 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3200431 3200457 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3200057 3200144 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455"; -chr1 Cufflinks exon 3200057 3200144 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455"; -chr1 Cufflinks transcript 3201161 3201187 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3201161 3201187 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3201008 3201039 1000 . . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; -chr1 Cufflinks exon 3201008 3201039 1000 . . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; -chr1 Cufflinks transcript 3201597 3201666 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429"; -chr1 Cufflinks exon 3201597 3201666 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429"; -chr1 Cufflinks transcript 3201726 3201809 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714"; -chr1 Cufflinks exon 3201726 3201809 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714"; -chr1 Cufflinks transcript 3211522 3211561 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; -chr1 Cufflinks exon 3211522 3211561 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; -chr1 Cufflinks transcript 3212718 3212801 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857"; -chr1 Cufflinks exon 3212718 3212801 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857"; -chr1 Cufflinks transcript 3213119 3213242 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226"; -chr1 Cufflinks exon 3213119 3213242 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226"; -chr1 Cufflinks transcript 3240607 3240633 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks exon 3240607 3240633 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks transcript 3242480 3242512 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545"; -chr1 Cufflinks exon 3242480 3242512 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545"; -chr1 Cufflinks transcript 3242925 3243005 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333"; -chr1 Cufflinks exon 3242925 3243005 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333"; -chr1 Cufflinks transcript 3243109 3243154 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913"; -chr1 Cufflinks exon 3243109 3243154 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913"; -chr1 Cufflinks transcript 3254080 3254106 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3254080 3254106 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3277156 3277182 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3277156 3277182 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3277914 3278390 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057"; -chr1 Cufflinks exon 3277914 3278390 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057"; -chr1 Cufflinks transcript 3280118 3280144 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks exon 3280118 3280144 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks transcript 3280499 3280525 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3280499 3280525 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3282505 3282531 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3282505 3282531 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3282651 3282677 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3282651 3282677 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3282761 3282832 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000"; -chr1 Cufflinks exon 3282761 3282832 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000"; -chr1 Cufflinks transcript 3284967 3284993 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3284967 3284993 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3290799 3290859 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492"; -chr1 Cufflinks exon 3290799 3290859 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492"; -chr1 Cufflinks transcript 3299444 3299640 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700"; -chr1 Cufflinks exon 3299444 3299640 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700"; -chr1 Cufflinks transcript 3290920 3291273 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797"; -chr1 Cufflinks exon 3290920 3291273 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797"; -chr1 Cufflinks transcript 3299692 3299733 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714"; -chr1 Cufflinks exon 3299692 3299733 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714"; -chr1 Cufflinks transcript 3307749 3307775 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3307749 3307775 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3318621 3318647 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks exon 3318621 3318647 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks transcript 3330528 3330554 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; -chr1 Cufflinks exon 3330528 3330554 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; -chr1 Cufflinks transcript 3351241 3351311 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; -chr1 Cufflinks exon 3351241 3351311 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; -chr1 Cufflinks transcript 3355908 3356119 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792"; -chr1 Cufflinks exon 3355908 3356119 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792"; -chr1 Cufflinks transcript 3356181 3356225 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000"; -chr1 Cufflinks exon 3356181 3356225 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000"; -chr1 Cufflinks transcript 3363077 3363176 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000"; -chr1 Cufflinks exon 3363077 3363176 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000"; -chr1 Cufflinks transcript 3363388 3363446 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881"; -chr1 Cufflinks exon 3363388 3363446 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881"; -chr1 Cufflinks transcript 3364872 3364919 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500"; -chr1 Cufflinks exon 3364872 3364919 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500"; -chr1 Cufflinks transcript 3367211 3367237 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3367211 3367237 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3369581 3369607 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3369581 3369607 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3375002 3375028 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3375002 3375028 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3379889 3379915 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3379889 3379915 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3386740 3386836 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402"; -chr1 Cufflinks exon 3386740 3386836 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402"; diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_in3.gtf --- a/test-data/cuffcompare_in3.gtf +++ /dev/null @@ -1,100 +0,0 @@ -chr1 mm9_refFlat stop_codon 3206103 3206105 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat CDS 3206106 3207049 0.000000 - 2 gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat exon 3204563 3207049 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat CDS 3411783 3411982 0.000000 - 1 gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat exon 3411783 3411982 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat CDS 3660633 3661429 0.000000 - 0 gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat start_codon 3661427 3661429 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat exon 3660633 3661579 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat stop_codon 4334681 4334683 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat CDS 4334684 4340172 0.000000 - 2 gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4334224 4340172 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat CDS 4341991 4342162 0.000000 - 0 gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4341991 4342162 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat CDS 4342283 4342906 0.000000 - 0 gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat start_codon 4342904 4342906 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4342283 4342918 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4350281 4350473 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat stop_codon 4481797 4481799 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat CDS 4481800 4482749 0.000000 - 2 gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4481009 4482749 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat CDS 4483181 4483487 0.000000 - 0 gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat start_codon 4483485 4483487 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4483181 4483547 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4483853 4483944 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4485217 4486023 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4486372 4486494 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat stop_codon 4766545 4766547 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4766548 4766882 0.000000 - 2 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4763279 4766882 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4767606 4767729 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4772649 4772814 0.000000 - 1 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4774032 4774186 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4774032 4774186 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4775654 4775758 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat start_codon 4775756 4775758 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat stop_codon 4764533 4764535 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4764536 4764597 0.000000 - 2 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4763279 4764597 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4767606 4767729 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4772649 4772814 0.000000 - 1 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4774032 4774186 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4774032 4774186 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4775654 4775758 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat start_codon 4775756 4775758 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4763279 4764597 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat start_codon 4797995 4797997 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4797995 4798063 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4797974 4798063 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4798536 4798567 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4798536 4798567 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4818665 4818730 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4818665 4818730 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4820349 4820396 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4820349 4820396 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4822392 4822462 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4822392 4822462 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4827082 4827155 0.000000 + 2 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4827082 4827155 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4829468 4829569 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4829468 4829569 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4831037 4831213 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4831037 4831213 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4835044 4835094 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat stop_codon 4835095 4835097 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4835044 4836816 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat start_codon 4847995 4847997 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4847995 4848057 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4847775 4848057 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4857551 4857613 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4857551 4857613 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4868108 4868213 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4868108 4868213 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4876825 4876912 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4876825 4876912 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4879538 4879683 0.000000 + 1 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4879538 4879683 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4880821 4880877 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4880821 4880877 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4881996 4882150 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4881996 4882150 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4883498 4883644 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4883498 4883644 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4885015 4885086 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4885015 4885086 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4886437 4886442 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat stop_codon 4886443 4886445 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4886437 4887987 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat start_codon 4847995 4847997 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; -chr1 mm9_refFlat CDS 4847995 4848057 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1_dup1"; -chr1 mm9_refFlat exon 4847775 4848057 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; -chr1 mm9_refFlat CDS 4857551 4857613 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1_dup1"; diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out1.tmap --- a/test-data/cuffcompare_out1.tmap +++ /dev/null @@ -1,51 +0,0 @@ -ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 - -Xkr4 Xkr4 c CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 3634 -Xkr4 Xkr4 i CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 3634 -Xkr4 Xkr4 i CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 3634 -Xkr4 Xkr4 i CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 3634 -Xkr4 Xkr4 i CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 3634 -Xkr4 Xkr4 i CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 3634 -Xkr4 Xkr4 i CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 3634 -Xkr4 Xkr4 i CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 3634 -- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 - -- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 - -- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 - -- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 - -- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 - -- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 - -- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 - -- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 - -- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 - -- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 - -- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 - -- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 - -- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 - -- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 - -- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 - -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 3634 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 3634 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 3634 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 3634 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 3634 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 3634 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 3634 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 3634 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 3634 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 3634 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 3634 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 3634 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 3634 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 3634 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 3634 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 3634 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 3634 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 3634 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 3634 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 3634 diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out2.refmap --- a/test-data/cuffcompare_out2.refmap +++ /dev/null @@ -1,2 +0,0 @@ -ref_gene_id ref_id class_code cuff_id_list -Xkr4 Xkr4 c CUFF.13|CUFF.13.1 diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out3.tmap --- a/test-data/cuffcompare_out3.tmap +++ /dev/null @@ -1,51 +0,0 @@ -ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 - -- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 - -- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 - -- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 - -- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 - -- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 - -- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 - -- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 - -- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 - -- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 - -Xkr4 Xkr4 i CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 3634 -Xkr4 Xkr4 i CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 3634 -Xkr4 Xkr4 i CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 3634 -Xkr4 Xkr4 i CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 3634 -Xkr4 Xkr4 i CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 3634 -Xkr4 Xkr4 i CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 3634 -Xkr4 Xkr4 i CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 3634 -Xkr4 Xkr4 i CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 3634 -Xkr4 Xkr4 i CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 3634 -Xkr4 Xkr4 i CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 3634 -Xkr4 Xkr4 i CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 3634 -Xkr4 Xkr4 i CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 3634 -Xkr4 Xkr4 i CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 3634 -Xkr4 Xkr4 i CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 3634 -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 3634 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 3634 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 3634 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 3634 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 3634 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 3634 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 3634 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 3634 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 3634 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 3634 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 3634 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 3634 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 3634 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 3634 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 3634 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 3634 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 3634 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 3634 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 3634 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 3634 diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out4.refmap --- a/test-data/cuffcompare_out4.refmap +++ /dev/null @@ -1,1 +0,0 @@ -ref_gene_id ref_id class_code cuff_id_list diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out5.gtf --- a/test-data/cuffcompare_out5.gtf +++ /dev/null @@ -1,90 +0,0 @@ -chr1 Cufflinks exon 3204755 3204833 . - . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.13.1"; nearest_ref "Xkr4"; class_code "c"; tss_id "TSS1"; -chr1 Cufflinks exon 3111450 3111490 . . . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2"; -chr1 Cufflinks exon 3111546 3111576 . . . gene_id "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3"; -chr1 Cufflinks exon 3174766 3174792 . . . gene_id "XLOC_000004"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS4"; -chr1 Cufflinks exon 3187402 3187428 . . . gene_id "XLOC_000005"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS5"; -chr1 Cufflinks exon 3188522 3188548 . . . gene_id "XLOC_000006"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS6"; -chr1 Cufflinks exon 3189811 3190789 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS7"; -chr1 Cufflinks exon 3190859 3191434 . . . gene_id "XLOC_000008"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS10"; -chr1 Cufflinks exon 3191513 3192077 . . . gene_id "XLOC_000009"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS11"; -chr1 Cufflinks exon 3192251 3192336 . . . gene_id "XLOC_000010"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS13"; -chr1 Cufflinks exon 3192442 3192494 . . . gene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; tss_id "TSS14"; -chr1 Cufflinks exon 3192551 3192629 . . . gene_id "XLOC_000012"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; tss_id "TSS15"; -chr1 Cufflinks exon 3192650 3192676 . . . gene_id "XLOC_000013"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS16"; -chr1 Cufflinks exon 3192732 3192811 . . . gene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; tss_id "TSS17"; -chr1 Cufflinks exon 3192941 3193042 . . . gene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; tss_id "TSS18"; -chr1 Cufflinks exon 3194186 3194226 . . . gene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; tss_id "TSS19"; -chr1 Cufflinks exon 3194303 3194329 . . . gene_id "XLOC_000017"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; tss_id "TSS20"; -chr1 Cufflinks exon 3194707 3194733 . . . gene_id "XLOC_000018"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS21"; -chr1 Cufflinks exon 3195084 3195110 . . . gene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; tss_id "TSS22"; -chr1 Cufflinks exon 3195451 3195477 . . . gene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; tss_id "TSS23"; -chr1 Cufflinks exon 3197090 3197116 . . . gene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; tss_id "TSS24"; -chr1 Cufflinks exon 3197247 3197273 . . . gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS25"; -chr1 Cufflinks exon 3197347 3197373 . . . gene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS26"; -chr1 Cufflinks exon 3197426 3197452 . . . gene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS27"; -chr1 Cufflinks exon 3200023 3200191 . . . gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS28"; -chr1 Cufflinks exon 3200326 3200352 . . . gene_id "XLOC_000026"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29"; -chr1 Cufflinks exon 3200431 3200457 . . . gene_id "XLOC_000027"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30"; -chr1 Cufflinks exon 3201008 3201039 . . . gene_id "XLOC_000028"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31"; -chr1 Cufflinks exon 3201078 3201481 . . . gene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS32"; -chr1 Cufflinks exon 3201597 3201666 . . . gene_id "XLOC_000030"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33"; -chr1 Cufflinks exon 3201673 3201699 . . . gene_id "XLOC_000031"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34"; -chr1 Cufflinks exon 3201726 3201809 . . . gene_id "XLOC_000032"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35"; -chr1 Cufflinks exon 3211522 3211561 . . . gene_id "XLOC_000033"; transcript_id "TCONS_00000067"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS36"; -chr1 Cufflinks exon 3212214 3212292 . . . gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.15.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS37"; -chr1 Cufflinks exon 3212368 3212439 . . . gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.19.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS38"; -chr1 Cufflinks exon 3212718 3212801 . . . gene_id "XLOC_000036"; transcript_id "TCONS_00000068"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS39"; -chr1 Cufflinks exon 3213096 3213192 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.17.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40"; -chr1 Cufflinks exon 3213119 3213242 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000069"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.37.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40"; -chr1 Cufflinks exon 3240607 3240633 . . . gene_id "XLOC_000038"; transcript_id "TCONS_00000070"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.39.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS41"; -chr1 Cufflinks exon 3242480 3242512 . . . gene_id "XLOC_000039"; transcript_id "TCONS_00000071"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.41.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS42"; -chr1 Cufflinks exon 3242634 3242923 . . . gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.25.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS43"; -chr1 Cufflinks exon 3242925 3243005 . . . gene_id "XLOC_000041"; transcript_id "TCONS_00000072"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.43.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS44"; -chr1 Cufflinks exon 3243019 3243079 . . . gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.21.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS45"; -chr1 Cufflinks exon 3243109 3243154 . . . gene_id "XLOC_000043"; transcript_id "TCONS_00000073"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.45.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS46"; -chr1 Cufflinks exon 3243348 3243401 . . . gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.23.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS47"; -chr1 Cufflinks exon 3254080 3254106 . . . gene_id "XLOC_000045"; transcript_id "TCONS_00000074"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.47.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS48"; -chr1 Cufflinks exon 3256975 3257011 . . . gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.27.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS49"; -chr1 Cufflinks exon 3277156 3277182 . . . gene_id "XLOC_000047"; transcript_id "TCONS_00000075"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.49.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS50"; -chr1 Cufflinks exon 3277191 3277218 . . . gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS51"; -chr1 Cufflinks exon 3277914 3278390 . . . gene_id "XLOC_000049"; transcript_id "TCONS_00000076"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.51.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS52"; -chr1 Cufflinks exon 3280118 3280144 . . . gene_id "XLOC_000050"; transcript_id "TCONS_00000077"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.53.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS54"; -chr1 Cufflinks exon 3280499 3280525 . . . gene_id "XLOC_000051"; transcript_id "TCONS_00000078"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.55.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS55"; -chr1 Cufflinks exon 3280687 3280741 . . . gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS56"; -chr1 Cufflinks exon 3282505 3282531 . . . gene_id "XLOC_000053"; transcript_id "TCONS_00000079"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.57.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS57"; -chr1 Cufflinks exon 3282651 3282677 . . . gene_id "XLOC_000054"; transcript_id "TCONS_00000080"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.59.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS58"; -chr1 Cufflinks exon 3282761 3282832 . . . gene_id "XLOC_000055"; transcript_id "TCONS_00000081"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS59"; -chr1 Cufflinks exon 3284967 3284993 . . . gene_id "XLOC_000056"; transcript_id "TCONS_00000082"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS60"; -chr1 Cufflinks exon 3290489 3290553 . . . gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS61"; -chr1 Cufflinks exon 3290799 3290859 . . . gene_id "XLOC_000058"; transcript_id "TCONS_00000083"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS62"; -chr1 Cufflinks exon 3290920 3291273 . . . gene_id "XLOC_000059"; transcript_id "TCONS_00000084"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS63"; -chr1 Cufflinks exon 3299444 3299640 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000085"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS65"; -chr1 Cufflinks exon 3299610 3299664 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS66"; -chr1 Cufflinks exon 3299692 3299733 . . . gene_id "XLOC_000061"; transcript_id "TCONS_00000086"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS67"; -chr1 Cufflinks exon 3300052 3300078 . . . gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS68"; -chr1 Cufflinks exon 3307749 3307775 . . . gene_id "XLOC_000063"; transcript_id "TCONS_00000087"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS69"; -chr1 Cufflinks exon 3318621 3318647 . . . gene_id "XLOC_000064"; transcript_id "TCONS_00000088"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS70"; -chr1 Cufflinks exon 3319000 3319051 . . . gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS71"; -chr1 Cufflinks exon 3330528 3330554 . . . gene_id "XLOC_000066"; transcript_id "TCONS_00000089"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS72"; -chr1 Cufflinks exon 3351241 3351311 . . . gene_id "XLOC_000067"; transcript_id "TCONS_00000090"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS73"; -chr1 Cufflinks exon 3355888 3355914 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74"; -chr1 Cufflinks exon 3355908 3356119 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000091"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74"; -chr1 Cufflinks exon 3356181 3356225 . . . gene_id "XLOC_000069"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS75"; -chr1 Cufflinks exon 3363077 3363176 . . . gene_id "XLOC_000070"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS76"; -chr1 Cufflinks exon 3363215 3363278 . . . gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS77"; -chr1 Cufflinks exon 3363388 3363446 . . . gene_id "XLOC_000072"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78"; -chr1 Cufflinks exon 3363754 3363849 . . . gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS79"; -chr1 Cufflinks exon 3364872 3364919 . . . gene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80"; -chr1 Cufflinks exon 3367136 3367162 . . . gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS81"; -chr1 Cufflinks exon 3367211 3367237 . . . gene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82"; -chr1 Cufflinks exon 3367334 3367382 . . . gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS83"; -chr1 Cufflinks exon 3369581 3369607 . . . gene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84"; -chr1 Cufflinks exon 3375002 3375028 . . . gene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85"; -chr1 Cufflinks exon 3377212 3377262 . . . gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS86"; -chr1 Cufflinks exon 3379889 3379915 . . . gene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87"; -chr1 Cufflinks exon 3386740 3386836 . . . gene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88"; -chr1 Cufflinks exon 3391326 3391352 . . . gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS89"; -chr1 Cufflinks exon 3435842 3435880 . . . gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS90"; -chr1 Cufflinks exon 3447762 3447788 . . . gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS91"; -chr1 Cufflinks exon 3450907 3450965 . . . gene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS92"; -chr1 Cufflinks exon 3451052 3451109 . . . gene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS93"; diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out6.tracking --- a/test-data/cuffcompare_out6.tracking +++ /dev/null @@ -1,100 +0,0 @@ -TCONS_00000001 XLOC_000001 Xkr4|Xkr4 c q1:CUFF.13|CUFF.13.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000002 XLOC_000002 - u q1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000003 XLOC_000003 - u q1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|- - -TCONS_00000004 XLOC_000007 - u q1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|- - -TCONS_00000005 XLOC_000007 - u q1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|- - -TCONS_00000006 XLOC_000007 - u q1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|- - -TCONS_00000007 XLOC_000009 - u q1:CUFF.35|CUFF.35.1|100|96.747183|61.420107|132.074259|6.183206|- - -TCONS_00000008 XLOC_000009 - u q1:CUFF.37|CUFF.37.1|100|104.085013|53.596365|154.573660|6.652174|- - -TCONS_00000009 XLOC_000011 - u q1:CUFF.39|CUFF.39.1|100|23.912983|0.000000|51.525317|1.528302|- - -TCONS_00000010 XLOC_000012 - u q1:CUFF.41|CUFF.41.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000011 XLOC_000014 - u q1:CUFF.43|CUFF.43.1|100|10.561567|0.000000|25.497879|0.675000|- - -TCONS_00000012 XLOC_000015 - u q1:CUFF.45|CUFF.45.1|100|20.708956|2.186303|39.231609|1.323529|- - -TCONS_00000013 XLOC_000016 - u q1:CUFF.47|CUFF.47.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000014 XLOC_000017 - u q1:CUFF.49|CUFF.49.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000015 XLOC_000019 - u q1:CUFF.51|CUFF.51.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000016 XLOC_000020 - u q1:CUFF.53|CUFF.53.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000017 XLOC_000021 - u q1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000018 XLOC_000022 - u q1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000019 XLOC_000023 - u q1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000020 XLOC_000025 - u q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|- - -TCONS_00000021 XLOC_000026 - u q1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000022 XLOC_000029 - u q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|- - -TCONS_00000023 XLOC_000031 - u q1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000024 XLOC_000034 Xkr4|Xkr4 i q1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000025 XLOC_000035 Xkr4|Xkr4 i q1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|- - -TCONS_00000026 XLOC_000037 Xkr4|Xkr4 i q1:CUFF.17|CUFF.17.1|100|8.710571|0.000000|21.029179|0.556701|- - -TCONS_00000027 XLOC_000040 Xkr4|Xkr4 i q1:CUFF.25|CUFF.25.1|100|14.567679|5.354270|23.781089|0.931034|- - -TCONS_00000028 XLOC_000042 Xkr4|Xkr4 i q1:CUFF.21|CUFF.21.1|100|13.851236|0.000000|33.439842|0.885246|- - -TCONS_00000029 XLOC_000044 Xkr4|Xkr4 i q1:CUFF.23|CUFF.23.1|100|23.470150|0.000000|50.571145|1.500000|- - -TCONS_00000030 XLOC_000046 Xkr4|Xkr4 i q1:CUFF.27|CUFF.27.1|100|34.253732|0.000000|73.806535|2.189189|- - -TCONS_00000031 XLOC_000048 Xkr4|Xkr4 i q1:CUFF.61|CUFF.61.1|100|45.263860|0.000000|97.530065|2.892857|- - -TCONS_00000032 XLOC_000049 Xkr4|Xkr4 i q1:CUFF.63|CUFF.63.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000033 XLOC_000052 Xkr4|Xkr4 i q1:CUFF.65|CUFF.65.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000034 XLOC_000057 Xkr4|Xkr4 i q1:CUFF.67|CUFF.67.1|100|12.998852|0.000000|31.382005|0.830769|- - -TCONS_00000035 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.69|CUFF.69.1|100|10.058636|0.000000|24.283695|0.642857|- - -TCONS_00000036 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.71|CUFF.71.1|100|8.621688|0.000000|20.814595|0.551020|- - -TCONS_00000037 XLOC_000060 Xkr4|Xkr4 i q1:CUFF.73|CUFF.73.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000038 XLOC_000062 Xkr4|Xkr4 i q1:CUFF.75|CUFF.75.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000039 XLOC_000065 Xkr4|Xkr4 i q1:CUFF.77|CUFF.77.1|100|16.248565|0.000000|39.227507|1.038462|- - -TCONS_00000040 XLOC_000068 Xkr4|Xkr4 i q1:CUFF.79|CUFF.79.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000041 XLOC_000071 Xkr4|Xkr4 i q1:CUFF.81|CUFF.81.1|100|13.201959|0.000000|31.872349|0.843750|- - -TCONS_00000042 XLOC_000073 Xkr4|Xkr4 i q1:CUFF.83|CUFF.83.1|100|13.201959|0.000000|28.446269|0.843750|- - -TCONS_00000043 XLOC_000075 Xkr4|Xkr4 i q1:CUFF.85|CUFF.85.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000044 XLOC_000077 Xkr4|Xkr4 i q1:CUFF.87|CUFF.87.1|100|17.243375|0.000000|41.629191|1.102041|- - -TCONS_00000045 XLOC_000080 Xkr4|Xkr4 i q1:CUFF.89|CUFF.89.1|100|16.567165|0.000000|39.996674|1.058824|- - -TCONS_00000046 XLOC_000083 Xkr4|Xkr4 i q1:CUFF.91|CUFF.91.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000047 XLOC_000084 Xkr4|Xkr4 i q1:CUFF.93|CUFF.93.1|100|21.664754|0.000000|52.303342|1.384615|- - -TCONS_00000048 XLOC_000085 Xkr4|Xkr4 i q1:CUFF.95|CUFF.95.1|100|46.940300|0.000000|101.142289|3.000000|- - -TCONS_00000049 XLOC_000086 Xkr4|Xkr4 i q1:CUFF.97|CUFF.97.1|100|21.481154|0.000000|46.285454|1.372881|- - -TCONS_00000050 XLOC_000087 Xkr4|Xkr4 i q1:CUFF.99|CUFF.99.1|100|14.567679|0.000000|35.169489|0.931034|- - -TCONS_00000051 XLOC_000004 - u - q2:CUFF.1|CUFF.1.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000052 XLOC_000005 - u - q2:CUFF.3|CUFF.3.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000053 XLOC_000006 - u - q2:CUFF.5|CUFF.5.1|100|21.226627|0.000000|59.889707|1.205672|- -TCONS_00000054 XLOC_000007 - u - q2:CUFF.11|CUFF.11.1|100|32.531777|24.582998|40.480555|1.847804|- -TCONS_00000055 XLOC_000008 - u - q2:CUFF.7|CUFF.7.1|100|29.709524|19.806349|39.612698|1.687500|- -TCONS_00000056 XLOC_000009 - u - q2:CUFF.9|CUFF.9.1|100|34.072933|23.364686|44.781179|1.935341|- -TCONS_00000057 XLOC_000010 - u - q2:CUFF.13|CUFF.13.1|100|16.582060|0.000000|35.729373|0.941860|- -TCONS_00000058 XLOC_000013 - u - q2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000059 XLOC_000018 - u - q2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000060 XLOC_000024 - u - q2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000061 XLOC_000025 - u - q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|- -TCONS_00000062 XLOC_000027 - u - q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000063 XLOC_000028 - u - q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|- -TCONS_00000064 XLOC_000029 - u - q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000065 XLOC_000030 - u - q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|- -TCONS_00000066 XLOC_000032 - u - q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|- -TCONS_00000067 XLOC_000033 Xkr4|Xkr4 i - q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|- -TCONS_00000068 XLOC_000036 Xkr4|Xkr4 i - q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|- -TCONS_00000069 XLOC_000037 Xkr4|Xkr4 i - q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|- -TCONS_00000070 XLOC_000038 Xkr4|Xkr4 i - q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000071 XLOC_000039 Xkr4|Xkr4 i - q2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|- -TCONS_00000072 XLOC_000041 Xkr4|Xkr4 i - q2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|- -TCONS_00000073 XLOC_000043 Xkr4|Xkr4 i - q2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|- -TCONS_00000074 XLOC_000045 Xkr4|Xkr4 i - q2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000075 XLOC_000047 Xkr4|Xkr4 i - q2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000076 XLOC_000049 Xkr4|Xkr4 i - q2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|- -TCONS_00000077 XLOC_000050 Xkr4|Xkr4 i - q2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000078 XLOC_000051 Xkr4|Xkr4 i - q2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000079 XLOC_000053 Xkr4|Xkr4 i - q2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000080 XLOC_000054 Xkr4|Xkr4 i - q2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000081 XLOC_000055 Xkr4|Xkr4 i - q2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|- -TCONS_00000082 XLOC_000056 Xkr4|Xkr4 i - q2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000083 XLOC_000058 Xkr4|Xkr4 i - q2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|- -TCONS_00000084 XLOC_000059 Xkr4|Xkr4 i - q2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|- -TCONS_00000085 XLOC_000060 Xkr4|Xkr4 i - q2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|- -TCONS_00000086 XLOC_000061 Xkr4|Xkr4 i - q2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|- -TCONS_00000087 XLOC_000063 Xkr4|Xkr4 i - q2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000088 XLOC_000064 Xkr4|Xkr4 i - q2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000089 XLOC_000066 Xkr4|Xkr4 i - q2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|- -TCONS_00000090 XLOC_000067 Xkr4|Xkr4 i - q2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|- -TCONS_00000091 XLOC_000068 Xkr4|Xkr4 i - q2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|- -TCONS_00000092 XLOC_000069 Xkr4|Xkr4 i - q2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|- -TCONS_00000093 XLOC_000070 Xkr4|Xkr4 i - q2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|- -TCONS_00000094 XLOC_000072 Xkr4|Xkr4 i - q2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|- -TCONS_00000095 XLOC_000074 Xkr4|Xkr4 i - q2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|- -TCONS_00000096 XLOC_000076 Xkr4|Xkr4 i - q2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000097 XLOC_000078 Xkr4|Xkr4 i - q2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000098 XLOC_000079 Xkr4|Xkr4 i - q2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000099 XLOC_000081 Xkr4|Xkr4 i - q2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000100 XLOC_000082 Xkr4|Xkr4 i - q2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|- diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out7.txt --- a/test-data/cuffcompare_out7.txt +++ /dev/null @@ -1,33 +0,0 @@ -# Cuffcompare v2.0.2 | Command line was: -#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/002/dataset_2770.dat -R ./input1 ./input2 -# - -#= Summary for dataset: ./input1 : -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) -# (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 1 in 1 loci (1 multi-exon) -# Corresponding super-loci: 1 -#--------------------| Sn | Sp | fSn | fSp - Base level: 2.2 2.3 - - - Exon level: 0.0 0.0 0.0 0.0 - Intron level: 0.0 nan 0.0 nan -Intron chain level: 0.0 nan 0.0 nan - Transcript level: 0.0 0.0 0.0 0.0 - Locus level: 0.0 0.0 0.0 0.0 - -Matching intron chains: 0 - Matching loci: 0 - - Missed exons: 2/3 ( 66.7%) - Novel exons: 49/50 ( 98.0%) - Missed introns: 2/2 (100.0%) - Missed loci: 0/1 ( 0.0%) - Novel loci: 49/50 ( 98.0%) - -#= Summary for dataset: ./input2 : -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) -# (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 0 in 0 loci (0 multi-exon) - - Total union super-loci across all input datasets: 87 - (0 multi-transcript, ~1.1 transcripts per locus) diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_in1.sam --- a/test-data/cuffdiff_in1.sam +++ /dev/null @@ -1,400 +0,0 @@ -EAS38_8_212_338_985 0 chr1 3004981 0 35M * 0 0 CCAATGGGCCTCTATTTGCAGTGATGGGCGAGTAG hhhhhhhhhhhhhEhhhhYhhhhUhhh@Ih?BZ?e NM:i:2 -EAS38_8_8_215_414 0 chr1 3035356 0 35M * 0 0 TACCCCATAAAAGCCCCTGGCTTTCGCGCCTCGTG hhhhhhhhhhhhhhhhhhhhhhh`GI>PPIQPBOH NM:i:1 -EAS38_8_8_622_393 16 chr1 3065512 0 35M * 0 0 AAAAAAAAAAAAACAAAAAAAAAAAAAACAGCGAG hhHhhhhhhhhhhMhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_53_557_326 16 chr1 3075162 0 35M * 0 0 TAGAGAAATGGATACAGAAAGTGTGGTAATTTACA Ihehhhhh]hhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_259_911_538 0 chr1 3099409 0 35M * 0 0 TTTGGCTGGGAGACAATTAATGACTGCTTTTTTTT hhhhhhhhhhhh_hhhhhNhhP\hhaEhhHhNhhh NM:i:2 -EAS38_8_284_729_569 16 chr1 3113004 255 35M * 0 0 CTATCTGTTGCAAAGAGAACTTTCCTTGGTGTAAG EIIEKhRh@K_hahhhhhhh`ehhhhhhhhhhhhh NM:i:0 -EAS38_8_27_537_242 0 chr1 3118613 255 35M * 0 0 AGGACTCACATTCCCTTACTTTGTTTACAAAATGA hhh`hhhhhhhhhhhhhhhhhhhhhh]hhYXOhD` NM:i:0 -EAS38_8_38_947_12 0 chr1 3131368 0 35M * 0 0 TATTAGTCCCCTATCANATTTAGGATTGTTAATAA hhhhhhh_bchhhhUh;\hhhhh`EXcIVhNJZ]P NM:i:2 -EAS38_8_205_433_879 16 chr1 3136988 0 35M * 0 0 CATATCAATTGAACGGAACTAAAGTCTGTGACAGT hhhhchhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_155_191_162 16 chr1 3136999 0 35M * 0 0 AACGGAACTAAAGTCTGTGACAGTGGACATAGCTG hh_h\hhYhhhhhMhfhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_216_635_828 0 chr1 3137063 0 35M * 0 0 ATCTGGAATTATGTGATTATAATTTTCTTAGCATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_317_949_784 0 chr1 3137063 0 35M * 0 0 ATCTGGAATTATGTGATTATAATTTTCTTAGCATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhNchh NM:i:0 -EAS38_8_278_281_786 16 chr1 3137078 0 35M * 0 0 ATTATAATTTTCTTAGCATTTTCTTTGTAAAAAAA AhhhQhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_228_462_705 0 chr1 3137133 0 35M * 0 0 GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA hhhhhhhhhhhhhhhhhhh_hghhWhYh`LhhKbY NM:i:0 -EAS38_8_299_582_840 0 chr1 3137133 0 35M * 0 0 GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhWhhhhh NM:i:0 -EAS38_8_125_742_683 16 chr1 3137135 0 35M * 0 0 TGGTGTATAGTAAAAAGTAAAGAAATTCTGAGAGG GJCZSShchhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_208_212_874 0 chr1 3137137 0 35M * 0 0 GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG hhhhhhhhhhhhhhhhhhhhhhhhh[hhhhhhh`h NM:i:0 -EAS38_8_241_424_62 16 chr1 3137137 0 35M * 0 0 GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG hhhhhhhhehhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_245_195_910 16 chr1 3137137 0 35M * 0 0 GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG Bhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_234_890_706 0 chr1 3137138 0 35M * 0 0 TGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAGT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhUhh NM:i:0 -EAS38_8_317_909_810 16 chr1 3137175 0 35M * 0 0 TATTTTAGGATAATACATATATACATATGCAGTGT hhhhhhhaThhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_111_444_456 0 chr1 3137180 0 35M * 0 0 TAGGTTAATACATATATACATATGCAGTGTGTGTG hhhhhhhhhhhhhhhhhhhahhhhhhhhgehhhhH NM:i:1 -EAS38_8_134_193_731 0 chr1 3137180 0 35M * 0 0 TAGGATAATACATATATACATATGCAGTGTGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_138_869_374 0 chr1 3137180 0 35M * 0 0 TAGGATAATACATATATACATATGCAGTGTGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_36_257_907 0 chr1 3137192 0 35M * 0 0 TATATACATATGCAGTGTGTGTGCCAGTGGTGTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhNJDhS NM:i:0 -EAS38_8_50_322_852 0 chr1 3137192 0 35M * 0 0 TATATACATATGCAGTGTGTGTGCCAGTGGTGTTA hhhhhhhhhhhhhhhhhhhhhhhRcZhhhhVhShY NM:i:0 -EAS38_8_207_430_640 16 chr1 3146524 0 35M * 0 0 AAAAAACATCGGCACAACAATCAAAAAAAAAAAAA VE_AhhhhFhhhhh]hhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_289_914_684 0 chr1 3154024 255 35M * 0 0 TCACAGAAGGCTCACTTCCTTTCTGTCTGTGTCAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhdhhMGT NM:i:0 -EAS38_8_35_737_747 16 chr1 3174758 255 35M * 0 0 TTTTGGGTGAGATGGAATCTCAGAGTAGTTATTTT [hghdhMhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_75_492_572 16 chr1 3174758 255 35M * 0 0 TTTTGGGTGAGATGGAATCTCAGAGTAGTTATTTT [Vhhh^hhhhhhhhhhhdhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_187_160_172 16 chr1 3175562 255 35M * 0 0 TAGTCTGGTCTGTGGCTTCAGCGGTAGGATGGCCT BT\JAGMQVRN[QhYZGchhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_56_600_894 0 chr1 3175828 255 35M * 0 0 GAGAAAGAGGTGGGAAGGGAAAGAGAGAGAGAAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhShChDKhI NM:i:0 -EAS38_8_106_467_709 16 chr1 3181781 255 35M * 0 0 CTTTAGTACAGGTTACATTCCATACCTATAGCAAG hhhhhhhhhhh`hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_199_476_527 16 chr1 3181781 255 35M * 0 0 CTTTAGTACAGGTTACATTCCATACCTATAGCAAG E[dbhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_116_967_124 16 chr1 3187134 255 35M * 0 0 ATAGCTCTTCATCTAGGGGTGGGACTTTTGAGATT hghYhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_182_44_990 16 chr1 3187394 255 35M * 0 0 GAAATGCTCATTCTCATAGAGAAGAGATTGCCTAG EhhhaKhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_203_996_132 16 chr1 3187394 255 35M * 0 0 GAAATGATCATTCTCATAGAGAAGAGATTGCCTAG JXJ`_eFVVhhhhhchhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_318_612_118 0 chr1 3188522 255 35M * 0 0 GTATTCTTAATCTATTGTGTTTTGTTTGTTCTTTG hhhhhhhhhhhhhhhhhhShhhhIhhhWhh_hYhC NM:i:1 -EAS38_8_52_573_715 16 chr1 3188914 255 35M * 0 0 TTTGGAAGATAGTTTTCATTTCAGGACTGTCATTA hh]hDhh\hhhghhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_82_668_114 16 chr1 3189123 255 35M * 0 0 TAGATTCTGTTGAAAGCTGCTTGTGTAGGTGCTGG Jhfheh@_Nh`hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_229_732_980 16 chr1 3189293 255 35M * 0 0 ATATGTAGAAAAAGAAAGCAATTAGATGTATCATA hhhhWhhOhhhhhghhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_49_685_15 0 chr1 3189811 255 35M * 0 0 CTTTTAAAATGACCACAGTGTACTTTATTTAATTA hhhhhhhhhhhhhhhhhhhhhhhhhh]hhhPahZQ NM:i:2 -EAS38_8_228_500_937 0 chr1 3189812 255 35M * 0 0 TTTTAAAATGACCACAGTGTACTTTATTTAATGAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhLh NM:i:1 -EAS38_8_8_865_653 0 chr1 3189812 255 35M * 0 0 TTTTAAAATGACCACAGTGTACTTTATTTAATGAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_284_550_449 0 chr1 3189815 255 35M * 0 0 TGAAATGACCACAGTGTACTTTATTTAATGATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPhhhh NM:i:1 -EAS38_8_44_493_707 0 chr1 3189839 255 35M * 0 0 TTAATGATTTTTGTACTTTGTGTTGCAATAAAATA hhhhhhhhhhhhhhhhhhhhhhhhRhhhhhhhhhh NM:i:0 -EAS38_8_173_339_743 0 chr1 3189847 255 35M * 0 0 TTTTGTACTTTGTGTTGCAATAAAATAAAAAAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZhhhf NM:i:0 -EAS38_8_69_320_425 16 chr1 3189862 255 35M * 0 0 TGAAATAAAAAAAAAAAAAAATCTACAAAATTCAA _OahhShhhhAhhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_253_215_784 0 chr1 3189882 255 35M * 0 0 ATCTACAAAATTCAAATATATAAAATTTCAAGTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_254_492_492 0 chr1 3189882 255 35M * 0 0 ATCTACAAAATTCAAATATATAAAATTTCAAGTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhhhh NM:i:0 -EAS38_8_164_969_744 0 chr1 3189884 255 35M * 0 0 CTACAAAATTCAAATATATAAAATTTCAAGTTTTC hhhhhhhhhhhhhhhhhhhhhVhhWhTNchDhhgA NM:i:0 -EAS38_8_76_118_672 0 chr1 3189938 255 35M * 0 0 AGAAAAAAAATCAGATAACCGAGGAAAATTATTCA hhhhhhhhhhhhhhhhhhhhhhhh]hhhhhThhR] NM:i:0 -EAS38_8_322_903_184 16 chr1 3189967 255 35M * 0 0 TATTCATTATGAAGTACTACTTTCCACTTCATTTC O[ENehNVh`ahh]hhhhhhWhhhhhhhhhhhhhh NM:i:0 -EAS38_8_122_863_114 16 chr1 3189975 255 35M * 0 0 ATGAAGTACTACTTTCCACTTCATTTCATCACAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_328_905_544 0 chr1 3189975 255 35M * 0 0 ATGAAGTACTACTTTCCACTTCATTTCATCACAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhXhO NM:i:0 -EAS38_8_49_611_982 16 chr1 3189991 255 35M * 0 0 CACTTCATTTCATCACAAATTGTAACTTACTTAAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_149_471_590 0 chr1 3189993 255 35M * 0 0 CTTCATTTCATCACAAATTGTAACTTACTTAACTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhc NM:i:0 -EAS38_8_176_471_461 0 chr1 3189993 255 35M * 0 0 CTTCATTTCATCACAAATTGTAACTTACTTAACTG hhhhhhhhhhhhhhhhhhhhhhchhh`hhh[hhhO NM:i:0 -EAS38_8_330_91_472 16 chr1 3189999 255 35M * 0 0 TTAATCACAAATTGTAACTTACTTAACTGACCAAA hhOhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_330_964_788 16 chr1 3189999 255 35M * 0 0 TTCATCACAAATTGTAACTTACTTAACTGACCAAA aIhhhh`hhhhhhhhhhhhhBhhhhhhhchhhhhh NM:i:0 -EAS38_8_281_200_582 16 chr1 3190038 255 35M * 0 0 CTATGGTACTGCAGTATAGAAAATACTCCACACAC ONK[MhhhdhhQhhhhhhhMhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_241_125_175 16 chr1 3190056 255 35M * 0 0 GAAAATAATCCACACACTGTGCTTTGAGCTAGAGC HhhhhShIhhShhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_274_895_968 0 chr1 3190074 255 35M * 0 0 GTGCTTTGAGCTAGAGCACTTGGAGTCACTGCACA hhhhhhhhhhhhhhhhPhOhhhhPhhMTMXhLBMC NM:i:1 -EAS38_8_274_589_297 16 chr1 3190081 255 35M * 0 0 GAGCTAGAGCACTGGGAGTCACTGCCCAGGGCAGC ]W_IHUh_hh^WZDhhhhKhhh[hhhhhhhhhhhh NM:i:1 -EAS38_8_11_418_433 0 chr1 3190094 255 35M * 0 0 TGGAGTCACTGCCCAGGGCAGCAGCCTCCAACCAA hhhhhhhhhhhhhhhhhhbCchhb`PUPhJWIOGA NM:i:0 -EAS38_8_324_436_604 16 chr1 3190136 255 35M * 0 0 ACACTTACAAGTTGAATTCTAAAGGAAGGTCTGGT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_131_262_425 16 chr1 3190137 255 35M * 0 0 CACGTACAAGTTGAATTCTAAAGGAAGGTCTGGTT dVKEhhhhhhhWhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_5_661_318 16 chr1 3190137 255 35M * 0 0 CACTTACAAGTTGAATTCTAAAGGAAGGTCTGGTT F^O_ZhhhhhAhhhhhMh`hhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_109_581_805 0 chr1 3190144 255 35M * 0 0 AAGTTGAATTCTAAAGGAAGGTCTGGTTATGTGGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_279_908_963 0 chr1 3190154 255 35M * 0 0 CTAAAGGAAGGTCTGGTTATGTGGGGTTGGAATAT hhhhhhhhhhhhhhhhhhhhhhhhhhDhhhRDEhH NM:i:0 -EAS38_8_207_793_649 16 chr1 3190155 255 35M * 0 0 TAAAGGAAGGTCTGGTTATGTGGGGTTGGAATATG FThTO[ZcIHRhhShhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_249_136_550 0 chr1 3190167 255 35M * 0 0 TGGTTATGTGGGGTTGGAATATGTATATCTATATA hhhhhhhhhhhhhhhhhghhhhhhhhhhhhDhJhh NM:i:0 -EAS38_8_197_214_431 16 chr1 3190168 255 35M * 0 0 GGTTATGTGGGGTTGGAATATGTATATCTATATAT EUEU@QhJhhVgFUhhhhPhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_124_625_963 16 chr1 3190174 255 35M * 0 0 GTGGGGTTGGAATATGTATATCTATATATCTCTAT ]hdTChhhXhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_314_668_328 16 chr1 3190176 255 35M * 0 0 GGGGTTGGAATATGTATATCTATATATCTCTATAT hhhh]]hhhhOh_hhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_8_247_406 16 chr1 3190176 255 35M * 0 0 GGGGTTGGAATATGTATATCTATATATCTCTATAT fY]NUFQQhhVcRhhhhhhehhhhhhhhhhhhhhh NM:i:0 -EAS38_8_45_380_957 16 chr1 3190191 255 35M * 0 0 ATATCTATATATCTCTATATATATTTACATCAAAG hhhVhbhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_224_453_647 16 chr1 3190214 255 35M * 0 0 TTTACATCAAAGAATTTAATAACTCATTTAAATTT hKhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_120_914_892 0 chr1 3190236 255 35M * 0 0 CTCATTTAAATTTTTGTTTCAAATAAAATTCCAAA hhhhhhhhhhhhhhhhhhhhhhhhhhfhhhLWh]K NM:i:0 -EAS38_8_8_442_670 0 chr1 3190258 255 35M * 0 0 ATAAAATTCCAAATACATTTGTACAATGTTTACAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhRhhTe_\ NM:i:0 -EAS38_8_245_767_298 16 chr1 3190284 255 35M * 0 0 TGTTTACAAAGTAAGAGACAGGACTGGCAGGTTTG WOF`hhhhhhhbhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_94_374_121 16 chr1 3190284 255 35M * 0 0 TGTTTACAAAGTAAGAGACAGGACTGGCAGGTTTG Shh`hhRhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_256_414_787 0 chr1 3190333 255 35M * 0 0 CACCGTGATGTCCGGGTGATATATCTTCACGTTGC hhhhhhhhhhhhhhhhdhchhhhh`hhJRBhfhhJ NM:i:0 -EAS38_8_215_417_539 16 chr1 3190353 255 35M * 0 0 ATATCTTCACGTTGCCTGCACACACCTTATTTCTG VAHGh@XhBhhhRhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_167_839_349 0 chr1 3190379 255 35M * 0 0 TTATTTCTGAAATGGAGAGAGAAACTCAAGAATGT hhhhhhhhhhhhhhhhhhhhhdhhhhhPhhDhhCh NM:i:0 -EAS38_8_235_344_488 0 chr1 3190402 255 35M * 0 0 ACTCAAGAATGTCACCGACTATGCATCAGAATACT hhhhhhhhhhhhhhhhhLhhhhbfhGUILPJQQPL NM:i:0 -EAS38_8_287_803_220 0 chr1 3190402 255 35M * 0 0 ACTCAAGAATGTCACCGACTATGCATCAGAATACT hhhhhhhhhhhhhhhhhhhhhhhhdhgTMVEh\^N NM:i:0 -EAS38_8_23_488_181 16 chr1 3190434 255 35M * 0 0 ACTATGTACAGTTGAAGTTAGGGAGCTGAGAACCT hChhhhOhhhhgUhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_137_662_459 16 chr1 3190469 255 35M * 0 0 AGTGTTCTGTTCTCTTCTGGTTTGTCTTCATCTAC eOKeGUhIhVhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_228_762_237 16 chr1 3190469 255 35M * 0 0 AGTGGTCTGTTCTCTTCTGGTTTGTCTTCATCTAC ZhMhbWK\hgShShhhh^hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_65_836_536 16 chr1 3190469 255 35M * 0 0 AGTGTTCTGTTCTCTTCTGGTTTGTCTTCATCTAC ahYhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_100_122_849 0 chr1 3190545 255 35M * 0 0 CAAACATTGGAAAGAGGAAGGAGAAAAACACAAAA hhhhhhhhhhhhhhhhhhhhhXhhhhhhCdM[TUh NM:i:1 -EAS38_8_172_157_846 16 chr1 3190553 255 35M * 0 0 GGAAAGAGGAAGGAGAAAAGTACAAAATATTTAAG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_166_123_980 16 chr1 3190565 255 35M * 0 0 GAGAAAAGCACAAAATATTTAAGGCAAATTAAGCA FhThhhhLhhhhhhhhhhhhhhhbhhhhhhhhhhh NM:i:0 -EAS38_8_202_25_949 16 chr1 3190601 255 35M * 0 0 ATATGTATAGTCTCTTTGTGCCAGGAGGATGTGAC OKTX@[hhdGVhVhhhhMhdhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_135_382_764 0 chr1 3190604 255 35M * 0 0 TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT hhhhhhhhhhhhhhhhhhhhhhhhhOhhhhYHhhh NM:i:0 -EAS38_8_256_748_407 16 chr1 3190604 255 35M * 0 0 TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT RWEhhhhZhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_328_369_595 0 chr1 3190604 255 35M * 0 0 TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT hhhhhhhhhhhhhhhhhhhhhhhhhFahJORXhhh NM:i:0 -EAS38_8_13_985_934 16 chr1 3190609 255 35M * 0 0 AGTCTCTTTGTGCCAGGAGGATGTGACTTTCTTTT STZhQhhUhcdhhhhdSh^Zhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_13_657_254 0 chr1 3190659 255 35M * 0 0 GCTTTAAAAAATTCAAATAAAGCAAGTCTGGTGTG hhhhhhhhhhhhhhhhhhhhhhhhZhhhhhYh]h\ NM:i:0 -EAS38_8_97_368_634 0 chr1 3190659 255 35M * 0 0 GCTTTAAAAAATTCAAATAAAGCAAGTCTGGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_158_637_333 0 chr1 3190697 255 35M * 0 0 TGGGTTGCTTGTGTTGTTTTAATTTTTTTTGAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh@ZMhQ NM:i:0 -EAS38_8_7_431_889 0 chr1 3190697 255 35M * 0 0 TGGGTTGCTTGTGTTGTTTTAATTTTTTTTGAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_129_799_390 0 chr1 3190859 255 35M * 0 0 TAAAATAATGAGAGAATGGAGAACCAATGTAAGGA hhhhhhhhhhhhbhQMhhhXhJgFNJVKJLT>BI? NM:i:0 -EAS38_8_186_234_660 16 chr1 3190910 255 35M * 0 0 TCTGGAAGCAGGCTCACCAAGTATGATGGTTTCAT bb\hhhhhhhhdhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_99_392_34 16 chr1 3190940 255 35M * 0 0 TTCATACACAGAAAAACATTTGTTCTTTTGGATGC `dAhhhEUMhhhhhhhhhhThhhhhhhhhhhhhhh NM:i:1 -EAS38_8_141_299_800 0 chr1 3190964 255 35M * 0 0 CTTTTGGATGCCATTAGTTCAGCCAGTGTCAACAT hhhhhhhhhhhhhhhhhhhhhhhhahhhhhhhQh] NM:i:0 -EAS38_8_41_30_673 0 chr1 3190983 255 35M * 0 0 CAGCCAGTGTCAACATGACTAGTGGTTTCCCCAGC hhhhhhhhhhhhhhhhhhQhhhhhhJhh>SWHLEM NM:i:1 -EAS38_8_270_818_467 16 chr1 3191047 255 35M * 0 0 CTGCTTTCCAGGCTTCTCATCTATAGATAGAGAAG YADUL]DhhhhYhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_295_700_520 0 chr1 3191049 255 35M * 0 0 GCTTTCCAGGCTTCTCATCTATAGATAGAGAAGAC hhhhhhhhhhhhhhhhhhhhRhhhhhhah`IhRXG NM:i:0 -EAS38_8_326_937_869 0 chr1 3191049 255 35M * 0 0 GCTTTCCAGGCTTCTCATCTATAGATAGAGAAGAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhQMhFG? NM:i:1 -EAS38_8_156_546_203 0 chr1 3191080 255 35M * 0 0 AGACTTTTACAAGGTGTATGTATTGAATCCATTAT hhhhhhhhhhhhhhhhhhhfhhhhDhhVhhRhhPh NM:i:1 -EAS38_8_226_788_95 0 chr1 3191080 255 35M * 0 0 AGACTTTTACAAGGTGTATGTATTTAAGCCATTAT hhhhhhhhhhhhhhhhhhhhhhhhPhhSghchhhh NM:i:1 -EAS38_8_206_454_499 16 chr1 3191117 255 35M * 0 0 AAAATGACATTATTTATCATTATTAGAAATTCCAA hhhhZhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_126_432_418 0 chr1 3191141 255 35M * 0 0 AGAAATTCCAACCCTAGTTATGAAAGATTGAGGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhYhchR NM:i:0 -EAS38_8_255_473_525 0 chr1 3191143 255 35M * 0 0 AAATTCCAACCCTAGTTATGAAAGATTGAGGGAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhWhhhafh NM:i:0 -EAS38_8_293_908_459 16 chr1 3191160 255 35M * 0 0 ATGAAAGATTGAGGGAAAGTGATAAAGAACAAAAG hhehhhhhhYhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_126_512_733 0 chr1 3191163 255 35M * 0 0 AAAGATTGAGGGAAAGTGATAAAGAACAAAAGGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhN NM:i:0 -EAS38_8_132_357_350 0 chr1 3191163 255 35M * 0 0 AAAGATTGAGGGAAAGTGATAAAGAACAAAAGGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh^hL NM:i:0 -EAS38_8_225_963_686 16 chr1 3191186 255 35M * 0 0 GAACAAAAGGGAGGGATATTATTCTCTCATTTTTA UchhhhfhhhahNhahhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_91_183_721 0 chr1 3191203 255 35M * 0 0 ATTATTCTCTCATTTTTAACAGCATATTTGTCTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[ NM:i:0 -EAS38_8_91_184_720 0 chr1 3191203 255 35M * 0 0 ATTATTCTCTCATTTTTAACAGCATATTTGTCTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhX NM:i:0 -EAS38_8_37_742_366 16 chr1 3191253 255 35M * 0 0 TACTGTGTGGCTTCAAAGAAGATAGTCATCTCTGG h]hQhhB_hhRhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_164_833_223 16 chr1 3191267 255 35M * 0 0 AAAGAAGATAGTCATCTCTGGTTCTCTTACTGAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_20_3_646 16 chr1 3191299 255 35M * 0 0 AGAATAGAAAGTCTCTCCTTACTGAGAATAGGAAG hVhh_hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_305_336_434 16 chr1 3191299 255 35M * 0 0 AGAATAGAAAGTCTCTCCTTACTGAGAATAGGAAG hhhhhhhhhhhUhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_133_876_487 16 chr1 3191301 255 35M * 0 0 AATAGAAAGTCTCTCCTTACTGAGAATAGGAAGCC hhGhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_58_243_264 16 chr1 3191305 255 35M * 0 0 GAAAGTCTCTAATTACTGAGAATAGGAAGCCATCT hhhhh?UQLOIAhhhWhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_158_87_484 16 chr1 3191325 255 35M * 0 0 AATAGGAAGCCATCTTCATACCTGTCCCTCTGCAT gh@hChhhh`LhFhhghhRhhhhhghhhhhhhhhh NM:i:0 -EAS38_8_49_289_587 16 chr1 3191360 255 35M * 0 0 TTATTCTTGAGGTTACTGAGCCATCTGGCTACAGA hhh^XhKUhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_226_316_409 0 chr1 3191368 255 35M * 0 0 GAGGTTACTGAGCCATCTGGCTACAGAGAAGAAAA hhhhhhhhhhhhhhhhhhahhhah_UOhDENhC[G NM:i:0 -EAS38_8_27_871_685 16 chr1 3191375 255 35M * 0 0 CAGAGCCATCTGGCTACAGAGAAGAAAAGCAAGAG gAhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_323_782_711 16 chr1 3191375 255 35M * 0 0 CTGAGCCATCTGGCTACAGAGAAGAAAAGCAAGAG hGdhZhghhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_138_990_817 16 chr1 3191399 255 35M * 0 0 AAAAGCAAGAGTTGTTTTTTTATTTTTATTTTATT hhhhKhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_185_443_369 16 chr1 3191399 255 35M * 0 0 AAAAGCAAGAGTTGTTTTTTTATTTTTATTTTATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_16_393_343 16 chr1 3191400 255 35M * 0 0 AAAGCAAGAGTTGTTTTTTTATTTTTATTTTATTT hhhhVhhhhhI]hPJhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_50_691_313 16 chr1 3191400 255 35M * 0 0 AAAGCAAGAGTTGTTTTTTTATTTTTATTTTATTT hhhhhhhhhhhhhXhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_189_168_310 16 chr1 3191408 255 35M * 0 0 AGTTGTTTTTTTATTTTTATTTTATTTTTATTTTT hhWWhhh[hh_hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_247_520_310 16 chr1 3191408 255 35M * 0 0 AGTTGTTTTTTTATTTTTATTTTATTTTTATTTTT hhTRhhh]hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_8_620_387 0 chr1 3191411 3 35M * 0 0 TTTTTTTTTATTTTTATTTTATTTTTATTTTTTTA hhhhhhhhhhhhhhh`hhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_264_985_305 0 chr1 3191415 1 35M * 0 0 TTTTTATTTTTATTTTATTTTTATTTTTTTAATTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhOhh NM:i:1 -EAS38_8_290_750_320 16 chr1 3191505 255 35M * 0 0 CAGACAATGGCTTTAAGTGGGGCCTATATGAACTG BaFA>PbShGXfXhh_hJhh[hhhhhhhhhhhhhh NM:i:1 -EAS38_8_220_527_228 16 chr1 3191562 255 35M * 0 0 CGGTTTTGTGAAGGTAATATATCAGTAATATGGTT E[gYhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_181_540_123 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhOfhPhhEZDS NM:i:0 -EAS38_8_28_698_660 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhheRchhHhGh NM:i:0 -EAS38_8_304_298_316 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGTTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhhbchhhTchh NM:i:1 -EAS38_8_146_777_942 0 chr1 3191575 255 35M * 0 0 GTAATATATCAGTAATATGGTTGACATAAATAAGC hhhhhhhhhhhhhhhhhhhhhhhhahhhhhhhhhG NM:i:0 -EAS38_8_206_582_659 0 chr1 3191575 255 35M * 0 0 GTAATATATCAGTAATATGGTTGACATAAATAAAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhgh[hh@T NM:i:1 -EAS38_8_113_379_524 0 chr1 3191576 255 35M * 0 0 TAATATATCAGTAATATGGTTGACATAAATAAGCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhIh NM:i:0 -EAS38_8_197_772_581 16 chr1 3191611 255 35M * 0 0 GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_256_457_159 16 chr1 3191611 255 35M * 0 0 GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC hhhhhhUhhhgPhhghhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_315_836_955 0 chr1 3191675 255 35M * 0 0 TGAAAAGAATGTTAGTTGGCTGTAACCATAAAATT hhhhhhhhhhhhhhhhhhhLhhHhhhEMhghJhUW NM:i:0 -EAS38_8_255_763_380 16 chr1 3191702 255 35M * 0 0 ATAAAATGGGCAGTTGTATTTACAAATAATCACAT hhhhhhhBhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_279_818_155 0 chr1 3191716 255 35M * 0 0 TGTATTTACAAATAATCACATATATGATGCTTACA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhT^G NM:i:0 -EAS38_8_48_883_242 16 chr1 3191719 255 35M * 0 0 ATTTAAAAATAATCACATATATGATGCTTACAGAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_78_140_97 0 chr1 3191764 255 35M * 0 0 ATTTCTAAATAATCACATATGCTAAAAGCTAGTTT hhhhhhhhhhhhhhhhhhhhPhhh\ThGhhDILh] NM:i:1 -EAS38_8_322_980_805 16 chr1 3191782 255 35M * 0 0 ATGCTAAAAGCTAGGTTTTTCTAATACACTTTTAT hSYhhhhhh\hhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_319_99_291 16 chr1 3191786 255 35M * 0 0 TAAAAGCTAGGTTTTTCTAATACACTTTTACTTTC hhhhhhhdhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_64_224_620 0 chr1 3191811 255 35M * 0 0 TTTTATTTTCATGGAGGGCTCTAGAGGTTTCCACG hhhhhhhhhhhhhPhhhhhhhhhhZh]>hhCPJQJ NM:i:1 -EAS38_8_108_348_710 0 chr1 3191850 255 35M * 0 0 ATAGAAACCACTGAAAAGAGACTCAACTCTTTTTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh\ NM:i:0 -EAS38_8_231_364_552 0 chr1 3191864 255 35M * 0 0 AAAGAGACTCAACTCTTTTTCCCCCCAGCAATATT hhhhhhhhhhhhhhhhhhhhhhhhhhfhhhRhEhh NM:i:0 -EAS38_8_116_293_619 0 chr1 3191865 255 35M * 0 0 AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhhhX NM:i:0 -EAS38_8_145_345_869 0 chr1 3191865 255 35M * 0 0 AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhchhXhhh NM:i:0 -EAS38_8_275_299_203 0 chr1 3191865 255 35M * 0 0 AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA hhhhhhhhhhhhhhhhhhhhhhhhhHBhhBhXh^\ NM:i:0 -EAS38_8_14_653_187 16 chr1 3191901 255 35M * 0 0 GTTGCTCTGGGCTGCTCTATGCATATGGCATGTTG NQKhhRTYh@hNdhhWMhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_123_560_667 16 chr1 3191909 255 35M * 0 0 GTGCTGCTCTATGCATATGGCATGTTGTTGGTACC eThh]hhfhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_158_848_347 16 chr1 3191913 255 35M * 0 0 GGCTCTATGCATATGGCATGTTGTTGGTACCTGTA @U\EWWhRbhhhhbhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_259_577_716 0 chr1 3191933 255 35M * 0 0 TTGTTGGTACCTGTACCATTCTCTTCCATTGAGAA hhhhhhhhhhhhhhhRhhhhhhhhh]hhhhhKhhh NM:i:0 -EAS38_8_37_266_444 16 chr1 3191981 255 35M * 0 0 GGTGGAGGAGCTGTTCAGCTCTCTCTAACCTATTT EfQhWOhh`hhWhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_298_155_843 16 chr1 3191988 255 35M * 0 0 GAGCTGTTCAGCTCTCTCTAACCTATTTAGATTTT Lhh`hhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_171_911_326 16 chr1 3192010 255 35M * 0 0 CTATTTAGATTTTATCTTTCACTTTGTGATAGAAT [hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_213_546_978 16 chr1 3192010 255 35M * 0 0 CTATTTAGATTTTATCTTTCACTTTGTGATAGAAT afhhhhh\hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_165_431_451 0 chr1 3192012 255 35M * 0 0 ATTTAGATTTTATCTTTCACTTTGTGATAGAATCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhh]Chhhh NM:i:0 -EAS38_8_130_352_184 16 chr1 3192020 255 35M * 0 0 TTTATCTTTCACTTTGTGATAGAATCTCTCTATAG hfdhhYhhhghJhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_303_420_658 16 chr1 3192025 255 35M * 0 0 CTTTCACTTTGTGATAGAATCTCTCTATAGAATGT hKhhhUhhhhhhhhhhhhh]hhhhhhhhhhhhhhh NM:i:0 -EAS38_8_11_860_892 16 chr1 3192043 255 35M * 0 0 ATCTCTCTATAGAATGTTCTCTCCACCACCTCCTG LLhXhchhhh^@hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_166_250_850 16 chr1 3192043 255 35M * 0 0 ACCTCTCTATAGAATGTTCTCTCCACCACCTCCTG M@X?CGhhhhhLhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_41_436_855 0 chr1 3192251 255 35M * 0 0 TACCTTTTACCCACTTACTGTTCTTACATGACCTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhbAhhh NM:i:0 -EAS38_8_1_614_740 0 chr1 3192310 255 35M * 0 0 GCACTGTAGATATTTTTGAGGAGTCACATAATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_1_615_739 0 chr1 3192310 255 35M * 0 0 GCACTGTAGATATTTTTGAGGAGTCACATAATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_11_667_100 0 chr1 3192520 255 35M * 0 0 CTCCTCAAGGGAAAATTTGGAAAGTATTTCATATT hhhhhhhhhhhhhhhhhhh\hhhHhhhhhhhhhhh NM:i:0 -EAS38_8_142_397_982 16 chr1 3192642 255 35M * 0 0 CTGTTAGCACAGTTCAATGATACATTCTTATTTTA hVShThOhhhhGhhhhhhhAhFhhhhhhhhhhhhh NM:i:2 -EAS38_8_201_45_850 16 chr1 3192642 255 35M * 0 0 CTGTTAGCACAGTTCAATGGTGCATTCTTATTTTA hfMfYhhhVhh[hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_198_171_959 0 chr1 3192730 255 35M * 0 0 TAGTCATTTAGGCAAGGAAATAGACATTGTTTTGA hhhhhhhhhhhhhhhhhhhhhhhfZhhhhhhhhTR NM:i:0 -EAS38_8_300_863_946 16 chr1 3193601 255 35M * 0 0 ATTCCTTTCTTCTTTGTTGCTATCATTGAACCACA BGbhah[IhhhhhhfOhh^hhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_311_818_593 0 chr1 3193885 255 35M * 0 0 CACAGATGCACAGATTGATGATCTCTAGGAAAAAG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZ]hh NM:i:0 -EAS38_8_126_604_962 0 chr1 3194707 255 35M * 0 0 TGGATCAAACAATTTAAACAACTTTAGCTTTACAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKWh NM:i:1 -EAS38_8_95_901_210 0 chr1 3194707 255 35M * 0 0 TGGATCAAACAATTTAAACAACTTTAGCTTTACAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_145_407_869 16 chr1 3195051 255 35M * 0 0 TAGGTTGCAGTTGCTCTATGTGATGTATTTCTCTT ShP?MhHhhZhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_111_861_260 16 chr1 3196449 255 35M * 0 0 TTTTTTCCTGGAGTGCATAATGGATACATTTGATG \OhfhMhhShhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_167_257_42 16 chr1 3197418 255 35M * 0 0 AATTAAGGCATCAGTGTTCTGAACTGTGTGATAGC hhhAhhhhUhVhhhbhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_233_573_175 16 chr1 3197418 255 35M * 0 0 AATTAAGGCATAAGTGTTCTGAACTGTGTGATAGC hhDIhhhh[h_BhhVhhhdhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_305_871_204 16 chr1 3199438 255 35M * 0 0 AGTTGCTCACTTTCATGAGTAGCTTTGACTAATTA hXGMDTVdhhYhZhhPhhhhhhhhchhhhhhhhhh NM:i:0 -EAS38_8_231_724_560 0 chr1 3200057 255 35M * 0 0 TACAGCAATAACACATGGCAAATTCTTAATAATGA hhhhhhhhhhhhhhhhhhhhQhhhhhgJhShQeAA NM:i:0 -EAS38_8_203_543_728 0 chr1 3200118 255 35M * 0 0 CCACAAGGAAATCTATAGGCAAACAAAATAACCAA hhhhhhhhhhhhhhhhhhhhhhh^Xhhh_hh\@Ch NM:i:0 -EAS38_8_229_849_498 0 chr1 3200118 255 35M * 0 0 CCACAAGGAAATCTATAGGCAAACAAAATAACTAA hhhhhhhhhhhhhhhhhhhbhfhhY`hQcaK?hBV NM:i:1 -EAS38_8_119_995_590 0 chr1 3200431 255 35M * 0 0 CTTATTTCTGTGGGCACATGGCTGGTTGCCACTTC hhhhhhhhhhhhhhhhhhhhhhhhDVhEEJICIh@ NM:i:1 -EAS38_8_253_690_533 0 chr1 3200431 255 35M * 0 0 CTTATTTCTGTGGGCACATGGCTGCTTGCCCCTTC hhhhhhhhhhhhhhhhhhhhhhhhIhRHM@GQMR? NM:i:1 -EAS38_8_2_361_608 16 chr1 3200848 255 35M * 0 0 CAAATGTTGGGTAGCAGATTGGTGTCATAAGTCAA G^h^PNLLKh@hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_19_443_443 16 chr1 3201005 255 35M * 0 0 GGTCCACCTTGGTCCTGCTGTGCTGTCAGCTTCTG N\MhhAVhQYhh]hhShhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_240_860_321 0 chr1 3201008 255 35M * 0 0 CCACCTTGGTCCTGCTGTGCTGTCAGCTTTTGTCT hhhhhhhhhhhhhhhhhhehhhhSGhHhP@YI`CL NM:i:1 -EAS38_8_159_889_369 16 chr1 3201153 255 35M * 0 0 TATATAGAAATAGTCGTGGCTAATGGCAAAGATAT Nh`hPhhhhhhhhNhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_6_649_343 16 chr1 3201153 255 35M * 0 0 TATATAGAAATAGTCGTGGCTAATGGCAAAGATAT hhhhhhhhhhhhhhhhhhhZhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_159_13_859 16 chr1 3201231 255 35M * 0 0 CATTAGAAAAAATTCACAGGATTCTTGTCTAAACA hhghhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_206_389_817 0 chr1 3201597 255 35M * 0 0 CATGCATTTCTAAGTTTATCTCTGTGTAGATGCAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhZhahhh NM:i:0 -EAS38_8_8_834_910 16 chr1 3201632 255 35M * 0 0 GTAAGAGAGTCAGTCTTTCTGTCTGTCTGTTTCTG KTEPRY\hhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_193_381_989 0 chr1 3201726 255 35M * 0 0 GGCAAATCTGTAGAAATTGATATCTCTTTATGTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_218_286_583 16 chr1 3201770 255 35M * 0 0 CAGGGATCAAATTCAGGTCAAGTTTGCATCTTTTT hh[a\h\hhhh^hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_231_842_613 16 chr1 3201775 255 35M * 0 0 ATCAAGTTCAGGTCAAGTTTGCATCTTTTTTCAGT hahhhOhbhhhKhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_69_697_617 16 chr1 3201775 255 35M * 0 0 ATCAAATTCAGGTCAAGTTTGCATCTTTTTTCAGT heghhhOhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_315_783_294 16 chr1 3205321 255 35M * 0 0 CTAAAAGTAAAAACAAATCCTGAAATATGTAGAAA ERhhhhhXhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_208_943_432 16 chr1 3206163 255 35M * 0 0 CCTTGGAGGAGATGGGGAACATTCAAAAGCTAAAA bVQHbOhahhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_17_380_277 0 chr1 3209126 255 35M * 0 0 TTGGTGTGCTTATCCGACACTGTAGGTAGAAACCA hhhhhhhhhhhhhhhh]hPh\NhhJQhEKCEOJhG NM:i:1 -EAS38_8_156_409_184 16 chr1 3211514 255 35M * 0 0 CAAGAAAGATTGATGAGACACAGTTGATAGAGGGA HKhThhhhhhOhhghhhhLhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_189_963_938 0 chr1 3211535 255 35M * 0 0 AGTTGATAGAGGGATGATAAATAATCCTTTCCTTT hhhhhhhhhhhhhhhhahhh^hhdSGTTZ`>D[XR NM:i:0 -EAS38_8_194_593_290 0 chr1 3212718 255 35M * 0 0 GCTTAAGACACTTTGCATCCCTCTTTTGTAACATT hhhhhhhhhhhhhhhhhhhhhhhhhhhWhRK^Jhb NM:i:0 -EAS38_8_54_951_1001 0 chr1 3212775 255 35M * 0 0 ACTTTCCTTTTCAGGAAAAAAAATGTATATAATAT hhhhhhhhhhhhhhhhhhh[hhhhhIHhhdbaSOJ NM:i:0 -EAS38_8_55_222_593 16 chr1 3213111 255 35M * 0 0 CTCACTGCCTCCCTCTTAGGACTCTTACACTGAAA h>hPhf`ZhYhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_192_865_198 16 chr1 3213157 255 35M * 0 0 AGTCAATGCAAGAAAGCAGATGCTTCCATCTTGCT _JHhOhFhBhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_257_284_263 16 chr1 3213208 255 35M * 0 0 AAAAAAAACAAAACAAATCTCCACTTTTTGTAAAT hXhMhhhhOhhhhIhhhfhPhQhhhhhhhhhhhhh NM:i:2 -EAS38_8_14_341_452 0 chr1 3234830 255 35M * 0 0 CCTTGATGTCTTGATGGTTGAAATAGGTTACATTT hhhhhhhhhhhhhhhhhhhh`hhh^IhhhN`Lhhh NM:i:0 -EAS38_8_171_140_943 0 chr1 3239649 255 35M * 0 0 TCCCTGTTAGATTCAAATGTTACTTTATAGTTAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh^h NM:i:0 -EAS38_8_98_123_525 16 chr1 3240599 255 35M * 0 0 ACATCCCTCCCTAAATAAACCACAATCCACCCCCA hdhLDhEMhhfhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_178_873_141 16 chr1 3242478 255 35M * 0 0 TTTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT OVhhRhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_215_180_235 16 chr1 3242478 255 35M * 0 0 TGTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT hThhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_7_814_774 16 chr1 3242478 255 35M * 0 0 TTTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT Jhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_315_926_983 16 chr1 3242791 255 35M * 0 0 ACCTCCTCCTATAGCTTCTAGAGACAACAGACCTT @<BEAZIMRhHhIdhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_163_191_986 16 chr1 3242917 255 35M * 0 0 AATCATATTTTGACCTCAATTAGCCTTGGGGTTGA hhTRhSaeh\UAThhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_173_800_35 16 chr1 3242917 255 35M * 0 0 AATAATATTTTGACCTCAATTAGCCTTGGGGTTGA hh=FhRhVhOhShGhcZhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_25_295_514 0 chr1 3242979 255 35M * 0 0 GCTCTTCTGTCAAGAGTACCTGAAATTTATCTGTG hhhhhhhhhhhhhhhhhhhhhhhehhhhhhZhhhc NM:i:0 -EAS38_8_260_745_595 0 chr1 3242979 255 35M * 0 0 GCTCTTCTGTCAAGAGTACCTGAAATTTATCTGTG hhhhhhhhhhhhhhhhhhhhhhLhhhhhhhhhhfM NM:i:0 -EAS38_8_162_854_426 16 chr1 3243101 255 35M * 0 0 GAAAAAACCTGTCTTGGTCTGAGGTCTGGGCCACT >hhhhhPhhU_XhXZhhhhehhhhhhhhhhhhhhh NM:i:0 -EAS38_8_120_168_509 16 chr1 3243120 255 35M * 0 0 TGAGGTCTGGGCCACTGTTATTCAGAGTGAACAAC AZc^hCcMhhhWhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_219_315_931 16 chr1 3243676 255 35M * 0 0 TTTGTTGAAGGAGAACACAATGAGAGGTGCATATT ]OhYhhchhahhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_180_247_88 16 chr1 3244868 255 35M * 0 0 GCATACTTAAAATTAGGCTGCAATCAGTCTTCCTT _@hhhCJhhhhhhIhhhhShhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_144_513_481 0 chr1 3252847 255 35M * 0 0 AATGGCATTCAGTTAGCTTTAGTGACTGATCCCAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhBC NM:i:0 -EAS38_8_125_631_236 0 chr1 3253217 255 35M * 0 0 TGAGGCATGACCTCCTTTCACTGAATCTTAGTCTT hhhhhhhhhhhhhhhhhhhhhhhhehhhhhLChhh NM:i:1 -EAS38_8_312_169_822 16 chr1 3253312 255 35M * 0 0 AAGGCTAAAATTGCTGTTACCAGCTGCTATGCTTG [JNDIONDhWhhhhhhIhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_10_227_417 0 chr1 3253759 255 35M * 0 0 CAAATTTTAGCTCCTTTCCCAGTTTCCCTCTGGAA hYhhhhhhhhhhhhhhhh`hG_heh\V^hXhUBH? NM:i:0 -EAS38_8_144_231_566 0 chr1 3253759 255 35M * 0 0 CAAATTTTAGCTCCTTTCCCAGTTTCCCTCTGGAA hhhhhhhhhhhhhhhhhhXhghhhhROZWKbU\MM NM:i:0 -EAS38_8_208_276_857 16 chr1 3254072 255 35M * 0 0 TCAACTTCACAAGGAATTTGGAGTGACTGGCCTCC VdMOhLchXhhhh^hhhZhhhhhhh_hhhhhhhhh NM:i:0 -EAS38_8_6_640_930 16 chr1 3254072 255 35M * 0 0 TCAACTTCACAAGGAATTTGGAGTGACTGGCCTCC IHhOhJThchhhhWhhh_hhYhhhhhhhhehhhhh NM:i:0 -EAS38_8_261_856_180 0 chr1 3254263 255 35M * 0 0 GTTCCGCAACACCTGCCCTCACATTCCACTGAACT hhhhhhhhhhhhhhhhhhhhMhThh[NCKQD?DJK NM:i:1 -EAS38_8_97_169_815 0 chr1 3254597 3 35M * 0 0 ATCAGGCTACTTTCAGCAAGCACTTCTTGTCATCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhAh^hUh NM:i:1 -EAS38_8_250_270_899 0 chr1 3259536 255 35M * 0 0 CTAGATTAGCAGGTAATTTCTAAATCACACATTTA hhhhhhhhhhhhhhhhhhhhhhhhhahUJOhhYhb NM:i:0 -EAS38_8_267_436_563 0 chr1 3273793 255 35M * 0 0 TTTTTTTGTTTGTTTGTTTGTTTTTATACAACAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhh NM:i:1 -EAS38_8_244_916_490 16 chr1 3274218 255 35M * 0 0 GAGCCTAAACCAACCAACCAATGAATATACATAGG ThCYE@AhhhOhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_111_703_424 16 chr1 3274366 255 35M * 0 0 ACAGGGCACATGTTCTTCTAGCTGAGCTGCCTTGT L[gE[hhhhhghhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_224_315_306 16 chr1 3274921 255 35M * 0 0 GGAACTGTGCAAATTGTGTAACTGGAGAAAATAAT hhhh^hh_hhhhhhhhhhhhh`hhhhhhhhhhhhh NM:i:0 -EAS38_8_256_842_769 0 chr1 3277156 255 35M * 0 0 AATGATATTGGTTTGAAGTTCTTTAGCCCCATATT hhhhhhhhhhhhhhhhhhhhhhhhhhhh\hhh]hh NM:i:0 -EAS38_8_292_619_933 0 chr1 3277156 255 35M * 0 0 AATGATATTGGTTTGAAGTTCTTTAGCCTCATATT hhhhhhhhhhhhhhhhhhhhhhhhhhbOLhMhhhh NM:i:1 -EAS38_8_212_928_881 0 chr1 3277700 0 35M * 0 0 TCCTTTTCCTTTCCTTCCTTCCTTCCATCCTTCCT hhhhhhhdZghhaehhTVhhZhhhNT?h^MX]OBQ NM:i:2 -EAS38_8_223_507_484 0 chr1 3277914 255 35M * 0 0 TTCTGAAACTTGAGTACAGTGTTATTACCAATATT hhhhhhhhhhhhhhhhhhhLhhhhhhhKhLbheha NM:i:0 -EAS38_8_264_464_724 0 chr1 3277925 255 35M * 0 0 GAGTACAGTGTTATTACCAATATTCCCCCATTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhh NM:i:0 -EAS38_8_97_398_795 0 chr1 3277927 255 35M * 0 0 GTACAGTGTTATTACCAATATTCCCCCATTTTTCC hhhhhhhhhhhhhhhhhhhhhhhLhhhVhhhhh^h NM:i:0 -EAS38_8_271_224_790 16 chr1 3277983 255 35M * 0 0 AGTGATGTCCTAACATGCTTGCTCTCTCATAACCA FhhQ`hhhhhhhhhhhhhhhhhghhhhhhhhhhhh NM:i:0 -EAS38_8_249_919_47 16 chr1 3277988 255 35M * 0 0 TGTCCTAACATGCTTGCTCTCTCATAACCAGACTT K=DFHUhLXhaJSbfLPfhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_264_398_810 16 chr1 3278029 255 35M * 0 0 AGTTTTGTTAGGTTTGCTGGTCTTTTAAAAGGTCT ZghhHhhhhTh[hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_202_252_118 16 chr1 3278057 255 35M * 0 0 AAGGTCTAGATTTTTGTTTCATTATTTTTTTTCTG hhhTDhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_195_472_45 0 chr1 3278134 255 35M * 0 0 CTTTTATTATATTCTTCCTCTTCGTTATTTTGAAT hhhhhhhhhhhhhhhhhhhhhhhPhhh]hhhWENh NM:i:1 -EAS38_8_200_268_981 0 chr1 3278134 255 35M * 0 0 CTTTTATTATATTCTTCCTCTTCGTTAGTTTGAAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheh NM:i:0 -EAS38_8_87_755_875 16 chr1 3278180 255 35M * 0 0 TTCTCTTAAGTATATGTTCTTATTAACTATTTTTT hhhUhhhhhThhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_184_481_627 16 chr1 3278254 255 35M * 0 0 GAGGCATTTTAGTGTTATGAACTCCCCTTGGCACT NH?=BNI[BT^YdUZ[hKJhhhPhhhhhhhhhhhh NM:i:0 -EAS38_8_241_955_483 16 chr1 3278295 255 35M * 0 0 GACACAGATAGGTTTTTATGTGCTATACTTACATT DbHYMhVhhhVhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_24_420_629 0 chr1 3278309 255 35M * 0 0 TTTATGTGCTATACTTACATTCAGTTCAATGTAAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhfhhhhhh NM:i:0 -EAS38_8_307_620_12 16 chr1 3278356 255 35M * 0 0 TTAGACTTCATTTTCTTCTTCTTTTTGGTTGTGAG IOhKhhJdLhhhJhIeTVZhhhhhhhfWhhhhhhh NM:i:0 -EAS38_8_55_835_895 0 chr1 3278373 255 35M * 0 0 CTTCTTTTTGGTTGTGAGCCTAGCCTTCAACGGTT hhhhhhhhhhhhhhhhhhWWhhhMTIhPTHIhc>D NM:i:1 -EAS38_8_230_275_815 16 chr1 3278376 0 35M * 0 0 TTTTTTGTTTGTGAGCCTAGCCTTCAACGGCTGAG \_NF]RQGZhWPOXPhhhahhhhhhhMhhXhhhhh NM:i:2 -EAS38_8_24_167_957 16 chr1 3278397 255 35M * 0 0 CTTCAACGTCTGAGCCATCTCTCCAGCCCTCTTCT VFA`N?hQ@hhLhehhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_253_546_769 0 chr1 3278576 255 35M * 0 0 TTCCCACTCTCTGGGGCCTCAAGTCTCTCAAATTA hhhhhhhhhhhhhhhhhhhhKRZhhhhh`KMhRTM NM:i:2 -EAS38_8_283_280_992 0 chr1 3278576 255 35M * 0 0 TTCCCACTCTCTGGGGCCTCAAGTCTCTCAAATGT hhhhhhhhhhhhhhhhhhhYhhhFHcBQJHUNK?C NM:i:0 -EAS38_8_4_499_790 0 chr1 3278607 255 35M * 0 0 ATGTTAGGCACATCTCCCACTGATTCCAGACCAGG hhhhhhhhhhhhhhhhe[hhhhUhcVOP`I?LTXH NM:i:0 -EAS38_8_166_353_693 0 chr1 3278725 255 35M * 0 0 GGTTAGTTGAGATTGCTGGTCTTTCTATGGGTTGC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhhhFS NM:i:0 -EAS38_8_227_305_410 16 chr1 3278920 255 35M * 0 0 TCAGACCTCTGCTGATCACCTGCATAGTTGGAGAT KJhH@NRIA_B`hhhhhhhhThhhhhhhhhhhhhh NM:i:1 -EAS38_8_151_783_299 16 chr1 3279317 255 35M * 0 0 CTTTTTTGTTCTATAGATATCAATTATTTACCCAC BTS^WdIUehQhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_130_64_600 0 chr1 3280118 255 35M * 0 0 GGTTTCGAGAAAATGTTTTGAAGTGTTTATGCGCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhchKOhSh NM:i:0 -EAS38_8_204_14_612 0 chr1 3280118 255 35M * 0 0 GGTTTCGAGAAAATGTTTTGAAGTGTTTATTCGCT hhhhhhhhhhhhhhhhhhhhfhhhhhhhhhBQhL\ NM:i:1 -EAS38_8_242_889_996 0 chr1 3280118 255 35M * 0 0 GGTTTCGAGAAAATGTTTTGAAGTGTTTATGCGCT hhhhhhhhhhhhhhhhhhhhh^hVhaahgeh@Z?N NM:i:0 -EAS38_8_82_262_363 0 chr1 3280320 255 35M * 0 0 AACATATTTTAAATTCCTCTCAGATTAAGAGAATT hhhhhhhhhhhhehhhhhhhh^hWhKhShWD@hhB NM:i:2 -EAS38_8_111_150_178 0 chr1 3282505 255 35M * 0 0 AGATACATAGAAAAGCTACTTGACTTTAGGTCAAC hhhhhhhhhhhhhhhhhhhhhUfhhhhhQOhh\Sh NM:i:0 -EAS38_8_260_477_698 0 chr1 3282505 255 35M * 0 0 AGATACATAGAAAAGCTACTTGACTTTAGGTCAAC hhhhhhhhhhhhhhhhhhhhhhhhhhhXhhhh`hM NM:i:0 -EAS38_8_187_894_354 16 chr1 3282753 255 35M * 0 0 CTGCACTTGTTTAGAGAAGTGCTGTCTACATGAAG dhNhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_219_350_890 0 chr1 3282806 255 35M * 0 0 TTTTGGAACTTAGGCAAGAATGTTCTTTGGCTCCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPVh NM:i:0 -EAS38_8_185_258_316 16 chr1 3282902 255 35M * 0 0 TGAGAGCTAAATGTAAAGCTCAGTAATGCCAGCTC IJhhhhh^hhhhMhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_5_912_317 16 chr1 3284777 255 35M * 0 0 CTCTCGCTCTCTCTCTCTCTCCCCTCACTCCTTTC BPWFbChNSRhFhShehOh_hhhhhhhhhhhhhhh NM:i:1 -EAS38_8_119_362_614 0 chr1 3284967 255 35M * 0 0 TGTACCCTGAGATCAAGTACTTATTGCTTTCACTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_276_838_443 0 chr1 3284967 255 35M * 0 0 TGTACCCTGAGATCAAGTACTTATTGCTTTCACTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhahhhh NM:i:0 -EAS38_8_74_720_526 0 chr1 3286259 255 35M * 0 0 CAAATTGTAGAAAATTTGCATGTGTACTGAACACA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhL NM:i:0 -EAS38_8_273_582_300 16 chr1 3289456 255 35M * 0 0 TCTTCAGTTCTTTGTTAAATATATCATCTGGGTCT HhYchhhQhRhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_232_852_815 0 chr1 3290417 255 35M * 0 0 TTTTTTTTTTTAACTTTCATATGTAGTAGTTATTT hhhhhhhhhhhhh^hhhKhhhhhhhGV^hh[MHhh NM:i:2 -EAS38_8_121_748_181 0 chr1 3290799 255 35M * 0 0 ACCACACCCTGCTGCTCCATATTTCTTATCTTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhh\Bhhhhhh NM:i:1 -EAS38_8_36_138_632 0 chr1 3290826 255 35M * 0 0 AGCTTTTTTTTTTTAACAGCTACTGGGTGGTTTGC hhhhhhhhhhhhhhhhhhhhhOhhbhCXHZLI\BF NM:i:1 -EAS38_8_141_369_534 0 chr1 3290833 255 35M * 0 0 TTTTTTTAACAGCTACTGGGTGGTCTGCATAGCTT hhhhhhhhhhhhhhhhhhhhhhhhhhhfPRLdhhS NM:i:0 -EAS38_8_84_402_647 0 chr1 3290833 255 35M * 0 0 TTTTTTTAACAGCTACTGGGTGGTCTGCCTAGCTT hhhhhhhhhhhhhhhhhhhhhhhhhhVhBhThahe NM:i:1 -EAS38_8_169_576_313 16 chr1 3290912 255 35M * 0 0 ATGCTTCTTTCCACAGTTGAGTGGAATTGTAGGGG hPhRWPJhVLhhhhhh[hhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_279_571_717 16 chr1 3290912 255 35M * 0 0 ATGCTTCTTTCCACAGTTGAGTGGAATTGTAGGGG he\hhYhaOYhhThhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_234_793_825 16 chr1 3290951 255 35M * 0 0 AAAAGACATTTCTGAGTTCTAGCACTCTCAGGTCT hhhhRhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_217_210_636 16 chr1 3290952 255 35M * 0 0 AANGACATTTCTGAGTTCTAGCACTCTCAGGTCTG hh;PYhhWXhh^hhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_168_998_377 0 chr1 3290961 255 35M * 0 0 TCTGAGTTCTAGCACTCTCAGGTCTGGCTTTGACA hhhhhhWhhhhhhhhhhhhTe\YThhOIWJaC@A? NM:i:0 -EAS38_8_179_44_982 16 chr1 3290986 255 35M * 0 0 GCCTTTGACATTAGCTTCCTGACAGGCTGGCAGGT ?@[_GhH[hhhhhEhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_210_147_536 0 chr1 3291026 255 35M * 0 0 TCCTGAAGGTCAGGACTGTGCAAAACTGTCAGGCA hhhhhhhhhhhhhhhhhhhhhhQg`hh^hbGYYPH NM:i:0 -EAS38_8_228_906_499 0 chr1 3291047 255 35M * 0 0 AAAACTGTCAGGCAGCTATTTCAGGAGTGCCTTTT hhhhhhhhhhhhhThhh_hhhhUThYZPVED[@C@ NM:i:2 -EAS38_8_223_934_468 16 chr1 3291092 255 35M * 0 0 GCCCTGGATGATTTTTGAATGGGAATAATCCCTAT RXhf\Phh`hhhhhVhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_27_794_86 16 chr1 3291130 255 35M * 0 0 TCCATATAGGCTCATATATTTAAACACCTAGTCAT X@FSSZhhhADhShhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_205_713_101 16 chr1 3291163 255 35M * 0 0 ATTGTTGGTGGCACTGTCTGTAAGGATCACGAACC CEJLUB`WcgZ]hLhheHahhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_269_175_878 16 chr1 3291192 255 35M * 0 0 CAAACCCATTAGAAGGTAACAACATGCTAAAAAAA eChhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_127_466_820 0 chr1 3291247 255 35M * 0 0 GTGAGGGCTTGTGTTCTCTCTGCTTCCTCTGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhV_hTeSWhhh NM:i:0 -EAS38_8_29_659_107 0 chr1 3291649 255 35M * 0 0 TCCTGAGTTGGGAGGACAGATGAGAAGGGCTTTTT hhhhhhhhhhhhhhhXhhhShhh`PFVhALNChJd NM:i:2 -EAS38_8_210_520_140 16 chr1 3299511 255 35M * 0 0 GAAATAAAGAAAATTCTAATCTACAGGCTGACCAT VhhLDhhhhhhhhVLHShhPhfhhhhhhhhhhhhh NM:i:2 -EAS38_8_45_100_198 0 chr1 3299523 255 35M * 0 0 ATTCTAATCTACAGGCTGACCATACTGTATTTCAC hhhhhhhhhhhhhhhhhhhhhhhZhhIh^hhhhHh NM:i:0 -EAS38_8_145_894_137 0 chr1 3299538 255 35M * 0 0 CTGACCATACTGTATTTCACTAATATAATGGTGTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhRChhhU NM:i:0 -EAS38_8_231_634_172 16 chr1 3299568 255 35M * 0 0 GTGACAGTGATGCCAGAGAGCTCTAGCTGTGGCTG MHS?]hVChhPhHVhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_68_279_670 16 chr1 3299606 255 35M * 0 0 TGAATACTGGGTAGAAAATAAAAAAATTTACGGAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_157_544_34 16 chr1 3299684 255 35M * 0 0 TCATAAGATCGGGTAGTTAGTAAACCCTGCCTAGA ?MhFhhHMRZGSdhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_317_518_457 0 chr1 3299798 255 35M * 0 0 GATTTCTGTCTACTAGATCAAAACCTGATAACATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhMhh NM:i:0 -EAS38_8_87_383_194 16 chr1 3300173 255 35M * 0 0 AAACTACAAAATTGTGGATGTTTGGCTGTTCTTTT hhhSZhhhhhhKhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_220_990_452 16 chr1 3300259 255 35M * 0 0 TGCACCATCTTAGGAGTGAGGGAGGCAGCTGAGTG NHPUJ]hhSPa`ChhhYhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_168_713_356 0 chr1 3307749 255 35M * 0 0 GGTTAACCCGAAGCCAAACTTTTCTTTGTAATTTC hhhhhhhhhhhhhhhhhRhhhhhhhHhRhhIhhhJ NM:i:1 -EAS38_8_222_724_349 0 chr1 3307749 255 35M * 0 0 GGTTAACCCGAAGCCAAACTTTTCTGTGTAATTTC hhhhhhhhhhahhhh`eGhhhhhhhJhPhNKhhhQ NM:i:0 -EAS38_8_223_971_288 16 chr1 3310176 255 35M * 0 0 AATAATCATCACCTGAATGTCATGATCTAAAGGCT hhChhAhh\Ghhh[hhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_288_770_517 0 chr1 3310786 255 35M * 0 0 AGGTTTTGAGTTTTTGATCCAGAGGCTATGTTTAT hhhhhhhhhhhhhhhhgh\h]hQgQH\FS`HRJEW NM:i:0 -EAS38_8_310_958_947 16 chr1 3311201 255 35M * 0 0 CAATTTTTGATCATTCATCTTGTTTTCTTAACAAT hP\hJhh_Hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_140_291_179 16 chr1 3313701 255 35M * 0 0 ACCGCTGCCTTCCTTTCTTCTCTCCTTCCTTTCTT PW`@dP@hYhKhhhhchh]hZhahhhhhhhhhhhh NM:i:2 -EAS38_8_113_205_724 16 chr1 3318613 255 35M * 0 0 ACCTGGAAGAATTTCATAAAAATTCCCTTCCCAGC HhedLQhhbhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_236_727_634 16 chr1 3318613 255 35M * 0 0 ACCTGGAAGAATTTCATAAAAATTCCCTTCCCAGC Sd]QXehhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_21_827_590 0 chr1 3319045 255 35M * 0 0 TACAAACCAAGAGAAAAATCTGAAAATGAAAAATT hhhhhhhhhhhhhhhhhhhhhh_hhhhhhghhhhh NM:i:0 -EAS38_8_204_62_686 0 chr1 3321977 255 35M * 0 0 AAGCTGGCAATGTTTGGGATATAAACAAGCAAACA hhhhhhhhhhhhhhhhhhhhhhhhhhhahhhh[Yh NM:i:0 -EAS38_8_86_854_652 16 chr1 3324385 255 35M * 0 0 GCAGTGGCTGAGTGATATAACACAGGGATGCAGGT hhhhhhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_192_343_954 0 chr1 3329232 255 35M * 0 0 CTGCCCTTTTTCTCCCTGCCTATTCATTATAGTTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhU NM:i:0 -EAS38_8_6_774_928 0 chr1 3330010 255 35M * 0 0 GCACTGTAGCCAGGAGTGACACACAGCAAGGATGC hhhhhhhhhhhhhhhhhhhhhhhN`hUhhhhT`h? NM:i:0 -EAS38_8_256_461_804 16 chr1 3330063 1 23M11637N12M * 0 0 TTTGTTTGTTTGTTTGTTTGTTTGTTTTGACAGGG dhh@ZhhRhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 XS:A:+ NS:i:2 -EAS38_8_288_334_735 0 chr1 3330212 0 35M * 0 0 TTATAGCTATAAAAAGTAACATTCTTTGATTGGTC hhQhhhhhKhhQ`hhNKaXAXUaGQQVLOWKRFC> NM:i:1 -EAS38_8_11_615_231 0 chr1 3330440 255 35M * 0 0 ATTGGTTACAAAAAAGTTAGCTTTAACTTTGTAAC hhhhhhhhhhhhhhhhhhhhhhhhIhhhhTLhehR NM:i:1 -EAS38_8_284_883_215 0 chr1 3330528 255 35M * 0 0 ACTAGGCCTCTAGAGTACTTCTAAATTGAGATATT hhhhhhhhhhhhhhhhhhhhhhYhhhhIWEKh`hh NM:i:0 -EAS38_8_30_530_423 16 chr1 3330584 255 35M * 0 0 AGTAGACTTATAGAGATAAGCATTAAAATTTGTAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_202_722_286 16 chr1 3330653 255 35M * 0 0 ACTTTGTAACGTTAAAGTGATGTTTCTGGTATTGA NB[KZhhcYhhhdhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_214_253_466 16 chr1 3330653 255 35M * 0 0 ACTTGGTAACGTTAAAGTGATGTTTCTGGTATTGA hSN[DRShhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_4_564_326 16 chr1 3330653 255 35M * 0 0 ACTTTGTAACGTTAAAGTGATGTTTCTGGTATTGA ZXSVTYQhehh\hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_142_357_440 16 chr1 3330660 255 35M * 0 0 AACGTTAAAGTGATGTTTCTGGTATTGATCTTTAA hhhhhdhhhhhhhhhhh_hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_317_782_44 16 chr1 3330660 255 35M * 0 0 AACGTTAAAGTGATGTTTCTGGTATTGATCTTTAA hhFHbhhhhhhbhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_137_536_758 16 chr1 3330697 255 35M * 0 0 TAATAAATTGTTTAAAATTGGGTTTTGCTAACCAA `hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_129_924_268 16 chr1 3330838 255 35M * 0 0 CAATTCACCTATATATTGTAATTAGGATAATTACA BhhhDhhCZhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_48_834_938 0 chr1 3331062 255 35M * 0 0 GTTGTTCTAAATAAAGATTAAATTCAGAATTTATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_154_283_922 0 chr1 3331674 255 35M * 0 0 TTAACTAGTAAAGAACAAAAGGCTTTGCAGAAAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh_hhX NM:i:0 -EAS38_8_215_43_278 0 chr1 3331674 255 35M * 0 0 TTAACTAGTAAAGAACAAAAGGCTTTGCAGAAATA hhhhhhhhhhhhhhhhhhh\hhhhhhKhhVONhB@ NM:i:1 -EAS38_8_227_874_535 16 chr1 3341199 255 35M * 0 0 AGACCAAGATGATGGGAACATCTTCTCCACCCCAT =>?NBTPFLEDVHOaEhhhh\hghhYhhhhhhhhh NM:i:2 -EAS38_8_255_514_861 0 chr1 3341232 255 35M * 0 0 ATCAGAATTCCCAAGTCCCTGGGTCTTCAAGTCTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhY^h_RhH NM:i:0 -EAS38_8_135_67_741 16 chr1 3341341 255 35M * 0 0 AACTCAGCTGTTGTATGCTGCCTGGTTGGTGACTC @FHPQGOXhYO[Whhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_230_743_701 16 chr1 3341490 255 35M * 0 0 GCTTCTGTCCATTTGTTGGGTATGAGTATCTGCAT NhLahhUKhhhhhcWhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_212_374_788 0 chr1 3341507 255 35M * 0 0 GGGTATGAGTATCTGCATCTTACTCTTTCAGCTGC hhhhhhhhhhhhhhhhghhhhhhhhhhhh\hHhh[ NM:i:0 -EAS38_8_250_863_818 0 chr1 3341507 255 35M * 0 0 GGGTATGAGTATCTGCATCTTACTCTTTCAGGTGC hhhhhhhhhhhhfhh[Ph]hh]\^N`XhLQE>LGD NM:i:1 -EAS38_8_48_225_977 0 chr1 3341551 255 35M * 0 0 TTCTCAGAAGGTAGTTATGCTAGGCTCCTGTCTGC hhhhhhhhhhhhhhhhhhhhhhhhOhSYh\MF]hI NM:i:0 -EAS38_8_83_343_929 16 chr1 3341762 255 35M * 0 0 TCCCCTATTTCTCTACTGAAGGAGGACTCTACCAC TRhhhhhhhbhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_96_862_886 16 chr1 3341818 255 35M * 0 0 CCCCATGATTGTTTTCTTCTCCCTCCCATGTTGAA hhhh^hJhhhhhhhhhbhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_134_781_817 0 chr1 3342105 255 35M * 0 0 ACTCTTTAATAGAGTCTCCTGAAGAGGTAAAAATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_155_230_356 16 chr1 3342124 255 35M * 0 0 TGAAGAGGTAAAAATTTTAATTTTGACAGTCCAAT ]hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_179_463_472 16 chr1 3347662 255 35M * 0 0 TACCCTTGCGTCAAGGTGTGTTTTCTTACTCAAAT OG?[DIQhbAhdhLhhhhRhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_4_219_976 16 chr1 3347662 255 35M * 0 0 TATCCTTGCCTCAAGGTGTGTTTTCTTACTCAAAT hhhhhhhchhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_79_243_815 16 chr1 3349048 0 35M * 0 0 AAAAAGAGAAACCCTGTCTCAGAAAGAAAAAAAAA ]WhAhHh_hhhhhhehhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_133_197_589 0 chr1 3349165 255 35M * 0 0 CACCAGTTCTCCTGTGCATCCTCAGGAGAAATCAT hhhhhhhhhhhhhhhhhhhhhhhhhhUhKSPhUJh NM:i:0 -EAS38_8_188_649_421 0 chr1 3351241 255 35M * 0 0 GTAGATGGACAAACATCTCCCTCACGCATTCTCAG hhhhhhhhhhhhhhhhhhhhhhhhhhhhahhhbP> NM:i:0 -EAS38_8_268_213_808 0 chr1 3355908 255 35M * 0 0 ATCTAACTAAGTAAACTATGTTATAGGAAAGAAAT hhhhhhhhhhhhhhhhhhhh^hhhhhhhhhhZhhZ NM:i:0 -EAS38_8_11_161_707 0 chr1 3355956 255 35M * 0 0 TTTGTCACATGATCAGCATAGTAGATGATGTGTCT hhhhhhhhhhhhhhhhhhhhhhhhhhhPhhhhhHh NM:i:0 -EAS38_8_291_670_580 16 chr1 3356011 255 35M * 0 0 GAAGCAGTTAAAATTGTGTGTGTGTGGTTCTGGAT hV_OXh[VIhXNhP^hhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_44_851_834 16 chr1 3356011 255 35M * 0 0 GAAGCAGTTAAAATTGTGTGTGTGTGTTTCTGGAT ECD@MDGhJXDSAChdhPh]hUhbhhEhhhhhHhh NM:i:1 -EAS38_8_105_754_762 0 chr1 3356093 255 35M * 0 0 TATAGATGTAGTTTATCTCCTAATCCCACCCTTCC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_219_312_881 16 chr1 3356191 255 35M * 0 0 TTTAATTACTTTCCCATCAAAGGCCCATTGAGCAG XZNhNLhHhhZhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_299_450_385 0 chr1 3356483 255 35M * 0 0 ATTCTGGTGGGCTTTCGAGTGTTTCAGTTTCATCT hhhhhhhhhhhhhhhhhVhhhhhhhhhhhhhhhAh NM:i:1 -EAS38_8_52_623_649 0 chr1 3356578 255 35M * 0 0 GGAGCATATGTGAGTAAGCAAATGATGTTCTTGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhh]hEUNE NM:i:1 -EAS38_8_117_306_426 16 chr1 3359531 255 35M * 0 0 TCAGAGTGTCCACCTCATTCCTCTGGGTCAGTCTT @EN_DgWhhhh_hhhhhhdhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_120_120_744 16 chr1 3361583 255 35M * 0 0 CAAAGACAAGTAGGATAATGCTGAAAGCCCAAGCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_307_422_12 0 chr1 3362018 255 35M * 0 0 CTGAAAAATTACAGTGTTCTTGTACTGGACACTAC hhhhhhhhhhhhhhhdhSahhKDYGhECFJF@TI? NM:i:2 -EAS38_8_101_691_200 0 chr1 3363077 255 35M * 0 0 CTTTTTTCCATTTTAATGTTTGCATGCAAATCTTA hhhhhhhhhhhhhhhhhXhNhh`hhhhhMhhChhI NM:i:2 -EAS38_8_205_648_802 0 chr1 3363077 255 35M * 0 0 CTTTTTTCCATTTTAATGTGTGCATGCAAATGTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZ NM:i:0 -EAS38_8_265_441_688 0 chr1 3363150 255 35M * 0 0 CAGGAATCAATCTCAACCACTTTTCATCTTACTCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhOhhch NM:i:0 -EAS38_8_53_996_162 0 chr1 3363150 255 35M * 0 0 CAGGAATCAATCTCAACCACTTTTCATCTTACTCA hhhhUhh_hYhUhc^LEHALV^]]MIVE_MMB[MO NM:i:0 -EAS38_8_28_805_359 0 chr1 3363388 255 35M * 0 0 CCAACACCTTATTATCACTTATTTTTGTCATTCTA hhhhhhhhhhhhhhhhhhhhhhhhhhIhhhh@hhZ NM:i:1 -EAS38_8_229_300_432 16 chr1 3363412 255 35M * 0 0 TTGTGATGCTATATATGTGTGCATTAACCACTGCC RObh>QWGShUahhhhBUhNhPhhhhhhhhhhhhh NM:i:2 -EAS38_8_247_121_676 16 chr1 3363412 255 35M * 0 0 TTGTCATGCTATATATTTGTGCATTAACCACTGCC QQMhgLRNfhh[hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_180_822_42 16 chr1 3363658 255 35M * 0 0 GAGTAACTGCTGCATGTTAATCTATGTCATCCCTA MXE@dhhIP__Xhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_83_317_544 0 chr1 3364348 255 35M * 0 0 GCATTTCTGAGCCTGGGTGATCTTACTTTATATTC hhhhhhhhhhhhhhhhhhhhhhhhchhhhhhhhhb NM:i:0 -EAS38_8_194_299_688 16 chr1 3364585 255 35M * 0 0 AAGGATGTTATAATTGAATCATATGGAAGTTCTTT ^hh_h_hhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_42_578_279 0 chr1 3364694 255 35M * 0 0 AAGATGTATTTTTATTTGTTTACTGTATAATTTCC hhhhhhhhhhhhhhhhhhhhhhhhChhhh_hhCP\ NM:i:2 -EAS38_8_309_762_904 16 chr1 3364864 255 35M * 0 0 AAAAGGACATCTGAATTACCTACTTGTTTTTATCA hhhhhFhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_236_498_116 16 chr1 3364885 255 35M * 0 0 ACTTGTTTTTATCAGGTTGGTCTGTAAGCATATCT LI_hhQhhMahh\hhbhFhhh\hhhhhhhhhhhhh NM:i:0 -EAS38_8_184_968_83 0 chr1 3365051 255 35M * 0 0 TAATTGCCAGGAGTTCATTGTTTTCCATATTGTCT hhhhhhhhhhhhhhhhfhhhhhhhh]EhVhhHhUh NM:i:0 -EAS38_8_194_34_599 16 chr1 3367203 255 35M * 0 0 ATTGTGGATATAAGTGGAGAAAGAGCAAGAAAAAA hhHhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_73_896_111 16 chr1 3367203 255 35M * 0 0 ATTGTGGATATAAGTGGAGAAAGAGCAAGAAAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_115_579_578 16 chr1 3369573 255 35M * 0 0 TCAGAGCATTTGGATTTTGGTCTTTAGATTAAGGT ^hhhhhhhhXhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_260_546_322 16 chr1 3369573 255 35M * 0 0 TCAGAGCATTGGGATTTTGGTCTTTAGATTAAGGT >>NELH=IJ@@@QIMBDDKOS\KJfhhh[Phhhhh NM:i:1 -EAS38_8_168_10_541 16 chr1 3375680 255 35M * 0 0 CCGTGCAGACATTCTGATGTTGGGTAATATCAAAT LT>IKNhhhWhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_316_251_752 0 chr1 3377312 255 35M * 0 0 TCACAATATTGTCTATACTTCTAAACATCCTCAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhh NM:i:0 -EAS38_8_127_130_231 0 chr1 3379889 255 35M * 0 0 AATAAATTTCTCTTGTTTGCAAGCTATCTACTCTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhbhhhhe NM:i:1 -EAS38_8_262_614_438 0 chr1 3379889 255 35M * 0 0 AATAAATTTCTCTTGTTTGCAAGCTATCTACTCTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhA NM:i:1 -EAS38_8_152_675_620 0 chr1 3379983 255 35M * 0 0 ATCACACTTCAATTTTCATTTTCCAGCAAAAGCTT hhhhhhhhhhhhhhhhhhhhhhhhhhhghZhhhhh NM:i:2 -EAS38_8_315_641_621 16 chr1 3380977 255 35M * 0 0 CATTTATTCTATGTCAATTTATCTTTTGAGTATAA hhhhhhahhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_223_839_518 16 chr1 3381656 255 35M * 0 0 GTCCTTTTTCTAGTGTCGTGTTTAAGCTCCCGTGA PVLMUG`YLSVhaNhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_189_893_589 16 chr1 3382043 255 35M * 0 0 GCAGAGCCTCTGTGTCATTGCCTGGCAGGTAGGAG =L`KeShhhhdhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_228_882_739 0 chr1 3383793 255 35M * 0 0 TGGTGAGTATTGGAACGACTAAATCAGTGTATTAA hhhhhhhhhhhhhhh]hhfhhhh]^]hehbghNHO NM:i:0 -EAS38_8_290_281_824 16 chr1 3386732 255 35M * 0 0 GTAGAAAACTGGATTTTTTTTTTTTGGTGATATAG `GUEhEhhhd\hhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_in2.sam --- a/test-data/cuffdiff_in2.sam +++ /dev/null @@ -1,400 +0,0 @@ -EAS38_1_126_860_867 16 chr1 3009675 0 35M * 0 0 ATAGTCCCTTACTGCTTTTAGTATTCTATCTTTAT WFGAeC\gVShhhLh`hhPbPhhhhhhhhhhhhhh NM:i:2 -EAS38_1_125_842_97 0 chr1 3023056 0 35M * 0 0 ATCTTCTTCAATTTGTTTCTTCAGAGACTTTAATT hhhhhhhhhhhhhhhhhhhhhhhJhhNhhh_KINh NM:i:2 -EAS38_1_261_52_728 16 chr1 3035247 0 35M * 0 0 AATCCCCCACCCCACAGGAACAAAGTCCTGATGCA @???GIH@C?HXINLQJ=VVhhgTFHfhYhhJLhb NM:i:2 -EAS38_1_71_500_217 16 chr1 3081731 0 35M * 0 0 AGGAGATAAATAACTAATAAAAAATGAAAAAAAAA h?DhLhFhfhKhRFhhhShhhhhhThhhhhhhhhh NM:i:2 -EAS38_1_2_666_566 0 chr1 3111450 255 35M * 0 0 CCACTCACAAGACAAGACCAGGATCCTGGAGAGAT hhhhhhhhhhhhhhNh^Yh]d]GRNVYURK^JU>I NM:i:0 -EAS38_1_220_990_991 0 chr1 3111546 255 35M * 0 0 AAAAGCTGAGAGTCAGCATGAATCAAGAGATAGAA hhchhMabNhP_>BKXQSNKDRD?@@TBJJ=GL@G NM:i:1 -EAS38_1_133_518_728 0 chr1 3111550 255 35M * 0 0 GCTGAGAGTCAGCATGAATCCAGAGATAGAAAAAG hhhhhhhhhhhhhhhhhhhOhQhhhNL^ZT[PLNN NM:i:0 -EAS38_1_219_471_934 0 chr1 3117684 255 35M * 0 0 TGTCCTTTGGCTTACAGAAGTTTTATAATTTTATG hhhhhhhhhhhhhhhhhhhhhhhhRhhehhhh]hH NM:i:0 -EAS38_1_180_265_430 16 chr1 3131249 0 35M * 0 0 TGATCAGCCCTTTGGCATTCCTCAGTTGAGAATTC GICHVhhCY`\TYhhhh[fdhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_155_516_677 0 chr1 3137065 0 35M * 0 0 CTGGAATTATGTGATTATAATTTTCTTATCATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhh`Dhhhhhh NM:i:1 -EAS38_1_156_788_924 0 chr1 3137065 0 35M * 0 0 CTGGAATTATGTGATTATAATTTTCTTAGCATTTT hhhhhhhhhhhhhhhhhhhhhhhhbhhhh]Shhhh NM:i:0 -EAS38_1_219_907_956 0 chr1 3137065 0 35M * 0 0 CTGGAATTATGTGATTATAATTTTCTTAGCATTTT hhhhhhhhhhh\hhhhhhhhRhhh^hhg`h\hhhh NM:i:0 -EAS38_1_224_924_816 0 chr1 3137074 0 35M * 0 0 TGTGATTATAATTTTNTTAGCATTTTCTTCGTAAA hhhhhhhhhhhhhhh;hhhhh`hhhhhhhXhhhg] NM:i:2 -EAS38_1_128_932_926 16 chr1 3137133 0 35M * 0 0 GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA XYV[Lhfhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_146_271_903 16 chr1 3137133 0 35M * 0 0 TTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA HVhT[`hhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_127_823_362 0 chr1 3137183 0 35M * 0 0 GATAATACATATATACATATGCAGTGTGTGTGCCA hhhhhhhhhhhhhhhhhhhhhhhXhhhhhhhNU[H NM:i:0 -EAS38_1_282_34_255 16 chr1 3137183 0 35M * 0 0 GATAATACATATATAAATATGCAGTGTGTGTGCCA KhNhhLhQh\h`hJhCh`h^hLhhdhhhhhhhheh NM:i:1 -EAS38_1_215_971_567 0 chr1 3137204 0 35M * 0 0 CAGTGTGTGTGCCAGTGGTGTTAACAATACTAATA hhhhh[hhhhhhhhh\hSQeLYcVFKGAKH]XD^H NM:i:1 -EAS38_1_143_6_639 16 chr1 3137450 0 35M * 0 0 ATGTTCCCACACGGTCTATCTCCCTGACAAATCCC RH?>EJUcHhhILIhFhhYShb`hhhhhhhhchhh NM:i:2 -EAS38_1_132_603_749 0 chr1 3154107 255 35M * 0 0 TATATTTGGAAAAAAAAAGAAAGGAGTGTAGAGTC hhhhhhhhhhhhhhhhhhhhhhhhhhehhhhPhSS NM:i:0 -EAS38_1_238_595_598 0 chr1 3178632 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_238_595_598 0 chr1 3178639 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_238_595_598 0 chr1 3178646 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_238_595_598 0 chr1 3178653 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_118_1000_212 0 chr1 3179061 0 35M * 0 0 ATGTGATTTTAAATCATAGTCTTGCTTTTCCATTG hhhhhhhhhhhhghhhEMDPKhhLNh[hhMPNETJ NM:i:2 -EAS38_1_311_90_296 16 chr1 3179539 255 35M * 0 0 ACATAGGAAATGGAAGAGTACTTTATTATTATTAT bEhIhhhhTCNhhhhhhhVhRQhhhhhhhhhhhhh NM:i:1 -EAS38_1_221_489_194 16 chr1 3183282 3 35M * 0 0 ACTGACAGAAAAGAGACAGAGGTAGGACTTCTAGG >>FL[@RL@^WSRYUP@`UZeSLhhRQbOGWThhh NM:i:2 -EAS38_1_221_489_194 16 chr1 3183945 3 35M * 0 0 ACTGACAGAAAAGAGACAGAGGTAGGACTTCTAGG >>FL[@RL@^WSRYUP@`UZeSLhhRQbOGWThhh NM:i:2 -EAS38_1_205_642_159 16 chr1 3186543 255 35M * 0 0 CACATGCCTTTTTCATTTTTTCCAAGTGCCATCTG KhUhSHT]VS]_hFhhMhDbheHhhhhhhhhhhhh NM:i:0 -EAS38_1_26_282_635 16 chr1 3188051 255 35M * 0 0 TTCTGATCCTCAGGATCTGGAGTTACAGATGGTTG ECaSghKhh]ZhhhhdhVhhhh]hhhhhhhhhhhh NM:i:0 -EAS38_1_221_487_440 16 chr1 3188179 255 35M * 0 0 TTACTAAATTTTGTAATACTACTTAGTCTGGAAAA Oge[WhhhTKRShhhhbhhYhhchhh]hhhhhhhh NM:i:0 -EAS38_1_7_602_714 16 chr1 3188938 255 35M * 0 0 GACTGTCATTACATTATTTTAGTAGTTGTATTTTC A\h^SLhhChQhhhhhhhhUhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_239_803_441 16 chr1 3189316 255 35M * 0 0 AGATGTATCATAGCTCAGAAAGTACATTTGTAAGA hhhVhWhRJhYhh^Wbhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_318_649_84 16 chr1 3189316 255 35M * 0 0 AGATGTATCATAGCTCAGAAAGTACATTTGTAAGA hhh\hhhhKhhhhKMhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_178_556_269 0 chr1 3189808 255 35M * 0 0 CTTTTTTTAAAATGACCACAGTGTACTTTATTTAA hhhhhhhhhhhhhhhhhhhhLhhhXhhhhZhhhhX NM:i:2 -EAS38_1_184_810_767 16 chr1 3189830 255 35M * 0 0 GTACTTTATTTAATGATTTTTGTACTTTGTGTTGC dhah]hhhhhhhhhchh_hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_307_56_994 16 chr1 3189841 255 35M * 0 0 AATGATTTTTGTACTTTGTGTTGCAATAAAATAAA hh[Shhhhhh`hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_1_924_497 16 chr1 3189853 255 35M * 0 0 ACTTTGTGTTGAAATAAAATAAAAAAAAAATCTAC SNT[Za]ahh]Lhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_95_808_182 0 chr1 3189880 255 35M * 0 0 AAATCTACAAAATTCAAATATATAAAATTTCAAGT hhhhhhhhhhhhhhhehhhhhhhhhMhhhhh\h^h NM:i:0 -EAS38_1_43_924_188 0 chr1 3189887 255 35M * 0 0 CAAAATTCAAATATATAAAATTTCAAGTTTTCTTT hhhhhhhhh^Xhhhh?hh[RhhhhOMDhhhhhhhh NM:i:0 -EAS38_1_11_826_352 16 chr1 3189890 255 35M * 0 0 AATTCAAATATATAAAATTTCACGTTTTCTTTGTT hhIQAhhhShchchhhhUNU[hChhehhhhbhAhh NM:i:2 -EAS38_1_131_730_378 16 chr1 3189892 255 35M * 0 0 TTCAAATATATAAAATTTCAAGTTTTCTTTCTTTT HIhhhhhhhhhhhhhhhZhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_317_700_555 16 chr1 3189893 255 35M * 0 0 ACAAATATATAAAAGTTCAAGTTTTCTTTCTTTTA ?hhhhhh[hThhhhHhYhEhhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_46_519_952 0 chr1 3189903 255 35M * 0 0 AAAATTTCAAGTTTTNTTTCTTTTAAAGTTTTACA hhhhhhhhhhhhhhh;hhhhhhhhhhhhhhhhhPf NM:i:1 -EAS38_1_26_849_836 0 chr1 3189906 255 35M * 0 0 ATTTCAAGTTTTCTTTCTTTTAAAGTTTTACAAGA hhhhhhhhhhhhhhhhhhhhhdhhhhhhhhhhNXU NM:i:0 -EAS38_1_271_964_726 0 chr1 3189906 255 35M * 0 0 ATTTCAAGTTTTCTTACTTTTAAAGTTTTACAAGA hhhhhhhhhhhhhhhCXhhhhhhhHhhhhhhVhhh NM:i:1 -EAS38_1_305_225_753 16 chr1 3189909 255 35M * 0 0 TCAAGTTTTCTTTCTTTTAAAGTTTTACAAGAAAA Zhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_231_735 16 chr1 3189912 255 35M * 0 0 AGTTTTCTTTCTTTTAAAGTTTTACAAGAAAAAAA hhVhhhhhh_hhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_55_110 0 chr1 3189915 255 35M * 0 0 TTTCTTTCTTTTAAATTTTTACAATAAAAAAAATC hhhhhhhhhhhhUPh\hhhhdhLRcCLTRW@FMhh NM:i:2 -EAS38_1_230_130_609 16 chr1 3189915 255 35M * 0 0 TTTCTTTCTTTTAAAGTTTTACAAGAAAAAAAATC TDMO]K^FLYWWhhhh[S^Rhhhh^hhhhhhhhhh NM:i:0 -EAS38_1_203_262_383 16 chr1 3189917 255 35M * 0 0 TCTTTCTTTTAAAGTTTTACAAGAAAAAAAATCAG ]hJh[ahhhPhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_23_872_103 0 chr1 3189918 255 35M * 0 0 CTTTCTTTTAAATTTTTACAATAAAAAAAATCAGA hhhhhhhhhb_[Dhhhhhh[XAT[hUfKFhhVTM> NM:i:2 -EAS38_1_74_546_492 0 chr1 3189937 255 35M * 0 0 AAGAAAAAAAATCAGATAACCGAGGAAAATTCTTC hhhhhhhhhhhhhhh`h]hhhhThaRPOOhhBhhX NM:i:1 -EAS38_1_177_466_463 0 chr1 3189943 255 35M * 0 0 AAAAATCAGATAACCGAGGAAAATTATTCATTATG hhhhhhhhhhhhhhhhOhMSIIhhhdhh\hhhfhB NM:i:0 -EAS38_1_326_846_82 0 chr1 3189943 255 35M * 0 0 AAAAATCAGATAACCGAGGAAAATTATTCATTATT hhhhhhhhhhhhhhhh]hJdRdhhhZhhhYhbhhG NM:i:1 -EAS38_1_235_891_810 0 chr1 3189957 255 35M * 0 0 CGAGGAAAATTATTCATTATGAAGTACTACTTTCC hhhhhhhhhhhhhhhhhhhhhhhhh_HhOJhhPWI NM:i:0 -EAS38_1_73_865_289 16 chr1 3189961 255 35M * 0 0 GAAAATTATTCATTATGAAGTACTACTTTCCACTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_201_984_898 0 chr1 3189963 255 35M * 0 0 AAATTATTCATTATGAAGTACTACTTTCCACTTCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_37_723_474 16 chr1 3189968 255 35M * 0 0 ATTCATTATGAAGTACTACTTTCCACTTCATTTCA hHEJhFThZhhhhXhUShhhhhhhhhXhhhhhhhh NM:i:0 -EAS38_1_183_791_724 0 chr1 3189973 255 35M * 0 0 TTATGAAGTACTACTTTCCACTTCAGTTCATCACA hhhhhhhhhhhhhhhhhafhhhhdWBhhPYhHPh[ NM:i:1 -EAS38_1_69_87_770 16 chr1 3189978 255 35M * 0 0 AAGTACTACTTTCCACTTCATTTCATCACAAATTG hhJhghhhhhhghhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_54_211_781 16 chr1 3189984 255 35M * 0 0 TACTTTCCACTTCATTTCATCACAAATTGTAACTT hghhhLhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_203_766_573 16 chr1 3189985 255 35M * 0 0 ACTTTCCACTTCATTTCATCACAAATTGTAACTTA SQPbUhhZhhhhhhhWhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_195_866_158 0 chr1 3189991 255 35M * 0 0 CACTTCATTTCAACACAAATTGTAACTTACTTAAC hhhhhhRhhhhh@hchHOThhRh[F`hhPShbNSI NM:i:1 -EAS38_1_122_739_820 16 chr1 3190001 255 35M * 0 0 CATCACAAATTGTAACATACTTAACTGACCAAAAA hhXhfYhhhhSORhhhAghhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_144_950_152 16 chr1 3190008 255 35M * 0 0 AATTGTAACTTACTTAACTGAACAAAAAAACTATG hhIIc_hhI[\hHghhhYhhhHhhhhhhhhhhhhh NM:i:1 -EAS38_1_168_613_587 0 chr1 3190008 255 35M * 0 0 AATTGTAACTTACTTAACTGACCAAAAAAACTATG hhhhhhhhhhhhhhhhhhhhgh`SNhfhhRahZf\ NM:i:0 -EAS38_1_134_699_616 16 chr1 3190013 255 35M * 0 0 TAACTTACTTAACTGACCAAAAAAACTATGGTACT hhhQhMhhehhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_777_789 0 chr1 3190014 255 35M * 0 0 AACTTACTTAACTGACCAAAAAAACTATGGTACTG hhhhhhhhhhhhhhhWfh\`hHhhShgYhXGZIQU NM:i:0 -EAS38_1_66_446_787 0 chr1 3190014 255 35M * 0 0 AACTTACTTAACTGACCAAAAAAACTATGGTACTG hhhhhhhhhhhhhhhhhhhhhhh]dhhhhdghShh NM:i:0 -EAS38_1_179_978_676 16 chr1 3190032 255 35M * 0 0 AAAAAACTATGGTACTGCAGTATAGCAAATACTCC hhhhhghWhZhFhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_308_776_503 16 chr1 3190032 255 35M * 0 0 AAAAAACTATGGTACTGCAGTATAGCAAATACTCC hhhhhh^?hRhThhhghbhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_172_693_734 16 chr1 3190040 255 35M * 0 0 ATGGTACTGCAGTATAGCANATACTCCACACACTG hLD?UFaLLhaJhhhh[hh;hhhhhhhhhhhhhhh NM:i:1 -EAS38_1_239_423_396 16 chr1 3190040 255 35M * 0 0 AGGGTACTGAAGTATAGCAAATACTCCACACACTG _AH?>LADTCZh^h]hhDhhhZhhehhhhhhhhhh NM:i:2 -EAS38_1_284_912_582 16 chr1 3190042 255 35M * 0 0 GGTACTGCAGTATAGCAAATACTCCACACACTGTG LhhhhhhhhhhhhhhWhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_209_687_576 0 chr1 3190073 255 35M * 0 0 TGTGCTTTGAGCTAGAGCACTTGGAGTCACTGCCC hhhhhhhhhhhhhhhdhhZdhhYhPMhRPIeMWGP NM:i:0 -EAS38_1_185_490_551 16 chr1 3190085 255 35M * 0 0 TAGAGCACTTGGAGTCACTGCCCAGGGCAGCAGCC FJDFJGJJODb\`hJQ_hNghhhhhhhh`hhhhhh NM:i:0 -EAS38_1_65_838_419 0 chr1 3190102 255 35M * 0 0 CTGCCCAGGGCAGCAGCCTCCAACCAAGAAAGACA hhhhhhhhhhh]_hKhhchceBdGaOCG@?BGIIP NM:i:0 -EAS38_1_323_255_975 0 chr1 3190107 255 35M * 0 0 CAGGGCAGCAGCCTCCAACCAAGAAAGACACACTT hhhhhhhh\hhUShNYh]@Uh\hMXMaJ?YRRBFH NM:i:0 -EAS38_1_296_538_461 0 chr1 3190126 255 35M * 0 0 CAAGAAATACACACTTACAAGTTGAATTCTAAAGG hhhhhhhhhhhhhhhhhh]hhhhh\hhhhhMhbhh NM:i:1 -EAS38_1_132_195_514 16 chr1 3190129 255 35M * 0 0 GAAAGACACACTTACAAGTTGAATTCTAAAGGAAG chbhhhShFhhYhhghhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_155_895_725 16 chr1 3190140 255 35M * 0 0 TTTCAAGTTGAATTCTAAAGGAAGGTCTGGTTATG VhO[ghWSchhh_hZhhhhhhhhhXhhhhhhhhhh NM:i:1 -EAS38_1_193_609_633 16 chr1 3190140 255 35M * 0 0 TTACAAGTTGAATTCTAAAGGAAGGTCTGGTTATG Q`hbhhh[hhhhShhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_135_816_228 16 chr1 3190142 255 35M * 0 0 AAAAGTTGAATTCTAAAGGAAGGTCTGGTTATGTG fC_]SH_VhhIABLhhhhfhhhWfZhhhhhhhhhh NM:i:1 -EAS38_1_145_593_539 0 chr1 3190150 255 35M * 0 0 AATTCTAAAGGAAGGTCTGGTTATGTGGGGTTGTA hhhhhhhhhhhhhhhhhhhhhhhhQh`ShhhhhAH NM:i:1 -EAS38_1_121_577_810 16 chr1 3190177 255 35M * 0 0 GGGTTGGAGTATGTATATCTATATATCTCTATATA KJM]OSdhbXhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_194_207_828 0 chr1 3190207 255 35M * 0 0 ATATATATTTACATCAAAGAATTTAATAACTCATT hhhhhhhhhhhhhhhhhhhhhhhhchhTh_h_`hh NM:i:0 -EAS38_1_113_803_974 0 chr1 3190221 255 35M * 0 0 CAAAGAATTTAATAACTCATTTAAATTTTTGTTTC hhhhhhhhhhhhhhhchQhhhhhgOhh_hhh_hhL NM:i:0 -EAS38_1_160_812_510 16 chr1 3190244 255 35M * 0 0 AATTTTTGTTTCAAATAAAATTCCAAATACACTTG hhWOhG]h^hhQhhhhhhhhh_\hhhhhhhhBhhh NM:i:1 -EAS38_1_40_88_508 16 chr1 3190249 255 35M * 0 0 TTGTTTCAAATAAAATTCCAAATACATTTGTACAA QhhgVhdhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_84_935_631 16 chr1 3190249 255 35M * 0 0 TTGTTTCAAATAAAATTCCAAATACATTTGTACAA ^]hJhZWhhhhhhhhhUhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_36_762_603 0 chr1 3190263 255 35M * 0 0 ATTCCAAATACATTTGTACAATGTTTACAAAGTAA hhhhhhhhhhhhhhhhhhhhhh^hhhhahX\]_hb NM:i:0 -EAS38_1_16_788_728 16 chr1 3190265 255 35M * 0 0 TCCAAATACATTTGTACAATGTTTACAAAGTAAGA @hEhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_172_782_398 16 chr1 3190269 255 35M * 0 0 AATACATTTGTACAATGTTNACAAAGTAAGAGACA hhZhhhaZhhWhhhhhheh;hThhhhehhhhhhhh NM:i:1 -EAS38_1_319_78_862 16 chr1 3190274 255 35M * 0 0 ATTTGTACAATGTTTACAAAGTAAGAGACAGGACT dLhZM_ehdhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_27_817_428 16 chr1 3190276 255 35M * 0 0 TTGTAAAATGTTTACAAAGTAAGAGACAGGACTGG VPhchChh_ghfhhEhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_188_256_713 0 chr1 3190325 255 35M * 0 0 AGGCCAGGCACCGTGATGTCCGGGTGATATATCTT hhhhhhhhhhhhhhhKhhaMhUhhNgA_E[GhM[G NM:i:0 -EAS38_1_315_859_502 16 chr1 3190329 255 35M * 0 0 CAGGAACCGTGATGTCCGGGTGATATATCTTCACG BNSIKHNI\SK]VdXZR`Uhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_152_381_800 16 chr1 3190355 255 35M * 0 0 ATCTTCACGTTGCCTGCACACACCTTATTTCTGAA ZVhQIhhhhhhXhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_282_558_872 0 chr1 3190364 255 35M * 0 0 TTGTCTGCACACACCTTATTTCTGAAATGGAGAGA hhh=hhhhhhhhh_hhhhhhhYhh`hhhhhQhhhC NM:i:1 -EAS38_1_215_759_830 0 chr1 3190407 255 35M * 0 0 AGAATGTCACCGACTATGCATCAGAATACTATGTA hhhhhhhhhhhhhhhhhhh_hh[hUWhhbh^hhXc NM:i:0 -EAS38_1_277_471_798 16 chr1 3190412 255 35M * 0 0 GTCACCGACTATGCATCAGAATACTATGTACAGTT KJYK\eYhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_279_405_802 16 chr1 3190418 255 35M * 0 0 GACTATGCATCAGAATACTATGTACAGTTGAAGTT Chhhhhhhhhhhhhhhhhhhhhhhhh`hhhhhhhh NM:i:0 -EAS38_1_75_573_457 16 chr1 3190428 255 35M * 0 0 CAGAATACTATGTACAGTTGAAGTTAGGGAGCTGA Zhdhh_dhYhRh\hhhhUKhhhhhUhhhhhhhhhh NM:i:0 -EAS38_1_238_427_419 16 chr1 3190444 255 35M * 0 0 GTTGAAGTTAGGGAGCTGAGAACCTAGTGGTCTGT XKEQdhhNKZhhhhhhdhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_24_788_817 0 chr1 3190444 255 35M * 0 0 GTTGAAGTTAGGGAGCTGAGAACCTAGTGGGCTGT hhhhhhhhhhhhhQhHhhUeK_AGXKhNfe>=ITO NM:i:1 -EAS38_1_307_22_417 16 chr1 3190449 255 35M * 0 0 AGTTAGGGAGCTGAGAACCTAGTGGTCTGTTCTCT KU@DX`XWbV@JhghhTETVhh^hTWh_hh[hhhh NM:i:0 -EAS38_1_104_731_910 0 chr1 3190455 255 35M * 0 0 GGAGCTGAGAACCTAGTGGTCTGTTCTCTTCTGGT hhhhhhhhhhhJYhhhhhhZOhhhhBhF\hFhhaO NM:i:0 -EAS38_1_189_367_978 16 chr1 3190466 255 35M * 0 0 CCTAGTGTTCTGTTCTCTTCTGGTTTGTCTTCATC HhCMIbQEShcKTYhhh\hhhYPhhhhhhhhhhhh NM:i:1 -EAS38_1_288_697_269 0 chr1 3190470 255 35M * 0 0 GTGGTCTGTTCTCTTCTTGTTTGTCTTCATCTACC hhhhhhhhhhhhhhhhhBChhhDhhhhhQhhhI?c NM:i:1 -EAS38_1_239_232_371 16 chr1 3190490 255 35M * 0 0 GTGTCTTAATCTACCAGCTATTACTCCTCTTTTGC DKK?ADHAhKCIhVhhhB_hchhhbhhZhhhhhhh NM:i:2 -EAS38_1_17_329_620 16 chr1 3190509 255 35M * 0 0 ATTACTCCTCTTTTGCTCAGAGATAAATTTAAAAT h^E_hMhchhhThVhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_145_66_863 0 chr1 3190520 255 35M * 0 0 TTTGCTCAGAGATAAATTTAAAATACAAACATTGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhc NM:i:0 -EAS38_1_318_476_736 0 chr1 3190562 255 35M * 0 0 AAGGAGAAAAGCACAAAATATTTAAGGCAAATTAA hhhhhhhhhhhhhhhhhhhhhhhhfhh^hF\hhhH NM:i:0 -EAS38_1_91_887_139 16 chr1 3190577 255 35M * 0 0 AAATATTTAAGGCAAATTAAGCAAATATGTACAGT hhhhhK^ThhZhThhh\hhhhZhhhhhhhhhhhhh NM:i:0 -EAS38_1_42_628_869 16 chr1 3190582 255 35M * 0 0 TTTAAGGCAAATTAAGCAAATATGTACAGTCTCTT EYEhhBDYhhh^hhhLhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_266_296_122 16 chr1 3190587 255 35M * 0 0 GGAAAATTAAGAAAATATGTACAGTCTCTTTGTGC hUJhhh@ehhhFhhhShIhehhhh`h\hhbhhhhh NM:i:2 -EAS38_1_296_47_651 0 chr1 3190588 255 35M * 0 0 GCAAATTAAGCAAATATGTACAGTCTCTTTTTTCC hhhhhhhhhhhhhhhhhhhhh[hhhhhhhhDhIRE NM:i:2 -EAS38_1_298_622_554 16 chr1 3190612 255 35M * 0 0 CTCTGTGTGCCAGGAGGATGTGACTTTCTTTTTAA QXfIBXhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_55_346_335 16 chr1 3190613 255 35M * 0 0 TCGGTGTGCCAGGAGGATGTGACTTTCTTTTTAAA KABCGhGh@hhhhhhhhhh^hhhhhhhhhhhhhhh NM:i:2 -EAS38_1_144_104_681 16 chr1 3190646 255 35M * 0 0 AATCCCAAACCATGCTTTAAAAAATTCAAATAAAG hhVhJThhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_307_505_905 0 chr1 3190650 255 35M * 0 0 CCAAACCATGCTTTAAAAAATTCAAATAAAGCAAG hhhhhhhhhhhhhhhhhhhhhhhhShhhh_h\`hh NM:i:0 -EAS38_1_4_468_915 0 chr1 3190667 255 35M * 0 0 AAATTCAAATAAAGCAAGTCTGGTGTGAGTTGGGT hhhhhhhhhhhhhhhhhhhhhhhahfhJhhhhhha NM:i:0 -EAS38_1_177_100_872 0 chr1 3190682 255 35M * 0 0 AAGTCTGGTGTGAGTTGGGTTGCTTGTGTTGTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhThhhhh NM:i:0 -EAS38_1_201_448_983 0 chr1 3190733 255 35M * 0 0 TGTTTTGCACAAAATAACCATTTGGAATTTGCAGT hhhhhhhahhhhhhhhhZMhhhhhhNhhhhXGXhH NM:i:0 -EAS38_1_205_905_511 16 chr1 3190740 255 35M * 0 0 AACAAAATAACCATTTGGAATTTGCAGTGGAATAA hhFhhhhahhhhhhahhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_22_834_621 0 chr1 3190741 255 35M * 0 0 ACAAAATAACCATTTGGAATTTGCAGTGGAATAAT hhhhhhhhhhhhhhhhhYhhhhhh]h]h[NVhI`h NM:i:0 -EAS38_1_297_847_594 16 chr1 3190753 255 35M * 0 0 TTTGGAATTTGCAGTGGAATAATTTGTTAATTGTG `KYZ\hX^dhYhhhhbhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_105_929_305 16 chr1 3190768 255 35M * 0 0 GGAATAATTTGTTAATTGAGAAGTGTATGGTTTTG hhhhhhhQ]hhhhhh_hhEhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_323_29_609 0 chr1 3190771 255 35M * 0 0 ATAATTTGTTAATTGTGAAGTGTATGGTTTTGTAT hhhhhhhhhhhhhhhhhhhOhhhhhhhhhhh@hGh NM:i:0 -EAS38_1_174_674_495 0 chr1 3190781 255 35M * 0 0 AATTGTGAAGTGTATGGTTTTGTATTTTTAAACCA hhhhhhhhhhhhhhhhhhhhhFhhhhhhLUPaeSG NM:i:1 -EAS38_1_156_965_73 16 chr1 3190814 255 35M * 0 0 CAAAAAACAGTAGCTGAGGTAGTTAAATGTGAAAC DhhhCghNhhhhhRhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_264_136_776 0 chr1 3190842 255 35M * 0 0 GTGAAACTTACACAACTTAAAATAATGAGAGAATG hhhhhhhhhh`hbhhYhhbh_eh_hhbM\O]IVYR NM:i:0 -EAS38_1_269_103_855 16 chr1 3190853 255 35M * 0 0 ACAACTTAAAATAATGAGAGAATGGAGAACCAATG ShhhhhXhhhhchhLhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_133_823_893 0 chr1 3190856 255 35M * 0 0 GCTTAAAATAATGAGAGAATGGAGAAACAATGTAA hhhhhhhhhhhhhhhbhhVhhhahQZ@KZhSUKgH NM:i:2 -EAS38_1_316_626_26 0 chr1 3190872 255 35M * 0 0 GAATGGAGAACCAATGTAAGGAGCCCAGACTCTTG hhhhhhhhhh]hhhhh^hXNhhXLcGGFEMVIL\A NM:i:0 -EAS38_1_14_936_623 0 chr1 3190882 255 35M * 0 0 CCAATGTAAGGAGCCCAGACTCTTGCCATCTGGGA hhhhhhhhdhhhhYTbFhTWehhNJdKDJVREM?E NM:i:1 -EAS38_1_112_85_814 16 chr1 3190885 255 35M * 0 0 ATGTAAGGAACCCAGACTCTTGCCATCTGGAAGCA dBCDhhRNh?RhWhWhhWhZh[hhhhhhhhhhhhh NM:i:1 -EAS38_1_153_136_402 16 chr1 3190885 255 35M * 0 0 ATGTAAGGAGCCCAGACTCTTGCCATCTGGAAGCA QUhWhhh[hTahhhhQhhUhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_267_293_629 16 chr1 3190891 255 35M * 0 0 GGAGCCCAGACTCTTGCCATCTGGAAGCAGGCTCA Zg]YhEhhhhfd`hZhJhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_60_948_719 16 chr1 3190944 255 35M * 0 0 TACCCAGAAAAACATTTGTTCTTTTGGATGCCATT BAHQQhFehhhRhUPKJVf\hh^bWh_hhhhhhhh NM:i:0 -EAS38_1_279_273_497 0 chr1 3190975 255 35M * 0 0 CATTAGTTCAGCCAGTGTCAACATGACTAGTGGTT hhhhhhhhhhhhhhhZYhhhhahhh`Uh`ELGVVg NM:i:0 -EAS38_1_35_405_941 16 chr1 3190979 255 35M * 0 0 AGTTCAGCCAGTGTCAACATGACTAGTGGTTTCCC E??>bfB^hhOIT_hhhhhhUWhhhhh^hhhhhhh NM:i:0 -EAS38_1_307_828_462 16 chr1 3190995 255 35M * 0 0 ACATGACTAGTGGTTTCCCAAGCACTTGCTTGGAA hRhhhhh^hhhhhhhhGfhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_118_418_323 16 chr1 3191023 255 35M * 0 0 CGTGGAAGCAAAGATAAAGAAAGTCTGCTTTCCAG IS@dWhh]NhhhHhbhhhhhhhhZhchhhhghhhh NM:i:2 -EAS38_1_144_10_603 0 chr1 3191023 255 35M * 0 0 CTTGGAAGCAAATATAAAGAAAGTCTGCTTTCCAG hhhhhhhhhhZhhhhhhdhWhhhhhhh^hhhDhKU NM:i:0 -EAS38_1_219_965_773 16 chr1 3191038 255 35M * 0 0 AAAGAAAGTCTGCTTTCCACGCTTCTCATCTATAG hhhIhhh[ehXQhhhahhhJhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_56_375_762 16 chr1 3191134 255 35M * 0 0 CATTATTAGAAATTCCAACCCTAGTTATGAAAGAT hh_VhKZhMhhhSXbhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_148_601_688 16 chr1 3191142 255 35M * 0 0 GAAATTCCAACCCTAGTTATGAAAGATTGAGGGGA hhhhhTdhhhhhhhhhhhhhhhhhhhhhhhhhh>h NM:i:1 -EAS38_1_236_489_757 0 chr1 3191149 255 35M * 0 0 CAACCCTAGTTATGAAAGATTGAGGGAAAGTGATA hhhhhhhhhhhhhhhhhhThhhbhhhSKhhXhTh_ NM:i:0 -EAS38_1_144_552_470 0 chr1 3191153 255 35M * 0 0 CCTAGTTATGAAAGATTGAGGGAAAGTGATAAAGA hhhhhhhhhhhhhhehhhh`h\IPThhhThGKUML NM:i:0 -EAS38_1_288_225_365 16 chr1 3191173 255 35M * 0 0 GGAAAGTGATAAAGAACAAAAGGGAGGGATATTAT hhhhhh\hh`hhhhhhMhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_33_904_669 0 chr1 3191192 255 35M * 0 0 AAGGGAGGGATATTATTCTCTCATTTTTAACAGCA hhhhhhhhhhhhhhhhhhhhhhghhhhhhhhYKJH NM:i:0 -EAS38_1_123_430_125 16 chr1 3191220 255 35M * 0 0 AACAGCATATTTGTCTTAGCTTTAAATCCAGAGTA hhDh`Ch`h[UTh[RhehhcThhhhhhhhhhhhhh NM:i:0 -EAS38_1_179_676_404 16 chr1 3191241 255 35M * 0 0 TTAAATCCAGAGTACTGTTTGGCTTCAAAGAAGAT QhhhhLZUhhhhfhhbhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_120_22_725 0 chr1 3191250 255 35M * 0 0 GAGTACTGTTTGGCTTCAAAGAAGATAGTCATCTC hhhhhhhhhhhhhhhhfhhhhahhhhdhhhZhNhX NM:i:0 -EAS38_1_223_373_449 0 chr1 3191268 255 35M * 0 0 AAGAAGATAGTCATCACTGGTTCTCTTACTGAGAA hhhhhhhhhhhhhhhDhhhhZhhhhhh^hh[NFCQ NM:i:1 -EAS38_1_112_183_986 0 chr1 3191269 255 35M * 0 0 AGAAGATAGTCATCTCTGGTTCTCTTACTGAGAAT hhhhhhhhhhhhhhhfhhhehhhfhhX\hhVhbKg NM:i:0 -EAS38_1_172_99_819 16 chr1 3191287 255 35M * 0 0 GTTCTCTTACTGAGAATAGNAAGTCTCTCCTTACT U\VhOhhhhhhhhhhhhhh;hhhhhhhhhhhhhhh NM:i:1 -EAS38_1_210_930_591 16 chr1 3191287 255 35M * 0 0 GTTCTCTTACTGAGAATAGAAAGTCTCTCCTTACT LWK^Khh^ShNhhhhhhhhhhhhXhhhhhhhhhhh NM:i:0 -EAS38_1_100_778_539 16 chr1 3191290 255 35M * 0 0 CTCTTACTGAGAATAGAAAGTCTCTCCTTACTGAG hhfhhhThhhhhhhhhhhhh^hhhhhhhhhhhhhh NM:i:0 -EAS38_1_25_830_623 16 chr1 3191298 255 35M * 0 0 GAGAATAGAAAGTCTCTCCTTACTGAGAATAGGAA YhRhhLhhhhhh`h\hhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_304_473_442 0 chr1 3191304 255 35M * 0 0 AGAAAGTCTCTCCTTACTGAGAATAGGAAGCCATC `hhhThehhhhh\hhXYhgJ`ILQLDNBIAAM=HD NM:i:0 -EAS38_1_205_508_718 16 chr1 3191307 255 35M * 0 0 AAGTCTCTCCTTACTGAGAATAGGAAGCCATCTTC hhRBOThbhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_293_376_615 16 chr1 3191307 255 35M * 0 0 AAGTCTCTCCTTACTGAGAATAGGAAGCCATCTTC hhh@hFhOhhghhh[hh`hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_182_907_727 16 chr1 3191326 255 35M * 0 0 ATAGGAAGCNATCTTCATACCTGTCCCTCTGCATT hM^FJg`Mh;hhhhfhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_222_741_776 0 chr1 3191358 255 35M * 0 0 ATTTATTCTTGAGGTTACTGAGCCATCTGGCTACA hhhhhhhhhhhhhhChhYhTehDVghIhh][ZF?K NM:i:0 -EAS38_1_88_323_543 16 chr1 3191374 255 35M * 0 0 ACTGAGCCATCTGGCTACAGAGAAGAAAAGCAAGA X\Ghhe^JhNaXhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_66_197_743 16 chr1 3191383 255 35M * 0 0 TCTGGCTACAGAGAAGAAAAGCAAGAGTTGTTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_173_864_740 16 chr1 3191391 255 35M * 0 0 CAGAGAAGAAAAGCAAGAGTTGTTTTTTTATTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_124_858_171 16 chr1 3191398 255 35M * 0 0 GAAAAGCAAGAGTTGTTTTTTTATTTTTATTTTAT chhhhU\hhhhcOchhObh]hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_126_138_418 16 chr1 3191410 255 35M * 0 0 TTGTGTTTTTATTTTTATTTTATTTTTATTTTTTT U`hhBfhZZhhh`Yhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_221_397_462 0 chr1 3191429 255 35M * 0 0 TTTTTTTTATTTTTTTAAGTAGAAGCAAGATTCTC hhhhhhhhZhhhhhhhhVFhbKMSWhRG]?hhQh[ NM:i:1 -EAS38_1_216_901_971 0 chr1 3191444 255 35M * 0 0 TAAGTAGAAGCAAGATTCTCATTAAGGCTAACTAT hhhhhhhhhhhhhhhhhahZZhbhabfQ[MKFWGU NM:i:0 -EAS38_1_282_128_662 0 chr1 3191445 255 35M * 0 0 AAGTAGAAGCAAGATTCTCATTAAGGCTAACTATG hhhhhhhchhhhh]hhhhhVhhZhhhZhZ@MbMaL NM:i:0 -EAS38_1_77_686_871 0 chr1 3191446 255 35M * 0 0 AGTAGAAGCAAGATTCTCATTAAGGCTAATTATGT hhhhhhhhhhhhhhhdhhhhhhhhh^hh]@hhh`B NM:i:2 -EAS38_1_95_356_853 0 chr1 3191446 255 35M * 0 0 AGTAGAAGCAAGATTCTCATTAAGGCTAACTATGC hhhhhhhhhhhhhhhhhhhhhhPhhfh\HJGUhLN NM:i:0 -EAS38_1_315_80_525 0 chr1 3191449 255 35M * 0 0 AGATGCAAGATTCTCATTAAGGCTAACTATGCTAT hhhhhhhhhhhhhhhehhhR\Khh]]gh[hZ_hJh NM:i:1 -EAS38_1_211_797_532 0 chr1 3191471 255 35M * 0 0 CTAACTATGCTATTCTCCACTGCGCCCCATTGATC hhhhhhhhhhhhhhhhhhhhhfcIhLh[HhgUUhK NM:i:0 -EAS38_1_326_311_799 0 chr1 3191471 255 35M * 0 0 CTAACTATGCTATTCTCCACTGCGCCCCATTGATC hhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhVhG NM:i:0 -EAS38_1_107_806_891 16 chr1 3191478 255 35M * 0 0 TCCTATTCTCCACTGCGCCCCATTGATCAGACAAT LBfP^MWhAhh_hh^hZhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_121_349_512 0 chr1 3191489 255 35M * 0 0 ACTGCGCCCCATTGATCAGACAATGGCTTTAAGTG hhhhhhhhhhhhhhhhhhhhhBhhhhhhhhOOJeT NM:i:0 -EAS38_1_219_430_836 16 chr1 3191498 255 35M * 0 0 CATTGATCAGACAATGGCTTTAAGTGGGGCCTAAA c_WRRdUhhN[hhhdaWhOhhhghhhhhhhhhhhh NM:i:0 -EAS38_1_98_807_431 16 chr1 3191517 255 35M * 0 0 TTAAGTGGGGCCTAAATGAACTGTTGGACATCAGG PQg^SGhO[eOKhhhh`hhhYahhXhhhhhhhhhh NM:i:0 -EAS38_1_155_241_829 16 chr1 3191535 255 35M * 0 0 AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG ]QbLHKRRThhhWhhh[hdghhhhhhhhhhhhhhh NM:i:0 -EAS38_1_223_732_501 0 chr1 3191535 255 35M * 0 0 AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG hhhhhhhhhYhahh\EQghh\hPMJd_hSX[XhgE NM:i:0 -EAS38_1_320_444_109 16 chr1 3191535 255 35M * 0 0 AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG hbHUhhGhhhRhhhhhWZhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_103_761_542 0 chr1 3191537 255 35M * 0 0 CTGTTGGACATCAGGTTCATGAAAACGGTTTTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_245_218_950 0 chr1 3191539 255 35M * 0 0 GTTGGACATCAGGTTCATGAAAACGGTTTTGTGCA hhhhhhhhhchhhhhhhhhhhhhKhhhhhh_\R>f NM:i:1 -EAS38_1_54_654_789 0 chr1 3191548 255 35M * 0 0 CAGGTTCATGAAAACGGTTTTGTGAAGGTAATATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhLhChhh^ NM:i:0 -EAS38_1_242_532_556 0 chr1 3191553 255 35M * 0 0 TCATGAAAACGGTTTTGTGAAGGTAATATATCAGT hhhhhh]hhhhhhhhhZhTfchhO[LhUhXTCJJP NM:i:0 -EAS38_1_37_578_493 16 chr1 3191563 255 35M * 0 0 GGTTTGGTGAAGGTAATATATCAGTAATATGGTTG THOCeDUEhhZQgchhhhhhJhhhhhhhhhhhhhh NM:i:1 -EAS38_1_151_713_632 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhhh`hhhSThh NM:i:0 -EAS38_1_152_680_718 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhh^g\hhbhhh^ NM:i:0 -EAS38_1_152_24_706 0 chr1 3191573 255 35M * 0 0 AGGTAATATATCAGTAATATGGTTGACATAAATAA hhhhhhhhhhhhhhhhhhhhhhhhhOehhhWhhhW NM:i:0 -EAS38_1_330_686_422 16 chr1 3191575 255 35M * 0 0 GTAATATATCAGTAATATGGTTGACATAAATAAGC GLhhdhbhGJhh_hhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_275_44_659 0 chr1 3191579 255 35M * 0 0 TATATCAGTAATATGGTTGACATAAATAAGCTGGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhTcg NM:i:0 -EAS38_1_324_589_894 0 chr1 3191579 255 35M * 0 0 TATATCAGTAATATGGTTGACATAAATAAGATGGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhXhhhh NM:i:1 -EAS38_1_121_763_313 0 chr1 3191589 255 35M * 0 0 ATATGGTTGACATAAATAAGCTGGGAAATAGTTCT hhhhhhhhhhhhhhhhhhhhhhchhWFhhTChhfh NM:i:0 -EAS38_1_130_668_987 16 chr1 3191610 255 35M * 0 0 TGGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTT UT>Khbhbhhh[hhhhZhhfhhhhhhhhhhhhhBh NM:i:0 -EAS38_1_80_262_758 16 chr1 3191611 255 35M * 0 0 GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC PYdhhhMhh\HhhVhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_272_104_967 0 chr1 3191614 255 35M * 0 0 AAATAGTTCTTTTAGAAAGTAGAAGATTTTTCTCT hhhhhhhhhhhhhhhGhhhhhhhehXhhhhhZhZh NM:i:1 -EAS38_1_142_144_587 16 chr1 3191617 255 35M * 0 0 TAGTTCTTTTAGGAAGTAGAAGATTTTTCTCTTTG bhhhHPhNhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_282_509_344 16 chr1 3191618 255 35M * 0 0 AGTTCTTTTAGGAAGTAGAAGATTTTTCTCTTTGT hh^YdVSKWhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_3_797_743 0 chr1 3191619 255 35M * 0 0 GTTCTTTTAGGAAGCAGAAGATTTTTCTCTTTTTG hhhhhhhhhhhhhhAhhhhhXhhhhhhhfhhhHhb NM:i:2 -EAS38_1_311_266_241 16 chr1 3191633 255 35M * 0 0 TAGAAGATTTTTCTCTTTGTGTCTGTGTCTTTCAT LhhhhhhXGFHH_HhhhThhhdhhhhhhhhhhhhh NM:i:0 -EAS38_1_282_320_153 16 chr1 3191635 255 35M * 0 0 GAAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTT OQ\\PEA[JHNGRQJhhhhXNhhWhVhhUfhhhhh NM:i:0 -EAS38_1_74_839_687 16 chr1 3191635 255 35M * 0 0 GAAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTT MhhWhS[hhGhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_119_931_54 16 chr1 3191636 255 35M * 0 0 AAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTTG QJ?JRKXIZaOhYYdbhhhhbhhhfhhhhhhhhhh NM:i:0 -EAS38_1_171_559_793 16 chr1 3191638 255 35M * 0 0 GATTTTTCTCTTTGTGTCTGTGTCTTTCATTTGCC U_NhR[ZhhhRhWhhhhhh>hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_9_831_797 0 chr1 3191643 255 35M * 0 0 TTCTCTTTGTGTCTGTGTCTTTCATTTGCCTTTGT hhhhhhhhhhhhhhhhhhGhhhGChhhH>Kd?hEA NM:i:2 -EAS38_1_112_463_853 0 chr1 3191663 255 35M * 0 0 TTCATTTGCCTATGAAAAGAATGTTAGTTGGCTGT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhah^h NM:i:0 -EAS38_1_200_507_523 16 chr1 3191673 255 35M * 0 0 TATGAAAAGAATGTTAGTTGGCTGTAACCATAAAA @hW^hhhhehhKgXh\hh^hhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_307_105_716 0 chr1 3191676 255 35M * 0 0 GAAAAGAATGTTAGTTGGCTGTAACCATAAAATTG hhhhhhhhhhhhhhhhhhhhhhUh[_Hh]aQdhhZ NM:i:0 -EAS38_1_81_670_875 16 chr1 3191698 255 35M * 0 0 AACCATAAAATTGGCAGTTGTATTTACAAATAATC hehhhhhhhhhhhZhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_285_30_406 0 chr1 3191712 255 35M * 0 0 CAGTTGTATTTACAAATAATCACATATATTATGCT h_hhhhh_hhh]hQQShILhhYhQhIhHhCIh@U_ NM:i:1 -EAS38_1_45_791_522 16 chr1 3191716 255 35M * 0 0 TGTATTTACAAATAATCACATATATGATGCTTACA hh`hhXhhhhhhhhhfhhhHhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_43_819_567 16 chr1 3191719 255 35M * 0 0 ATTTACAAATAATCACATATATGATGCTTACAGAA hhQhhChhhhhhhhhhhhh@hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_26_772_717 0 chr1 3191761 255 35M * 0 0 CTCATTTCTAAATAATCACATATGCTAAAAGCTAG hhhhhhhhhhhhhhhhhhhhhZhhYhWfahSIhHS NM:i:0 -EAS38_1_130_865_419 0 chr1 3191766 255 35M * 0 0 TTCTAAATAATCACATATGCTAAAAGCTAGGTTTT hhhhhhhhhhhhhhhhhhhhh\`hhOhhELh_hhh NM:i:0 -EAS38_1_327_933_866 0 chr1 3191766 255 35M * 0 0 TTCTAAATAATCACATATGCTAAAAGCTAGGTTTT hhhhhhhhhhhhhhhhhhhhhhh]chYhPhLYhhh NM:i:0 -EAS38_1_126_547_811 16 chr1 3191773 255 35M * 0 0 TAATCACATATGCTAAAAGCTAGGTTTTTCTAATA hhhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_277_668_994 16 chr1 3191773 255 35M * 0 0 TAATCACATATGCTAAAAGCTAGGTTTTTCTAATA _hhJhhhhhhh]hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_181_734_387 16 chr1 3191780 255 35M * 0 0 ATATGCTAAAAGCTAGGTTTTTCTAATACACTTTT hNhNTARh`hhhIOhhhXeRMhLahhhhhhhhhhh NM:i:0 -EAS38_1_174_224_835 16 chr1 3191785 255 35M * 0 0 CTAAAAGCTAGGTTTTTCTAATACACTTTTACTTT hhhhhhhhhhdghhhhhhhhhhhhhhhhhhh>hhh NM:i:1 -EAS38_1_192_253_159 16 chr1 3191794 255 35M * 0 0 AGGTTTTTATAATACACTTTTATTTTCATGGAGGG hhc\PLNGAfhhhhhh[hZ[_hh[ahhhYhhhhhh NM:i:1 -EAS38_1_184_325_530 16 chr1 3191800 255 35M * 0 0 TTCTAATACACTTTTATTTTCATGGAGGGCTCTAG hGV[hhWhhhhhXh^hghhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_250_311_830 16 chr1 3191810 255 35M * 0 0 CTTTTATTTTCATGGAGGGCTCTAGAGGATTCCAC YLGJTUPJNNXgKQR_VKThhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_275_852_575 16 chr1 3191813 255 35M * 0 0 TTATTTTCATGGAGGGCTCTAGAGGATTCCACGTG JVeYM[E`hJSLV]SQVRChhhhhhhhhhhShhhh NM:i:0 -EAS38_1_77_390_526 0 chr1 3191818 255 35M * 0 0 TTCATGGAGGGCTCTAGAGGATTCCCCGTGGCATA hhhhhhhhhhhhhhhThNhhOhhOQA_^TEV=^EG NM:i:2 -EAS38_1_299_893_564 16 chr1 3191846 255 35M * 0 0 TGGAATAGAAACCACTGAAAAGAGACTCAACTCTT @aVhhKhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_294_440_933 16 chr1 3191865 255 35M * 0 0 TAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA O^EV?MhDhhUh\hYKVTKhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_278_780_674 16 chr1 3191873 255 35M * 0 0 CAACTCTTTTTCCCCCCAGCAATATTATGTTGCTC hhVWchcZHXMhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_86_970_279 0 chr1 3191876 255 35M * 0 0 CTCTTTTTCCCCCCAGCAATATTATGTTGCTCTGT hhhhhhhhhhhhhhPhheHhfhhehOhhEOhUhAF NM:i:0 -EAS38_1_148_146_536 0 chr1 3191881 255 35M * 0 0 TCTCCCCCCAGCAATATTATGTTGCTCTGTGCTGC hDhhhhhhh]hhhdhhhhhhhhhEhhhh\hEhhHG NM:i:1 -EAS38_1_224_888_484 16 chr1 3191884 255 35M * 0 0 CACCCCAGCAATATTATGTTGCTCTGTGCTGCTCT P?KJEARLNW`TdVWhF^OThhMgQ\hhhhfhhhh NM:i:1 -EAS38_1_223_648_752 0 chr1 3191887 255 35M * 0 0 CCCAGCAATATTATGCTGCTCTGTGCTGCTCTATG h_hhhhhhhhhhhhh=hhhhYhhOVghhB\AhWhM NM:i:1 -EAS38_1_300_220_617 0 chr1 3191891 255 35M * 0 0 GCAATATTATGTTGCTCTGTGCTGCTCTATGCATA hhdhhhhhhhhhhhhhhhhhh\hhhhZhhhhPKhL NM:i:0 -EAS38_1_63_467_696 16 chr1 3191897 255 35M * 0 0 TTATGTTGCTCTGTGCTGCTCTATGCATATGGCAT FHh^h]Fhe?hfhhchhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_24_141_869 0 chr1 3191905 255 35M * 0 0 CTCTGTGCTGCTCTATGCATATGGCATGTTGTTGG hhhhhhh^hhUhUhhhhYhhfhh_BPcfh`RXOLS NM:i:0 -EAS38_1_184_494_683 16 chr1 3191911 255 35M * 0 0 GCTGCTCTATGCATATGGCATGTTGTTGGTACCTG =Qab\ahVhchahhh]hhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_263_460_363 16 chr1 3191919 255 35M * 0 0 ATGCATATGGCATGTTGTTGGTACCTGTACCATTC h?UIhJhWhhOhghhKhDhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_80_670_426 16 chr1 3191919 255 35M * 0 0 ATGCATATGGCATGTTGTTGGTACCTGTACCATTC cPgPhNh\hhhh[hhhhUahhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_118_725_870 0 chr1 3191927 255 35M * 0 0 GGCATGTTGTTGGTACCTGTACCATTCTCTTCCAT hhhhhhhhhhhhhhhcghhhhRSQhhUhHhhGKLh NM:i:0 -EAS38_1_88_806_693 16 chr1 3191952 255 35M * 0 0 TCTCTTCCATTGAGAATTCTAAGCCATTATGTGGA fhhhhahhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_160_191_877 16 chr1 3191955 255 35M * 0 0 CTTCCATTGAGAATTCTAAGCCATTATGTGGAGGA hhXhhh\hhhhhhehhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_300_179_943 16 chr1 3191975 255 35M * 0 0 CCATTATGTGGAGGAGCTGTTCAGCTCTCTCTAAC h^IRPXZNMBIMZL[Ehh[hdhhQhchhhhhhhhh NM:i:0 -EAS38_1_208_195_556 0 chr1 3191986 255 35M * 0 0 AGGAGCTGTTCAGCTCTCTCTAACCTATTTAGATT hhhhhhhhhhhdhhhhhhhhhPhehhMhhhTH?bh NM:i:0 -EAS38_1_16_568_852 0 chr1 3191993 255 35M * 0 0 GTTCAGCTCTCTCTAACCTATTTAGATTTTATCTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhLhMhh NM:i:0 -EAS38_1_290_6_992 16 chr1 3192030 255 35M * 0 0 ACTTTGTGATAGAATCTCTCTATAGAATGTTCTCT F_UhhHhLhbeKhhhh^hhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_300_29_772 16 chr1 3192030 255 35M * 0 0 TCTTTGTGATAGAATCTCTCTATAGAATGTTCTCT Ahh`Vhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_109_466_314 0 chr1 3192031 255 35M * 0 0 CTTTGTGATAGAATCTCTCTATAGAATGTTCTCTC hhhhhhhhhhhfhhhhhhhhKhhGLXhRhhPhLhS NM:i:0 -EAS38_1_112_657_773 0 chr1 3192037 255 35M * 0 0 GATAGAATCTCTCTATAGAATGTTCTCTCCACCCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh]BG NM:i:2 -EAS38_1_137_971_213 16 chr1 3192048 255 35M * 0 0 TATATAGAATGTTCTCTCAACCACCTCCTGCTAGT C@BHTcZhaFFRSB\hVT@Oehhhhhhhhhhhhhh NM:i:2 -EAS38_1_185_636_515 16 chr1 3192048 255 35M * 0 0 TCTATAGAATGATCTCTCAACCACCTCCTGCTAGT F@J\Jd]Q\ABBAcA[Mhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_44_970_650 0 chr1 3192058 255 35M * 0 0 GTTCTCTCCACCACCCCCTGCTAGTCATACCAAAC hhhhhhhhhhhhhhThMhhhac\h[e_WRGfUIMH NM:i:1 -EAS38_1_92_965_745 0 chr1 3192064 255 35M * 0 0 TCCACCACCTCCTGCTAGTCATACCAAACCCACCC hhhhhhhhhhhhhhhhhhhhhhhJh_hhPIV_X?G NM:i:0 -EAS38_1_261_922_44 0 chr1 3192119 255 35M * 0 0 ACTTCAGTTTTTCTTTATAAAACTTAATCAAAACC hhhh_hhfhhhhhhEh_hTTY]hh@aJhOFMTOLM NM:i:2 -EAS38_1_123_430_987 16 chr1 3192133 255 35M * 0 0 GTATAAAACTGAATCAAAACCGATGTTTATTTTTA GZhdhhh]hhdhhdhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_234_381_448 0 chr1 3192142 255 35M * 0 0 TGAATCAAAACCGATGTTTATTTTTATGATAAAAA hhBhhh]hhhhhhhhhhhhFhhhhhThB_hQ]O@Y NM:i:0 -EAS38_1_46_449_600 0 chr1 3192148 255 35M * 0 0 AAAACCGATGTTTATNTTTATGATAAAAAGGATAT hhhhhhhahhhhhhh;hhhhhhfhThNh^OGWh]h NM:i:1 -EAS38_1_239_737_373 0 chr1 3192153 255 35M * 0 0 CGATGTTTATTTTTATTATAAAAAGGATATACTTT hhhhhhhhhhhhhhdhK[hhhRW\JMPhbhNhhhh NM:i:1 -EAS38_1_24_496_314 0 chr1 3192169 255 35M * 0 0 GATAAAAAGGATATACTTTTGTATTTTGTTGTAGA hhhhhhhhhhhhhhhhhhhhDhLhhhhHM[O]EA? NM:i:2 -EAS38_1_150_229_75 16 chr1 3192202 255 35M * 0 0 GAAAAAATATTGGTTTAAGAAGGAGATAAAAAGTC hhhhhhhJhA]hhSPARhhhhhhhhhbhhhhhhhh NM:i:1 -EAS38_1_170_110_874 16 chr1 3192248 255 35M * 0 0 AATTACCTTTTACCCACTTACTGTTCTTACATGAC hhhhXhh]hQhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_142_857_213 0 chr1 3192280 255 35M * 0 0 GACCTGACTATCCTAACAAACTCTATTCTAGCACT hhhhhhhhhhhhhhh\hQh_hhhhYhhhhRB]Wbh NM:i:0 -EAS38_1_7_223_584 0 chr1 3192314 255 35M * 0 0 TGTAGATATTTTTGAGGAGTCACATACTTTTCTAT hhhhhhhhhhhhhghhK^YhhhhJhhDhhhhhhMh NM:i:1 -EAS38_1_95_195_644 16 chr1 3192330 255 35M * 0 0 GAGTCACATAATTTTCTATGCTACAGTCATGCTTC hhhbPhZhhhhOhh`hhhYhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_219_903_777 0 chr1 3192346 255 35M * 0 0 TATGCTACAGTCATGATTCAGAAAGTCTAATGTCG hhhhhhhhhhhhhhhBhhhhhhhhhghh\hhhhJ[ NM:i:1 -EAS38_1_108_439_554 16 chr1 3192349 255 35M * 0 0 GCTACAGTCATGCTTCAGAAAGTCTAATGTCGTGA aThhhhhehhdhhXhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_239_516_540 0 chr1 3192442 255 35M * 0 0 TAATTTTAGAGAATCAGAGGAGATTATATTGTGTG hhhhhhhhhhhhhhhhhhhhNhLhhThhhheOfhW NM:i:1 -EAS38_1_196_124_875 16 chr1 3192460 255 35M * 0 0 GGAGATTATATTGGGTGTCAATACTGTAAGTATTC ?N[Mhh_hWhXh[LVhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_222_834_314 16 chr1 3192460 255 35M * 0 0 GGAGATTAGATTGGGTGTCGATACTGTAAGTATTC WDXGRJOR?hCMfKhR]OAIhPXZRh^hhhhhhSh NM:i:2 -EAS38_1_230_638_588 0 chr1 3192551 255 35M * 0 0 TATTTGAAGAGTATGGAATTTATTTTGTAAATGAA hhhhhhhhhhhhhhhhhhhhhWhhhhhh\`hhhG` NM:i:0 -EAS38_1_264_255_706 0 chr1 3192603 255 35M * 0 0 AGTACTGAATGGAGCCACATCATTCACATATTTCC hhhhhhhhhhhhhhhhhhhhhghhbhhdhfhhhdP NM:i:0 -EAS38_1_105_766_448 16 chr1 3192724 255 35M * 0 0 TTAGTTTAGTCATTTAGGCAAGGAAATAGACATTG Ghhhhhhhhhhhghhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_281_8_752 0 chr1 3192785 255 35M * 0 0 GCTCAGGTTGTTTTTCCTACCATCTCTCCACATTT hhhEhhhhhhhhhhhN\hh@MOhHU>WDGHW?WTd NM:i:1 -EAS38_1_273_517_672 16 chr1 3192933 255 35M * 0 0 ATAATATGGAGATGAATCAGCTCAAGAGTTCTGAG hhhhghCfdhhhhhhhhhhhhahhhhhhhhhhhhh NM:i:0 -EAS38_1_194_915_453 16 chr1 3192959 255 35M * 0 0 AGTCCTGAGCAGAAACACCATTCCACATTCTTCTG hbIGI_hhhOhhhhhfV\hhhdhhhhhhQhhhhhh NM:i:1 -EAS38_1_270_767_516 16 chr1 3193008 255 35M * 0 0 TGTTAGAAATGGTATAAAATCCCAGTTAAACCATT ThUchhhhhfhJhhhhhhhDOhchhhhhhhhhhhh NM:i:1 -EAS38_1_311_398_506 16 chr1 3193008 255 35M * 0 0 TGTTAGAAATGGTATAAAAACCCAGTTAAACCATT OWRbhhhhhUhZhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_77_151_681 16 chr1 3193008 255 35M * 0 0 TGTTAGAAATGGTATAAAAACCCAGTTAAACCATT WCP`hhhhhRhO\hhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_41_603 16 chr1 3193471 255 35M * 0 0 CACATTCCTTATAACACACTGTGAGGTAGGTGAAG ^bZV`R]hh_hOhhh`hhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_124_634_862 16 chr1 3193821 255 35M * 0 0 TTTCTGGGTATGATTGCTGTTAGCCTTTCTGTTTT h^HhhhDBhhhhhhhdhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_101_162_624 0 chr1 3194186 255 35M * 0 0 TTGCACTGTGTTTAGAAATCCCTCAAAAGGTTTGC hhhhhhhhhhhhhhhhhhhhhhhhW[hPfeUhhVY NM:i:0 -EAS38_1_235_609_726 0 chr1 3194200 255 35M * 0 0 GACATCCCTCAAAAGGTTTGCATAGCCAAATGCCT QJH]I]TaV[_X^\QIERLJHEG?H>JFFD@BCC? NM:i:1 -EAS38_1_162_13_894 16 chr1 3194295 255 35M * 0 0 GGGAATTGTTCACACAATTTGTGTGTTTTTCTGTC ?HCMeVTN?Sh[hRhhhhZhbhhhhhhhhhhhhhh NM:i:2 -EAS38_1_201_123_722 0 chr1 3194814 255 35M * 0 0 AACCATTATGTAAAGTATACTTTATAAATGTTTAA hhhhhhhhhhhhhhhhhhhhhhhhh]hhhhhhh\M NM:i:0 -EAS38_1_251_938_580 16 chr1 3195076 255 35M * 0 0 TATTTATCTTTGTACAACAAAGAGACTCTTAGCAG dYGWNFSQhWVPhhGhh`hhhehhhhhhhhhhhhh NM:i:1 -EAS38_1_8_777_292 16 chr1 3195076 255 35M * 0 0 TATTTATCTTTGTACAAAAAAGAGACTCTTAGCAG JQFAH@BLJGRNEhQhhDhhhfhhhh]]hhhhhhh NM:i:2 -EAS38_1_212_466_584 0 chr1 3195258 255 35M * 0 0 GCTATCCCAAAACCATATGTGCTGCTTGTATGAAC hhhhhhhhhghhhhfhhhh]hZhhhhhbhfhOD>M NM:i:1 -EAS38_1_137_805_954 0 chr1 3195451 255 35M * 0 0 GGAAAAGTCAGAACTTTGGGGTGATCAAACGTCTA hhhhhhhhhhhhhhhhhhhhhghhhCPhPIhMJYD NM:i:1 -EAS38_1_63_741_75 0 chr1 3195451 255 35M * 0 0 GGAAAAGTCAGAACTTTTGTGTGATCAACCGTCTA hhhhhhhhhhhVhhhhhFEJFhOHhSVRG@N_D_Q NM:i:2 -EAS38_1_146_999_561 16 chr1 3197082 255 35M * 0 0 GGAATCCATTGGCTGATCTTTTAAGAAGTAGTTCT SahhhRhhhXh\hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_295_1_556 16 chr1 3197082 255 35M * 0 0 GGAATCCATTGGCTGATCTTTTAAGAAGTAGTTCT bdhhMFhhgehhhhhhbIhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_133_696_323 16 chr1 3197239 255 35M * 0 0 CCTGCAATGAACCAACTGCTCCTTTCCCATTAATT ??FCJ??@DSCECKJ]JbhLXbXh\hUhhh^hhhf NM:i:2 -EAS38_1_184_992_275 0 chr1 3197347 255 35M * 0 0 GATTAATTAACTGCAATTCATCTCCAGTAAAATTT hhhhhhhhhhhhhhhShhhhhhhhh^`WILU_hhh NM:i:0 -EAS38_1_261_311_801 16 chr1 3197969 255 35M * 0 0 ATAAAAATTGAACAAAAAAAAGAAATGGGTTTCTT hchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_199_494_378 16 chr1 3198110 255 35M * 0 0 GCCATGCCAGAATGCTAGGACAATAGTTAAATTAA ?Dhh\hKPhhhhUhZhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_186_296_431 16 chr1 3199201 255 35M * 0 0 GTTAGCACTTTGTCACATATTCCACTGCTTTTAAA S>MhSKKDFJVhGHhPh]hdWhhhhhhhhhhhhhh NM:i:0 -EAS38_1_32_939_527 0 chr1 3199927 255 35M * 0 0 TTTCCCTAGTTTAGCTGTGATGCCTTTGACAAGCT hhhhhhhhhhhhhhhhhhhhhhghhhhVFYNVGYh NM:i:0 -EAS38_1_174_562_297 0 chr1 3200023 255 35M * 0 0 AAGGGAGATAGATCCCAGAGGTAAGGATCTTCAAG hbhRL^hCXHWNdNTMIH?IJG?DDE?C>KFH@B? NM:i:2 -EAS38_1_80_292_639 0 chr1 3200090 255 35M * 0 0 GATACTCTTAACTGATATGGGAATCAAGCCACACG hhhhhhhhhhhhhhhhhhhYcEhhh^d^TOhh]K? NM:i:1 -EAS38_1_146_971_305 16 chr1 3200157 255 35M * 0 0 ACGTTCAGCTTAGATTGTTTCTGAGTTTGTGTCCT RMOUAJ[YRHYh\hZhhhW[hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_103_633_813 16 chr1 3200318 255 35M * 0 0 TATAATATAATAAGGATCTAACATGTTGCTTTCTC YghhhNhUhh^hhThh]hhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_268_250_819 16 chr1 3200318 255 35M * 0 0 TATAATATAATAAGGATCTAACATGTTGCTTTCTC hhhhhVhhhhhhhgVhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_195_376_807 16 chr1 3200796 255 35M * 0 0 TCAGGGAGGGGGACTAAAGTGAGGTCACCTATTCC Ihe[Ihh]XahhhhhhhhhhhhFhhhhhhhhhhhh NM:i:1 -EAS38_1_92_137_414 0 chr1 3200902 0 35M * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTCTCTATTTTCC hhhhhhhhhhhhhhhhhhhhhhdhCA@hJ@IK@AE NM:i:2 -EAS38_1_142_636_259 0 chr1 3200903 0 35M * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTCCTATTTTCTA hhhhhhhhhhhhhhhhhhhhhhM?EM@>FLICF@@ NM:i:2 -EAS38_1_72_206_749 0 chr1 3200905 0 35M * 0 0 TTTTTTTTTTTTTTTTTTTTTTGATACTTTCCAAA hhhhhhhhhhhhhhhhhhhhhhBAN@UOE@YEE=@ NM:i:2 -EAS38_1_111_883_143 16 chr1 3201070 255 35M * 0 0 AAAGACAGTTGGAACTATTTTTAAAAGGCGCTTTA hhhhhQhhH`hchhfhhh\ghhhhhhhhhhhhhhh NM:i:0 -EAS38_1_255_841_137 0 chr1 3201133 255 35M * 0 0 CAGGCATCTCATCCAAGCTTTATATATAAATAGTC hhhhh\hhhhdhahDPDhhhhKhSh`LFPEePCYI NM:i:1 -EAS38_1_25_534_590 0 chr1 3201133 255 35M * 0 0 CAGGCATCTCATCCAAGCTTTATATAGAAATAGTC hhhhhUhhhhhh`hVYhYhchMgO^LWKGJHFDNE NM:i:0 -EAS38_1_11_826_739 0 chr1 3201151 255 35M * 0 0 CTAATATAGAAATAGTCGTGGCTAATGGCAAAGAT hhBhhhhhhhhhhhhhhhLhhR]`]TY^@DNPQ@D NM:i:2 -EAS38_1_200_667_750 0 chr1 3201166 255 35M * 0 0 TCGTGGCTAATGGCAAAGATATGTGATGAATGCAA hhhhhhhhhhhhhLRhIhbQ]fZYULURBNRG?EP NM:i:0 -EAS38_1_148_510_997 0 chr1 3201180 255 35M * 0 0 AAAGATATGTGATGAATGCAAGGGAGCATATATTT hhhhhhhhhhhehhhhhhZhMhhZD`FOXSV_SPZ NM:i:0 -EAS38_1_221_65_299 16 chr1 3201185 255 35M * 0 0 TATGTGATGAATGAAAGGGAGAATATATTTAGTCT BhG[Egh]hhhLhAhhhhhhhPhbhUhTWMhhSVh NM:i:2 -EAS38_1_149_164_972 0 chr1 3201186 255 35M * 0 0 ATGTGATGAATGCAAGGGAGGATATATTTAGTGTA hhhhhhhhhhhhNhhhhhdhCWh_MhhWOVhVBhU NM:i:2 -EAS38_1_269_935_919 16 chr1 3201203 255 35M * 0 0 AAACATATATTTAGTCTAGAAAGTAGTTCATTAGA FWQhh[hbhhbhhQXhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_289_238_636 0 chr1 3201226 255 35M * 0 0 TAGTTCATTAGAAAAAATTCACAGGATTCTTGTCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_125_517_695 16 chr1 3201271 255 35M * 0 0 TCAGAATTTGTTTCCACTCAGTAGCATCCAATGCA hJhHhhhWPehh\hhhhhchhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_22_489_754 16 chr1 3201281 255 35M * 0 0 TTTCCACTCGGTAGCATCCAATGCATTTGAAAGTG VNChUNhM\fDhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_122_450_662 16 chr1 3201346 255 35M * 0 0 TACACGTTTTCCTTGACTTAAGCCACGTGTTCAAT \PhJh`h[hKhhhhh`hhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_157_676_368 16 chr1 3201388 255 35M * 0 0 GAAGTAACATAAACTATTCAATTAGGCCACTTACA ghhYehhhhThhhhhh[Yhhh]hhhhhhhhhhhhh NM:i:0 -EAS38_1_4_358_468 16 chr1 3201390 255 35M * 0 0 AGTAAAAGAAACTATTCAATTAGGCCACTTACAAG hNDhhAhBhhhhWhMKdhhKbhhhhhhhhhhhhhh NM:i:2 -EAS38_1_15_825_658 16 chr1 3201447 255 35M * 0 0 AGTTCAGTCAAATCATGGAGCAAGGAATTCCATGT ]BZOJhZ`hhhhhhhhhhhhhhh]hhhhhhhhhhh NM:i:0 -EAS38_1_222_809_300 0 chr1 3201569 255 35M * 0 0 CAAAAAGTCATGGAAGTTTAAATTATCCCATGCAT hhhhh]hhhhhhS\c>hhhYhPhhhhhhhUhPhWh NM:i:1 -EAS38_1_116_429_381 16 chr1 3201665 255 35M * 0 0 TGTGTGTTTATTGAGAGTATGTGAGAAGATACCTG PhhhLhhchhh`hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_156_372_572 16 chr1 3201665 255 35M * 0 0 TGTGTGTTTATTGAGAGTATGTGAGAAGATACCTG hhhhhhhEhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_79_182_652 16 chr1 3201849 255 35M * 0 0 TACAAAAAGCTATCATATAACAATCCATCTATCAT IAYhhhhhbhXhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_186_626_713 16 chr1 3202147 255 35M * 0 0 CATTTATCAATCAATCTAATCTAACTTATCTATCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_16_258_505 16 chr1 3203603 255 35M * 0 0 TTCCAGCTGGGAGGGTGAGTCTTCAGAGTTCATCA ?AIDSAPEhhhhhhhhhhhhhhfhhhhhhhhhhhh NM:i:1 -EAS38_1_197_118_218 16 chr1 3204368 255 35M * 0 0 GGTGAGGTAGGCTGATGGATTTGTAGACTGGATTC VPGgUMhAXhh@GchGdhhOXLhfhhfhhhhhhhh NM:i:1 -EAS38_1_141_404_857 0 chr1 3204755 255 35M * 0 0 TTTTTAATGGCATACACATTGCATCTGTATGCTCT hhhhhhhhhhhhhhhhhhhhhhhh_hdhhhhIhEh NM:i:0 -EAS38_1_125_490_276 16 chr1 3204799 255 35M * 0 0 AATTGTGACCCAAAGTCTCTAGTAGACACATCATT h\]@VFQ@QPAhhhhGhhI_hhhhhhhhhhhhhhh NM:i:1 -EAS38_1_171_771_691 16 chr1 3205563 255 35M * 0 0 TATGGGTATTTTGCCTGCATATATGTCTATGCACC ]hOhKfhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_284_911_331 0 chr1 3210849 255 35M * 0 0 CTCTGTATTCTCTTCTTCTATTCACATCTCTACAA hhhhhhhhhhhhhhhhhhhbhhhhhbhhhhhFhhG NM:i:0 -EAS38_1_101_808_273 0 chr1 3212214 255 35M * 0 0 AGATGGTTGGTTGTAGTTTGACCCTTGAAGTTTAT hhhhhhhhhhhhhh^XhhhhJ]hhhhHLHR\hhKh NM:i:0 -EAS38_1_161_452_506 16 chr1 3212258 255 35M * 0 0 CCGGAGTTCCCGGTGTGTTGCTACTGGCATGGTGG HJ>@_ZEEc]R[hWhfhhThhhhh]hhhhhhhhhh NM:i:2 -EAS38_1_246_740_824 0 chr1 3212368 255 35M * 0 0 TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTG hhhhhhhhhhhhhh]hh[OhhhhhhOZZhMh_`Lh NM:i:0 -EAS38_1_328_863_236 0 chr1 3212368 255 35M * 0 0 TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTG hhhhhhhhhhhfhhhh[hhRIhahh`ghh[hhhhW NM:i:0 -EAS38_1_71_507_507 0 chr1 3212368 255 35M * 0 0 TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTT hhhhhhhhhhhhhhhhhhhg]LQhhhOhhShhHc? NM:i:1 -EAS38_1_156_360_657 0 chr1 3212393 255 35M * 0 0 AACTATTGTGAGTCTAGAGCTTCTCCAAATGCCTC hhhhhhhhhhhhhhhhhhhhhhXhVhChhhhhdbh NM:i:0 -EAS38_1_327_554_773 0 chr1 3212413 255 35M * 0 0 TTCTCCAAATGCCTCTTGTTACAAACATGCATATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_316_581_646 0 chr1 3213096 255 35M * 0 0 TTTTAATCTTATCTCCTCACTGCCTCCCTCTTAGG hhhhhhhhhhhhhhhhhgdhh_dRhhG^hfhYKJF NM:i:0 -EAS38_1_90_952_487 16 chr1 3214147 255 35M * 0 0 TCCCTGGATGAAGGAGGTTCAATTGGATTGAATTA DCQNQXOaeUhhUThcNhh`hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_191_680_14 0 chr1 3225128 255 35M * 0 0 ATATTTTCCAACAGGTAAGAAGTATGCAAGCTCCA hhMhhhhhhchhhJJUIhEOPPDHhE[T@@IDD?A NM:i:1 -EAS38_1_138_982_940 0 chr1 3233636 0 35M * 0 0 TACCTCTCGCCATCTGTCAATCTCTGGAGTCAGTT hJhhhhh^hahYhhhhJBhhhLhJhhVaXJAB_BL NM:i:2 -EAS38_1_158_9_677 16 chr1 3242626 255 35M * 0 0 AAAATAAATAAGAGAGAGGAGCCTTACTGTGCTTG hhhhPhhh^hhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_253_923_934 16 chr1 3242672 255 35M * 0 0 AACATTGTCTTTCTGCCAGGTTTCTGTGGAGCATA CIOHFhHOhO@LhTLhhhhKhh[hhhhhchXhhhh NM:i:1 -EAS38_1_5_178_743 16 chr1 3242672 255 35M * 0 0 AACATTTTCTGTCTGCCAGGTTTCTGTGGAGCATA QEDJM@C?]OOKhKRh^fUOR^Nhchehhhhhhhh NM:i:1 -EAS38_1_198_267_632 0 chr1 3242722 255 35M * 0 0 CGACACACCCCTTCTGCATACTGGCCTGTCACTGA hhhhhhhhhhhhhhhhhhhhhhhhhQhJT?ISHLA NM:i:2 -EAS38_1_19_755_678 0 chr1 3242782 255 35M * 0 0 GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACA hhhhhhhhhhVRhUZghFgEhYhLQROfI?OCIGE NM:i:0 -EAS38_1_243_907_786 0 chr1 3242782 255 35M * 0 0 GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACC hhhhhVhhNhhhhUahhWhJWhZOKhO\MPTGN?> NM:i:1 -EAS38_1_278_440_897 0 chr1 3242782 255 35M * 0 0 GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACA hhhhhhhhhhhhhehh_YhhhhhDhhDhNMEXANO NM:i:0 -EAS38_1_173_938_288 0 chr1 3242827 255 35M * 0 0 GCACTGGGCCTTTCTTCTGTGTCTGAGCTATTTCA hhhhhhhhhhhhhhhhhhhhhINhg?e\hVhhHhC NM:i:1 -EAS38_1_157_930_237 16 chr1 3242836 255 35M * 0 0 CTTTCTTCTGTGTCTGAGCTATTGCATTATATCTT PMUNNFZYHhFaVhUhhh^Shhhhhhhhhhhhhhh NM:i:0 -EAS38_1_266_172_602 16 chr1 3242889 255 35M * 0 0 TTCTAATCACTGATGCATTAATTAAAAGAATCATA XJLLBhchhNehhhhYhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_149_88_885 0 chr1 3243019 255 35M * 0 0 TTCTCTATATTCCTAGAGTTGTGTGGAAACTAATA hhhhhhhhhhhhhhhhhhhhhhhhhadLhObALgf NM:i:1 -EAS38_1_62_896_441 16 chr1 3243045 255 35M * 0 0 AAAATCATATGATACCATTTATGCTTGCCAGAACG hh_CZJh[hhhhhhhhhhXhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_12_294_576 16 chr1 3243367 255 35M * 0 0 AGAATAATAAATTATCCTATAAGCTGGGCTTGATG _hhhQhhahhhNNhDh[\hNhhhhWhhhhdhh>hh NM:i:1 -EAS38_1_2_533_514 16 chr1 3243367 255 35M * 0 0 AGAATAATAAATGATCCTATAAGCGGGGCTTGGTG hahhPh\ChZhhXhPhBNRZKhhh\hhhhhhhhhh NM:i:2 -EAS38_1_305_285_786 16 chr1 3243648 255 35M * 0 0 CAAAATATTGTTAGATTTGTTTGAGAGATTTGTTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_67_916_874 0 chr1 3243986 255 35M * 0 0 GATTATAATACCCTCGTTGAGATTTGTTTGTTATT hhhhhhhhhhhhhhhhhhh\hZhhhhhhhh^hfhh NM:i:0 -EAS38_1_123_564_954 16 chr1 3254091 255 35M * 0 0 GGAGTGACTGGCCTCCCCTCTTCTTTATAAAGCGT CDM?P<Mh@=FhhThhhhhhhdhhhhhhhhhhhhh NM:i:0 -EAS38_1_55_599_652 16 chr1 3254559 3 35M * 0 0 GTGTCAAGCTCTTGCAGAGCCTCTCAGGAGACAGC @AC=EhKFhAZMGW^Zhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_143_932_612 16 chr1 3256967 255 35M * 0 0 CCTAGAGACAAGGGCTGAAGCAGGCCAGTTATTTT JEEKSVIQNMSdN_h[dhhhhhehhhhhhhhhhhh NM:i:0 -EAS38_1_212_69_386 16 chr1 3256977 255 35M * 0 0 AGGGCTGAAGCAGGCCAGTTATTTTAGGAGAGCAG ROJUGJhhhhCUh]RJhhhhhh[hhhhhhhhhhhh NM:i:0 -EAS38_1_256_785_413 16 chr1 3256977 255 35M * 0 0 AGGGATGAAGCAGGCCAGTTATTTTAGGAGAGCAG U`MUAAebhaM[WbHHhhNhhfhh`hhhhhhhhhh NM:i:1 -EAS38_1_105_481_788 16 chr1 3268974 255 35M * 0 0 GCCCGAAAAAATCTGCTTTATATTGGCCACATACG DhGaahhhhhhhhhchhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_16_282_422 16 chr1 3273908 255 35M * 0 0 CAAATGGGACACCATTGTCTACATTTATGGTAAGT AOBNCFVEVCWFM_PCdOFGhRhXLahhhhehhhh NM:i:2 -EAS38_1_283_187_798 0 chr1 3274213 255 35M * 0 0 TTAGTGAGCCTGAACCAACCAACCAATGAATATAC hhhhhhhhhhhhhhVhhhPhhhLhhXhhZOhhhhY NM:i:0 -EAS38_1_329_178_196 0 chr1 3274786 255 35M * 0 0 GGAAGGCAGATCAGTATAGGTTACCAATAAAATTG hhhhhhhdhhhhhhhchh_@ERhhhEhhCgUWhha NM:i:1 -EAS38_1_300_318_77 16 chr1 3276576 255 35M * 0 0 GAAGAAGAAATATAAGCAGTCCAAGCAGGTTTCAG hhhhMhhhhhhhZKhhghhhARhhhhhhhhhhhhh NM:i:2 -EAS38_1_118_479_935 0 chr1 3276843 255 35M * 0 0 TTTTATCCTCTAGCATGTCAGTCAGGTACAGGGAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh?O NM:i:0 -EAS38_1_41_971_61 0 chr1 3277038 255 35M * 0 0 TGATAAAACAAAAATGTAGACCTTTTAACAGACCC hhhhh\`Z^NhV[]hO[ODJJHW`TbIE?GDBDE> NM:i:2 -EAS38_1_183_306_813 16 chr1 3277183 255 35M * 0 0 CCCATATTATCTTGGAGGTAGGATGATAGTGGTTT ehhhhhdhVNhZhhhhh[hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_288_251_841 16 chr1 3277184 255 35M * 0 0 CCATATTATCTTGGAGGTAGGATGATAGTGGTTTC U[h^hNhh]hehhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_40_672_870 16 chr1 3277184 255 35M * 0 0 CCATATTATCTTGGAGGTAGGATGATAGTGGTTTC Uhh]hMhhNhhgQ[h_Nhh_fhhhhhhhhhhhhhh NM:i:0 -EAS38_1_325_652_299 0 chr1 3278086 255 35M * 0 0 TTTCTGTTTTAAATTAATTACCTTTATTCCATGTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPhh NM:i:0 -EAS38_1_188_971_708 16 chr1 3278146 255 35M * 0 0 TCTTCCTCTTCGTTAGTTTGAATTTATTTCGTTCT P_QOhhWhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_295_186_302 16 chr1 3278229 255 35M * 0 0 CTTGTTGAGTGTTCTGCATGGAATAGAGGCATTTT CDG@ENd`[KQF@J?TEOBXYXaR\`V`hRhLhPh NM:i:1 -EAS38_1_314_975_553 16 chr1 3279235 255 35M * 0 0 ATTTGATAGGGACAGAATAAAAAGTGATAATTCTG hNJaVhahQDLhhhhhhRhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_220_655_831 16 chr1 3279355 255 35M * 0 0 AGAAAATACTTGCTTATTGCTGGAACACGTGACAT hShchXMRhK]Rhahhhhhhh^QhhhShhhhhhhh NM:i:0 -EAS38_1_267_333_743 16 chr1 3280494 255 35M * 0 0 CGTGATGCATCACCAGGGTATCCATGTATAGACTA FQNFhGVHhPfehVehKhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_165_158_507 16 chr1 3280679 255 35M * 0 0 GGGAACGTTATTTGGTGTCTATTGTGATTATTTCC hhbU`ZhhhhdX`hhYhhNhhhghhhhhhhhhchh NM:i:0 -EAS38_1_218_851_888 16 chr1 3280707 255 35M * 0 0 TATTTCCTAAATGCCCCTCNGTTTTTGTATGTTCT MPDILT_PI[`OLhc]hCh;hhh\VhKhhhdhhhh NM:i:1 -EAS38_1_144_853_896 16 chr1 3282690 255 35M * 0 0 GTATCACAAAGGCTCTTTTAACTCAAGAGTTTCTG MhhhhhhhhhXhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_232_504_623 0 chr1 3290489 255 35M * 0 0 TCCCTACATCTCTCCATGTTACTGTAAATGATAGT hhhhhhhhhhhhhhhhhhhhhhhh\Oee_PK`OV@ NM:i:1 -EAS38_1_238_304_582 0 chr1 3290527 255 35M * 0 0 TCATTCTTATTTAGCACTGAAATAATAACCGCCTA hhhhhhhhhhhhhMhhhhhhK]hRehha\DCGWhK NM:i:0 -EAS38_1_125_161_809 0 chr1 3290844 255 35M * 0 0 GCTACTGGGTGGTCTGCATAGCTTAGTGATACACT hh`bhhhhSYhhTE[QH@RFT>RJEVDCFLMCCBI NM:i:0 -EAS38_1_155_358_888 16 chr1 3290932 255 35M * 0 0 GTGGAATTGTAGGGGTGAAAAAAGACATTTCTGAG ghhRhhhhfhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_157_904_203 0 chr1 3291089 255 35M * 0 0 ACAGCCCTGGATGATTTTTGAATGGGAATAATCCC hhhhhhhhhhLhh]hhhhhM^hhNI_@hhQ^hUMW NM:i:0 -EAS38_1_180_814_759 16 chr1 3291152 255 35M * 0 0 AACACCTAGTCATTGTTGGTGGCACTGTCTGTAAG NNWAgXVhhVh_RYhhSeYJh_hhhhhhhhhhhhh NM:i:0 -EAS38_1_170_391_724 16 chr1 3291373 255 35M * 0 0 AAGTAAACCCTTTCTCCTGTAAGTTTCCTTTGGTC _hhWhgQhhhUbchhhhhhhhhhhhhhhhhhhXhh NM:i:0 -EAS38_1_315_950_278 16 chr1 3291611 255 35M * 0 0 TCCATGCCCAGTTTCAGGTGGGAAAACAACTAAGT QAchLb^ChhhhhYhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_330_167_763 16 chr1 3299360 255 35M * 0 0 AAAAATCTTTTTTCTTCTTCTTTCTTTCTTTCTAT hhhhhhhhLh__hhhhhhhhhhhhhhhhhhhhh=h NM:i:1 -EAS38_1_7_984_851 16 chr1 3299360 255 35M * 0 0 AAAAATCTTTTTTCTTCTTNTTTCTTTCTTTCTTT NLPMNN`LEdULNhVhhhh;Phhhhhhhhhhhhhh NM:i:1 -EAS38_1_133_814_850 0 chr1 3299443 1 35M * 0 0 TTTGAGACAGGGTTTCTTTATATAGCCATGGTTGG hhhhhhhhhhhhEhhChhhhhhhhhOTUhhf?SSG NM:i:2 -EAS38_1_303_411_338 16 chr1 3299602 255 35M * 0 0 GAGATGAATACTGGGTAGAAAATAAAAAAATTTAC ThYhFHhhI_JXh_XhhhhhhhYhhhhhhhhhhhh NM:i:0 diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out1.txt --- a/test-data/cuffdiff_out1.txt +++ /dev/null @@ -1,91 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -TCONS_00000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000011 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000014 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000015 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000016 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000017 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000018 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000019 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no -TCONS_00000021 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no -TCONS_00000023 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000024 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000025 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TCONS_00000026 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 3.99739e+06 1.82908e+06 -1.12794 0.781831 0.434314 1 no -TCONS_00000027 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no -TCONS_00000028 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000029 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000030 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000031 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000033 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000034 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000037 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000038 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000039 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000040 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000041 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000042 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000043 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000044 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000045 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000046 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000047 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000048 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000049 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000050 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000051 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000052 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000053 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no -TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no -TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no -TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no -TCONS_00000058 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000059 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000060 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000062 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000063 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000065 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TCONS_00000066 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.150149 no -TCONS_00000067 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000068 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no -TCONS_00000069 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 1.36901e+06 0 0 0 1 1 no -TCONS_00000070 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000071 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000072 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000073 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000074 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000075 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000076 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no -TCONS_00000077 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000078 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000079 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000080 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000081 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000082 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000083 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000084 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no -TCONS_00000085 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no -TCONS_00000086 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000087 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000088 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000089 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000090 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000091 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no -TCONS_00000092 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000093 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no -TCONS_00000094 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TCONS_00000095 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000096 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000097 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000098 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000099 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000100 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out10.txt --- a/test-data/cuffdiff_out10.txt +++ /dev/null @@ -1,88 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant -XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 LOWDATA 0 0 0 0 0 1 no diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out11.txt --- a/test-data/cuffdiff_out11.txt +++ /dev/null @@ -1,1 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out2.txt --- a/test-data/cuffdiff_out2.txt +++ /dev/null @@ -1,88 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.16621 no -XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no -XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no -XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no -XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no -XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.16621 no -XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.157299 no -XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.16621 no -XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no -XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no -XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.157299 no -XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.157299 no -XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.157299 no -XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no -XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.3664e+06 1.82908e+06 -1.55284 0.839459 0.401212 0.401212 no -XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no -XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no -XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.16621 no -XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.16621 no -XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no -XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no -XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no -XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no -XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.157299 no -XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out3.txt --- a/test-data/cuffdiff_out3.txt +++ /dev/null @@ -1,91 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS11 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no -TSS12 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no -TSS15 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no -TSS16 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS17 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS18 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS19 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS20 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TSS21 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS22 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS23 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS24 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS25 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS26 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS27 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS28 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS29 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS30 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no -TSS32 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS33 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS34 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS35 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no -TSS37 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TSS38 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS39 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.150149 no -TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS40 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS41 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS42 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TSS43 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no -TSS44 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 3.99739e+06 1.82908e+06 -1.12794 0.489836 0.62425 1 no -TSS45 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 1.36901e+06 0 0 0 1 1 no -TSS46 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS47 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS48 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no -TSS49 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS50 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS51 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS52 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS53 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS54 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS55 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS56 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS57 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no -TSS59 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS60 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS61 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS62 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS63 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS64 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS65 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS66 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS67 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS68 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no -TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no -TSS70 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no -TSS71 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS72 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS73 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS74 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS75 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS76 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS77 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS78 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS79 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS80 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no -TSS81 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS82 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no -TSS83 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS84 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TSS85 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS86 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS87 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS88 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS89 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS90 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS91 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS92 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS93 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS94 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS95 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS96 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS97 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS98 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS99 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out4.txt --- a/test-data/cuffdiff_out4.txt +++ /dev/null @@ -1,1 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/da46b521540d/ Changeset: da46b521540d User: Dave Bouvier Date: 2013-10-01 19:55:16 Summary: Remove migrated tools from tool_conf.xml.main. Affected #: 1 file diff -r 5019491835c7d196c5545a60aaf2061f629d8f07 -r da46b521540df29f936aa51cd03e75068eff1204 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -289,10 +289,6 @@ <label id="rna_seq" text="RNA-seq" /><tool file="ngs_rna/tophat_wrapper.xml" /><tool file="ngs_rna/tophat2_wrapper.xml" /> - <tool file="ngs_rna/cufflinks_wrapper.xml" /> - <tool file="ngs_rna/cuffcompare_wrapper.xml" /> - <tool file="ngs_rna/cuffmerge_wrapper.xml" /> - <tool file="ngs_rna/cuffdiff_wrapper.xml" /><tool file="ngs_rna/express_wrapper.xml" /><label id="filtering" text="Filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Extend the make_directory action to create the specified directory under the current working directory if it is not prefixed with $INSTALL_DIR.
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56e6257ba73d/ Changeset: 56e6257ba73d User: Dave Bouvier Date: 2013-10-01 17:51:58 Summary: Extend the make_directory action to create the specified directory under the current working directory if it is not prefixed with $INSTALL_DIR. Affected #: 1 file diff -r 1d1084581b6219ee8ae7968c8109c8132e32a915 -r 56e6257ba73d599a86be2e7731134b398bc79ad7 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -272,7 +272,11 @@ with lcd( current_dir ): action_type, action_dict = action_tup if action_type == 'make_directory': - td_common_util.make_directory( full_path=action_dict[ 'full_path' ] ) + if os.path.isabs( action_dict[ 'full_path' ] ): + full_path = action_dict[ 'full_path' ] + else: + full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) + td_common_util.make_directory( full_path=full_path ) elif action_type == 'move_directory_files': td_common_util.move_directory_files( current_dir=current_dir, source_dir=os.path.join( action_dict[ 'source_directory' ] ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: When installing repositories containing tools that have been migrated from the distribution to the tool shed, handle cases where the repository may have been successfully cloned, but is still in a New state.
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d1084581b62/ Changeset: 1d1084581b62 User: Dave Bouvier Date: 2013-10-01 16:59:42 Summary: When installing repositories containing tools that have been migrated from the distribution to the tool shed, handle cases where the repository may have been successfully cloned, but is still in a New state. Affected #: 1 file diff -r 7978a2884aa79c87650eb5aca1f934969f276fc0 -r 1d1084581b6219ee8ae7968c8109c8132e32a915 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -133,7 +133,7 @@ # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision> relative_clone_dir = os.path.join( self.tool_shed, 'repos', owner, name, changeset_revision ) clone_dir = os.path.join( self.tool_path, relative_clone_dir ) - if not self.__isinstalled( clone_dir ): + if not self.__iscloned( clone_dir ): repository_clone_url = os.path.join( self.tool_shed_url, 'repos', owner, name ) relative_install_dir = os.path.join( relative_clone_dir, name ) install_dir = os.path.join( clone_dir, name ) @@ -478,7 +478,15 @@ tool_shed_repository.name, tool_shed_repository.installed_changeset_revision ) clone_dir = os.path.join( self.tool_path, relative_clone_dir ) - if self.__isinstalled( clone_dir ): + cloned_ok = self.__iscloned( clone_dir ) + is_installed = False + # Any of the following states should count as installed in this context. + if tool_shed_repository.status in [ self.app.model.ToolShedRepository.installation_status.INSTALLED, + self.app.model.ToolShedRepository.installation_status.ERROR, + self.app.model.ToolShedRepository.installation_status.UNINSTALLED, + self.app.model.ToolShedRepository.installation_status.DEACTIVATED ]: + is_installed = True + if cloned_ok and is_installed: print "Skipping automatic install of repository '", tool_shed_repository.name, "' because it has already been installed in location ", clone_dir else: repository_clone_url = os.path.join( self.tool_shed_url, 'repos', tool_shed_repository.owner, tool_shed_repository.name ) @@ -489,9 +497,10 @@ tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) - suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) - cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) - if cloned_ok: + if not cloned_ok: + suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) + cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) + if cloned_ok and not is_installed: self.handle_repository_contents( tool_shed_repository=tool_shed_repository, repository_clone_url=repository_clone_url, relative_install_dir=relative_install_dir, @@ -592,7 +601,7 @@ return True return False - def __isinstalled( self, clone_dir ): + def __iscloned( self, clone_dir ): full_path = os.path.abspath( clone_dir ) if os.path.exists( full_path ): for root, dirs, files in os.walk( full_path ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Fill form by name rather than number when uploading files for tool functional tests.
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7978a2884aa7/ Changeset: 7978a2884aa7 User: Dave Bouvier Date: 2013-10-01 16:23:59 Summary: Fill form by name rather than number when uploading files for tool functional tests. Affected #: 1 file diff -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 -r 7978a2884aa79c87650eb5aca1f934969f276fc0 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -191,20 +191,20 @@ self.visit_url( "%s/tool_runner?tool_id=upload1" % self.url ) try: self.refresh_form( "file_type", ftype ) #Refresh, to support composite files - tc.fv("1","dbkey", dbkey) + tc.fv( "tool_form", "dbkey", dbkey ) if metadata: for elem in metadata: - tc.fv( "1", "files_metadata|%s" % elem.get( 'name' ), elem.get( 'value' ) ) + tc.fv( "tool_form", "files_metadata|%s" % elem.get( 'name' ), elem.get( 'value' ) ) if composite_data: for i, composite_file in enumerate( composite_data ): filename = self.get_filename( composite_file.get( 'value' ), shed_tool_id=shed_tool_id ) - tc.formfile( "1", "files_%i|file_data" % i, filename ) - tc.fv( "1", "files_%i|space_to_tab" % i, composite_file.get( 'space_to_tab', False ) ) + tc.formfile( "tool_form", "files_%i|file_data" % i, filename ) + tc.fv( "tool_form", "files_%i|space_to_tab" % i, composite_file.get( 'space_to_tab', False ) ) else: filename = self.get_filename( filename, shed_tool_id=shed_tool_id ) - tc.formfile( "1", "file_data", filename ) - tc.fv( "1", "space_to_tab", space_to_tab ) - tc.submit("runtool_btn") + tc.formfile( "tool_form", "file_data", filename ) + tc.fv( "tool_form", "space_to_tab", space_to_tab ) + tc.submit( "runtool_btn" ) self.home() except AssertionError, err: errmsg = "Uploading file resulted in the following exception. Make sure the file (%s) exists. " % filename Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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