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- 10008 discussions

02 Dec '09
details: http://www.bx.psu.edu/hg/galaxy/rev/6e742ffb16a5
changeset: 3134:6e742ffb16a5
user: jeremy goecks <jeremy.goecks at emory.edu>
date: Tue Dec 01 11:07:20 2009 -0500
description:
Improved loading state for AJAXed grids: when grid is loading, gray out table and prevent further user actions.
diffstat:
templates/grid_base.mako | 16 +++++++++++++++-
1 files changed, 15 insertions(+), 1 deletions(-)
diffs (47 lines):
diff -r e75b55cc9e08 -r 6e742ffb16a5 templates/grid_base.mako
--- a/templates/grid_base.mako Tue Dec 01 09:53:36 2009 -0500
+++ b/templates/grid_base.mako Tue Dec 01 11:07:20 2009 -0500
@@ -601,6 +601,7 @@
// If there's an operation in the args, do POST; otherwise, do GET.
var operation = url_args['operation'];
var method = (operation != null && operation != undefined ? "POST" : "GET" );
+ $('.loading-elt-overlay').show(); // Show overlay to indicate loading and prevent user actions.
$.ajax({
type: method,
url: "${h.url_for()}",
@@ -660,6 +661,9 @@
}
}
+ // Hide loading overlay.
+ $('.loading-elt-overlay').hide();
+
// Show message if there is one.
var message = $.trim( parsed_response_text[2] );
if (message != "")
@@ -711,6 +715,15 @@
.gray-background {
background-color: #DDDDDD;
}
+ .loading-elt-overlay {
+ background-color : white;
+ opacity : 0.5;
+ width : 100%;
+ height : 85%;
+ z-index : 14000;
+ position : absolute;
+ display: none;
+ }
</style>
</%def>
@@ -750,7 +763,8 @@
## Render grid.
<%def name="render_grid_table()">
<form action="${url()}" method="post" onsubmit="return false;">
- <table class="grid">
+ <div class='loading-elt-overlay'></div>
+ <table id='grid-table' class="grid">
<thead id="grid-table-header">
<tr>
<th></th>
1
0

02 Dec '09
details: http://www.bx.psu.edu/hg/galaxy/rev/fe853d8e062d
changeset: 3136:fe853d8e062d
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Tue Dec 01 16:18:25 2009 -0500
description:
Added some error checking to pileup_parser tool so that it exits with a meaningful message if the user tries to do some 6-column work on a 10-column file, or vice versa.
diffstat:
tools/samtools/pileup_interval.py | 16 ++++++++++++++--
1 files changed, 14 insertions(+), 2 deletions(-)
diffs (40 lines):
diff -r eb317734e391 -r fe853d8e062d tools/samtools/pileup_interval.py
--- a/tools/samtools/pileup_interval.py Tue Dec 01 11:49:07 2009 -0500
+++ b/tools/samtools/pileup_interval.py Tue Dec 01 16:18:25 2009 -0500
@@ -1,7 +1,7 @@
#! /usr/bin/python
"""
-Creates a pileup file from a bam file and a reference.
+Condenses pileup format into ranges of bases.
usage: %prog [options]
-i, --input=i: Input pileup file
@@ -18,6 +18,7 @@
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.cookbook import doc_optparse
+import sys
def stop_err( msg ):
sys.stderr.write( msg )
@@ -56,7 +57,18 @@
bases = []
while inLine.strip() != '':
lineParts = inLine.split('\t')
- seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex])
+ try:
+ seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex])
+ except IndexError, ei:
+ if options.format == 'ten':
+ stop_err( 'It appears that you have selected 10 columns while your file has 6. Make sure that the number of columns you specify matches the number in your file.\n' + str( ei ) )
+ else:
+ stop_err( 'There appears to be something wrong with your column index values.\n' + str( ei ) )
+ except ValueError, ev:
+ if options.format == 'six':
+ stop_err( 'It appears that you have selected 6 columns while your file has 10. Make sure that the number of columns you specify matches the number in your file.\n' + str( ev ) )
+ else:
+ stop_err( 'There appears to be something wrong with your column index values.\n' + str( ev ) )
# strout += str(startLoc) + '\n'
# strout += str(bases) + '\n'
# strout += '%s\t%s\t%s\t%s\n' % (seq, loc, base, cov)
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/e75b55cc9e08
changeset: 3133:e75b55cc9e08
user: Enis Afgan <afgane(a)gmail.com>
date: Tue Dec 01 09:53:36 2009 -0500
description:
Merge
diffstat:
lib/galaxy/config.py | 1 +
lib/galaxy/model/__init__.py | 10 +++++
lib/galaxy/model/mapping.py | 13 ++++++
lib/galaxy/model/migrate/versions/0029_user_actions.py | 47 +++++++++++++++++++++++
lib/galaxy/web/controllers/dataset.py | 2 +-
lib/galaxy/web/controllers/history.py | 2 +-
lib/galaxy/web/controllers/tag.py | 24 ++++++++---
lib/galaxy/web/framework/__init__.py | 17 ++++++++
lib/galaxy/web/framework/helpers/grids.py | 13 +++++-
templates/dataset/edit_attributes.mako | 2 +-
templates/history/view.mako | 2 +-
templates/root/history.mako | 2 +-
templates/tagging_common.mako | 8 ++--
universe_wsgi.ini.sample | 3 +
14 files changed, 128 insertions(+), 18 deletions(-)
diffs (335 lines):
diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/config.py
--- a/lib/galaxy/config.py Mon Nov 30 16:47:18 2009 -0500
+++ b/lib/galaxy/config.py Tue Dec 01 09:53:36 2009 -0500
@@ -79,6 +79,7 @@
self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', 'False' ) )
self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) )
self.log_memory_usage = string_as_bool( kwargs.get( 'log_memory_usage', 'False' ) )
+ self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",")
self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "main,test,tair" ).lower().split(",")
diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py Mon Nov 30 16:47:18 2009 -0500
+++ b/lib/galaxy/model/__init__.py Tue Dec 01 09:53:36 2009 -0500
@@ -1441,6 +1441,16 @@
def __init__( self, name=None, value=None ):
self.name = name
self.value = value
+
+class UserAction( object ):
+ def __init__( self, id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None):
+ self.id = id
+ self.create_time = create_time
+ self.user_id = user_id
+ self.session_id = session_id
+ self.action = action
+ self.params = params
+ self.context = context
## ---- Utility methods -------------------------------------------------------
diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py Mon Nov 30 16:47:18 2009 -0500
+++ b/lib/galaxy/model/mapping.py Tue Dec 01 09:53:36 2009 -0500
@@ -743,6 +743,15 @@
Column( "name", Unicode( 255 ), index=True),
Column( "value", Unicode( 1024 ) ) )
+UserAction.table = Table( "user_action", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "create_time", DateTime, default=now ),
+ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
+ Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ),
+ Column( "action", Unicode( 255 ) ),
+ Column( "context", Unicode( 512 ) ),
+ Column( "params", Unicode( 1024 ) ) )
+
# With the tables defined we can define the mappers and setup the
# relationships between the model objects.
@@ -1237,6 +1246,10 @@
assign_mapper( context, UserPreference, UserPreference.table,
properties = {}
)
+
+assign_mapper( context, UserAction, UserAction.table,
+ properties = dict( user=relation( User.mapper ) )
+ )
def db_next_hid( self ):
"""
diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/model/migrate/versions/0029_user_actions.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/model/migrate/versions/0029_user_actions.py Tue Dec 01 09:53:36 2009 -0500
@@ -0,0 +1,47 @@
+"""
+This migration script adds a user actions table to Galaxy.
+"""
+
+from sqlalchemy import *
+from migrate import *
+
+import datetime
+now = datetime.datetime.utcnow
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData( migrate_engine )
+
+def display_migration_details():
+ print ""
+ print "This migration script adds a user actions table to Galaxy."
+ print ""
+
+
+# New table to store user actions.
+UserAction_table = Table( "user_action", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "create_time", DateTime, default=now ),
+ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
+ Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ),
+ Column( "action", Unicode( 255 ) ),
+ Column( "context", Unicode( 512 ) ),
+ Column( "params", Unicode( 1024 ) ) )
+
+def upgrade():
+ display_migration_details()
+ metadata.reflect()
+ try:
+ UserAction_table.create()
+ except Exception, e:
+ print str(e)
+ log.debug( "Creating user_action table failed: %s" % str( e ) )
+
+def downgrade():
+ metadata.reflect()
+ try:
+ UserAction_table.drop()
+ except Exception, e:
+ print str(e)
+ log.debug( "Dropping user_action table failed: %s" % str( e ) )
\ No newline at end of file
diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/web/controllers/dataset.py
--- a/lib/galaxy/web/controllers/dataset.py Mon Nov 30 16:47:18 2009 -0500
+++ b/lib/galaxy/web/controllers/dataset.py Tue Dec 01 09:53:36 2009 -0500
@@ -87,7 +87,7 @@
link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced" ),
HistoryColumn( "History", key="history",
link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ),
- grids.TagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced" ),
+ grids.TagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ),
StatusColumn( "Status", key="deleted", attach_popup=False ),
grids.GridColumn( "Created", key="create_time", format=time_ago ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/web/controllers/history.py
--- a/lib/galaxy/web/controllers/history.py Mon Nov 30 16:47:18 2009 -0500
+++ b/lib/galaxy/web/controllers/history.py Tue Dec 01 09:53:36 2009 -0500
@@ -94,7 +94,7 @@
link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ),
attach_popup=True, filterable="advanced" ),
DatasetsByStateColumn( "Datasets (by state)", ncells=4 ),
- grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"),
+ grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ),
StatusColumn( "Status", attach_popup=False ),
grids.GridColumn( "Created", key="create_time", format=time_ago ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/web/controllers/tag.py
--- a/lib/galaxy/web/controllers/tag.py Mon Nov 30 16:47:18 2009 -0500
+++ b/lib/galaxy/web/controllers/tag.py Tue Dec 01 09:53:36 2009 -0500
@@ -28,28 +28,38 @@
@web.expose
@web.require_login( "Add tag to an item." )
- def add_tag_async( self, trans, id=None, item_class=None, new_tag=None ):
+ def add_tag_async( self, trans, id=None, item_class=None, new_tag=None, context=None ):
""" Add tag to an item. """
- item = self._get_item(trans, item_class, trans.security.decode_id(id))
- self._do_security_check(trans, item)
+ # Check that user owns item.
+ item = self._get_item(trans, item_class, trans.security.decode_id( id ) )
+ self._do_security_check( trans, item )
+ # Apply tag.
self.tag_handler.apply_item_tags( trans.sa_session, item, new_tag.encode('utf-8') )
trans.sa_session.flush()
+ # Log.
+ params = dict( item_id=item.id, item_class=item_class, tag=new_tag)
+ trans.log_action( unicode( "tag"), context, params )
+
@web.expose
@web.require_login( "Remove tag from an item." )
- def remove_tag_async( self, trans, id=None, item_class=None, tag_name=None ):
+ def remove_tag_async( self, trans, id=None, item_class=None, tag_name=None, context=None ):
""" Remove tag from an item. """
+
+ # Check that user owns item.
item = self._get_item(trans, item_class, trans.security.decode_id(id))
-
self._do_security_check(trans, item)
+ # Remove tag.
self.tag_handler.remove_item_tag( trans, item, tag_name.encode('utf-8') )
- #print tag_name
- #print unicode(tag_name)
trans.sa_session.flush()
+ # Log.
+ params = dict( item_id=item.id, item_class=item_class, tag=tag_name)
+ trans.log_action( unicode( "untag"), context, params )
+
# Retag an item. All previous tags are deleted and new tags are applied.
@web.expose
@web.require_login( "Apply a new set of tags to an item; previous tags are deleted." )
diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py Mon Nov 30 16:47:18 2009 -0500
+++ b/lib/galaxy/web/framework/__init__.py Tue Dec 01 09:53:36 2009 -0500
@@ -10,6 +10,7 @@
import base
import pickle
from galaxy import util
+from galaxy.util.json import to_json_string
pkg_resources.require( "simplejson" )
import simplejson
@@ -170,6 +171,22 @@
to allow migration toward a more SQLAlchemy 0.4 style of use.
"""
return self.app.model.context.current
+ def log_action( self, action, context, params):
+ """
+ Application-level logging of user actions.
+ """
+ if self.app.config.log_actions:
+ action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) )
+ try:
+ action.user = self.user
+ except:
+ action.user = None
+ try:
+ action.session_id = self.galaxy_session.id
+ except:
+ action.session_id = None
+ self.sa_session.add( action )
+ self.sa_session.flush()
def log_event( self, message, tool_id=None, **kwargs ):
"""
Application level logging. Still needs fleshing out (log levels and such)
diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/web/framework/helpers/grids.py
--- a/lib/galaxy/web/framework/helpers/grids.py Mon Nov 30 16:47:18 2009 -0500
+++ b/lib/galaxy/web/framework/helpers/grids.py Tue Dec 01 09:53:36 2009 -0500
@@ -200,6 +200,13 @@
trans.get_user().preferences[pref_name] = unicode( to_json_string( sort_key ) )
trans.sa_session.flush()
+ # Log grid view.
+ context = unicode( self.__class__.__name__ )
+ params = cur_filter_dict.copy()
+ params['sort'] = sort_key
+ params['async'] = ( 'async' in kwargs )
+ trans.log_action( unicode( "grid.view"), context, params )
+
# Render grid.
def url( *args, **kwargs ):
# Only include sort/filter arguments if not linking to another
@@ -340,17 +347,19 @@
# Generic column that supports tagging.
class TagsColumn( TextColumn ):
- def __init__( self, col_name, key, model_class, model_tag_association_class, filterable ):
+ def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ):
GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable)
self.model_tag_association_class = model_tag_association_class
# Tags cannot be sorted.
self.sortable = False
+ # Column-specific attributes.
self.tag_elt_id_gen = 0
+ self.grid_name = grid_name
def get_value( self, trans, grid, item ):
self.tag_elt_id_gen += 1
elt_id="tagging-elt" + str( self.tag_elt_id_gen )
div_elt = "<div id=%s></div>" % elt_id
- return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=item,
+ return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=item, elt_context=self.grid_name,
elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" )
def filter( self, db_session, query, column_filter ):
""" Modify query to filter model_class by tag. Multiple filters are ANDed. """
diff -r efed28fa6a5e -r e75b55cc9e08 templates/dataset/edit_attributes.mako
--- a/templates/dataset/edit_attributes.mako Mon Nov 30 16:47:18 2009 -0500
+++ b/templates/dataset/edit_attributes.mako Tue Dec 01 09:53:36 2009 -0500
@@ -59,7 +59,7 @@
</div>
<div style="clear: both"></div>
</div>
- ${render_tagging_element(data, "dataset-tag-area", use_toggle_link="false", in_form="true", input_size="30")}
+ ${render_tagging_element(data, "dataset-tag-area", "edit_attributes.mako", use_toggle_link="false", in_form="true", input_size="30")}
%endif
%for name, spec in data.metadata.spec.items():
%if spec.visible:
diff -r efed28fa6a5e -r e75b55cc9e08 templates/history/view.mako
--- a/templates/history/view.mako Mon Nov 30 16:47:18 2009 -0500
+++ b/templates/history/view.mako Tue Dec 01 09:53:36 2009 -0500
@@ -327,7 +327,7 @@
%if trans.get_user() is not None:
<div id='history-tag-area' class="tag-element"></div>
- ${render_tagging_element(history, "history-tag-area", use_toggle_link='false', get_toggle_link_text_fn='get_toggle_link_text', editable=user_owns_history)}
+ ${render_tagging_element(history, "history-tag-area", "history/view.mako", use_toggle_link='false', get_toggle_link_text_fn='get_toggle_link_text', editable=user_owns_history)}
%endif
%if not datasets:
diff -r efed28fa6a5e -r e75b55cc9e08 templates/root/history.mako
--- a/templates/root/history.mako Mon Nov 30 16:47:18 2009 -0500
+++ b/templates/root/history.mako Tue Dec 01 09:53:36 2009 -0500
@@ -325,7 +325,7 @@
%if trans.get_user() is not None:
<div id='history-tag-area' class="tag-element"></div>
- ${render_tagging_element(history, "history-tag-area", get_toggle_link_text_fn='get_toggle_link_text')}
+ ${render_tagging_element( tagged_item=history, elt_id="history-tag-area", elt_context="history.mako", get_toggle_link_text_fn='get_toggle_link_text' )}
%endif
%if not datasets:
diff -r efed28fa6a5e -r e75b55cc9e08 templates/tagging_common.mako
--- a/templates/tagging_common.mako Mon Nov 30 16:47:18 2009 -0500
+++ b/templates/tagging_common.mako Tue Dec 01 09:53:36 2009 -0500
@@ -1,10 +1,10 @@
## Render a tagging element if there is a tagged_item.
%if tagged_item is not None and elt_id is not None:
- ${render_tagging_element(tagged_item, elt_id=elt_id, in_form=in_form, input_size=input_size, tag_click_fn=tag_click_fn)}
+ ${render_tagging_element(tagged_item=tagged_item, elt_id=elt_id, elt_context=elt_context, in_form=in_form, input_size=input_size, tag_click_fn=tag_click_fn)}
%endif
## Render the tags 'tags' as an autocomplete element.
-<%def name="render_tagging_element(tagged_item, elt_id, use_toggle_link='true', in_form='false', input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable='true')">
+<%def name="render_tagging_element(tagged_item, elt_id, elt_context, use_toggle_link='true', in_form='false', input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable='true')">
<script type="text/javascript">
//
// Set up autocomplete tagger.
@@ -75,8 +75,8 @@
tag_click_fn: ${tag_click_fn},
<% tagged_item_id = trans.security.encode_id(tagged_item.id) %>
ajax_autocomplete_tag_url: "${h.url_for( controller='tag', action='tag_autocomplete_data', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}",
- ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}",
- ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}",
+ ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}",
+ ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}",
delete_tag_img: "${h.url_for('/static/images/delete_tag_icon_gray.png')}",
delete_tag_img_rollover: "${h.url_for('/static/images/delete_tag_icon_white.png')}",
add_tag_img: "${h.url_for('/static/images/add_icon.png')}",
diff -r efed28fa6a5e -r e75b55cc9e08 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample Mon Nov 30 16:47:18 2009 -0500
+++ b/universe_wsgi.ini.sample Tue Dec 01 09:53:36 2009 -0500
@@ -144,6 +144,9 @@
# Log events
log_events = True
+# Log user actions
+log_actions = True
+
# Configuration for debugging middleware
debug = True
use_lint = False
1
0

02 Dec '09
details: http://www.bx.psu.edu/hg/galaxy/rev/f98643c26eb7
changeset: 3130:f98643c26eb7
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Mon Nov 30 17:53:25 2009 -0500
description:
Framework for recording user actions for reports; framework is modelled after event recording. Currently two types of actions are recorded: (a) tagging/untagging and (b) filtering/searching in grids.
diffstat:
lib/galaxy/config.py | 1 +
lib/galaxy/model/__init__.py | 10 +++++
lib/galaxy/model/mapping.py | 13 ++++++
lib/galaxy/model/migrate/versions/0029_user_actions.py | 47 +++++++++++++++++++++++
lib/galaxy/web/controllers/dataset.py | 2 +-
lib/galaxy/web/controllers/history.py | 2 +-
lib/galaxy/web/controllers/tag.py | 24 ++++++++---
lib/galaxy/web/framework/__init__.py | 17 ++++++++
lib/galaxy/web/framework/helpers/grids.py | 13 +++++-
templates/dataset/edit_attributes.mako | 2 +-
templates/history/view.mako | 2 +-
templates/root/history.mako | 2 +-
templates/tagging_common.mako | 8 ++--
universe_wsgi.ini.sample | 3 +
14 files changed, 128 insertions(+), 18 deletions(-)
diffs (335 lines):
diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/config.py
--- a/lib/galaxy/config.py Mon Nov 30 15:33:45 2009 -0500
+++ b/lib/galaxy/config.py Mon Nov 30 17:53:25 2009 -0500
@@ -79,6 +79,7 @@
self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', 'False' ) )
self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) )
self.log_memory_usage = string_as_bool( kwargs.get( 'log_memory_usage', 'False' ) )
+ self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",")
self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "main,test,tair" ).lower().split(",")
diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py Mon Nov 30 15:33:45 2009 -0500
+++ b/lib/galaxy/model/__init__.py Mon Nov 30 17:53:25 2009 -0500
@@ -1441,6 +1441,16 @@
def __init__( self, name=None, value=None ):
self.name = name
self.value = value
+
+class UserAction( object ):
+ def __init__( self, id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None):
+ self.id = id
+ self.create_time = create_time
+ self.user_id = user_id
+ self.session_id = session_id
+ self.action = action
+ self.params = params
+ self.context = context
## ---- Utility methods -------------------------------------------------------
diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py Mon Nov 30 15:33:45 2009 -0500
+++ b/lib/galaxy/model/mapping.py Mon Nov 30 17:53:25 2009 -0500
@@ -743,6 +743,15 @@
Column( "name", Unicode( 255 ), index=True),
Column( "value", Unicode( 1024 ) ) )
+UserAction.table = Table( "user_action", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "create_time", DateTime, default=now ),
+ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
+ Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ),
+ Column( "action", Unicode( 255 ) ),
+ Column( "context", Unicode( 512 ) ),
+ Column( "params", Unicode( 1024 ) ) )
+
# With the tables defined we can define the mappers and setup the
# relationships between the model objects.
@@ -1237,6 +1246,10 @@
assign_mapper( context, UserPreference, UserPreference.table,
properties = {}
)
+
+assign_mapper( context, UserAction, UserAction.table,
+ properties = dict( user=relation( User.mapper ) )
+ )
def db_next_hid( self ):
"""
diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/model/migrate/versions/0029_user_actions.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/model/migrate/versions/0029_user_actions.py Mon Nov 30 17:53:25 2009 -0500
@@ -0,0 +1,47 @@
+"""
+This migration script adds a user actions table to Galaxy.
+"""
+
+from sqlalchemy import *
+from migrate import *
+
+import datetime
+now = datetime.datetime.utcnow
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData( migrate_engine )
+
+def display_migration_details():
+ print ""
+ print "This migration script adds a user actions table to Galaxy."
+ print ""
+
+
+# New table to store user actions.
+UserAction_table = Table( "user_action", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "create_time", DateTime, default=now ),
+ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
+ Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ),
+ Column( "action", Unicode( 255 ) ),
+ Column( "context", Unicode( 512 ) ),
+ Column( "params", Unicode( 1024 ) ) )
+
+def upgrade():
+ display_migration_details()
+ metadata.reflect()
+ try:
+ UserAction_table.create()
+ except Exception, e:
+ print str(e)
+ log.debug( "Creating user_action table failed: %s" % str( e ) )
+
+def downgrade():
+ metadata.reflect()
+ try:
+ UserAction_table.drop()
+ except Exception, e:
+ print str(e)
+ log.debug( "Dropping user_action table failed: %s" % str( e ) )
\ No newline at end of file
diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/web/controllers/dataset.py
--- a/lib/galaxy/web/controllers/dataset.py Mon Nov 30 15:33:45 2009 -0500
+++ b/lib/galaxy/web/controllers/dataset.py Mon Nov 30 17:53:25 2009 -0500
@@ -87,7 +87,7 @@
link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced" ),
HistoryColumn( "History", key="history",
link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ),
- grids.TagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced" ),
+ grids.TagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ),
StatusColumn( "Status", key="deleted", attach_popup=False ),
grids.GridColumn( "Created", key="create_time", format=time_ago ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/web/controllers/history.py
--- a/lib/galaxy/web/controllers/history.py Mon Nov 30 15:33:45 2009 -0500
+++ b/lib/galaxy/web/controllers/history.py Mon Nov 30 17:53:25 2009 -0500
@@ -94,7 +94,7 @@
link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ),
attach_popup=True, filterable="advanced" ),
DatasetsByStateColumn( "Datasets (by state)", ncells=4 ),
- grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"),
+ grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ),
StatusColumn( "Status", attach_popup=False ),
grids.GridColumn( "Created", key="create_time", format=time_ago ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/web/controllers/tag.py
--- a/lib/galaxy/web/controllers/tag.py Mon Nov 30 15:33:45 2009 -0500
+++ b/lib/galaxy/web/controllers/tag.py Mon Nov 30 17:53:25 2009 -0500
@@ -28,28 +28,38 @@
@web.expose
@web.require_login( "Add tag to an item." )
- def add_tag_async( self, trans, id=None, item_class=None, new_tag=None ):
+ def add_tag_async( self, trans, id=None, item_class=None, new_tag=None, context=None ):
""" Add tag to an item. """
- item = self._get_item(trans, item_class, trans.security.decode_id(id))
- self._do_security_check(trans, item)
+ # Check that user owns item.
+ item = self._get_item(trans, item_class, trans.security.decode_id( id ) )
+ self._do_security_check( trans, item )
+ # Apply tag.
self.tag_handler.apply_item_tags( trans.sa_session, item, new_tag.encode('utf-8') )
trans.sa_session.flush()
+ # Log.
+ params = dict( item_id=item.id, item_class=item_class, tag=new_tag)
+ trans.log_action( unicode( "tag"), context, params )
+
@web.expose
@web.require_login( "Remove tag from an item." )
- def remove_tag_async( self, trans, id=None, item_class=None, tag_name=None ):
+ def remove_tag_async( self, trans, id=None, item_class=None, tag_name=None, context=None ):
""" Remove tag from an item. """
+
+ # Check that user owns item.
item = self._get_item(trans, item_class, trans.security.decode_id(id))
-
self._do_security_check(trans, item)
+ # Remove tag.
self.tag_handler.remove_item_tag( trans, item, tag_name.encode('utf-8') )
- #print tag_name
- #print unicode(tag_name)
trans.sa_session.flush()
+ # Log.
+ params = dict( item_id=item.id, item_class=item_class, tag=tag_name)
+ trans.log_action( unicode( "untag"), context, params )
+
# Retag an item. All previous tags are deleted and new tags are applied.
@web.expose
@web.require_login( "Apply a new set of tags to an item; previous tags are deleted." )
diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py Mon Nov 30 15:33:45 2009 -0500
+++ b/lib/galaxy/web/framework/__init__.py Mon Nov 30 17:53:25 2009 -0500
@@ -10,6 +10,7 @@
import base
import pickle
from galaxy import util
+from galaxy.util.json import to_json_string
pkg_resources.require( "simplejson" )
import simplejson
@@ -170,6 +171,22 @@
to allow migration toward a more SQLAlchemy 0.4 style of use.
"""
return self.app.model.context.current
+ def log_action( self, action, context, params):
+ """
+ Application-level logging of user actions.
+ """
+ if self.app.config.log_actions:
+ action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) )
+ try:
+ action.user = self.user
+ except:
+ action.user = None
+ try:
+ action.session_id = self.galaxy_session.id
+ except:
+ action.session_id = None
+ self.sa_session.add( action )
+ self.sa_session.flush()
def log_event( self, message, tool_id=None, **kwargs ):
"""
Application level logging. Still needs fleshing out (log levels and such)
diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/web/framework/helpers/grids.py
--- a/lib/galaxy/web/framework/helpers/grids.py Mon Nov 30 15:33:45 2009 -0500
+++ b/lib/galaxy/web/framework/helpers/grids.py Mon Nov 30 17:53:25 2009 -0500
@@ -200,6 +200,13 @@
trans.get_user().preferences[pref_name] = unicode( to_json_string( sort_key ) )
trans.sa_session.flush()
+ # Log grid view.
+ context = unicode( self.__class__.__name__ )
+ params = cur_filter_dict.copy()
+ params['sort'] = sort_key
+ params['async'] = ( 'async' in kwargs )
+ trans.log_action( unicode( "grid.view"), context, params )
+
# Render grid.
def url( *args, **kwargs ):
# Only include sort/filter arguments if not linking to another
@@ -340,17 +347,19 @@
# Generic column that supports tagging.
class TagsColumn( TextColumn ):
- def __init__( self, col_name, key, model_class, model_tag_association_class, filterable ):
+ def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ):
GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable)
self.model_tag_association_class = model_tag_association_class
# Tags cannot be sorted.
self.sortable = False
+ # Column-specific attributes.
self.tag_elt_id_gen = 0
+ self.grid_name = grid_name
def get_value( self, trans, grid, item ):
self.tag_elt_id_gen += 1
elt_id="tagging-elt" + str( self.tag_elt_id_gen )
div_elt = "<div id=%s></div>" % elt_id
- return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=item,
+ return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=item, elt_context=self.grid_name,
elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" )
def filter( self, db_session, query, column_filter ):
""" Modify query to filter model_class by tag. Multiple filters are ANDed. """
diff -r 9d4945bbdcf5 -r f98643c26eb7 templates/dataset/edit_attributes.mako
--- a/templates/dataset/edit_attributes.mako Mon Nov 30 15:33:45 2009 -0500
+++ b/templates/dataset/edit_attributes.mako Mon Nov 30 17:53:25 2009 -0500
@@ -59,7 +59,7 @@
</div>
<div style="clear: both"></div>
</div>
- ${render_tagging_element(data, "dataset-tag-area", use_toggle_link="false", in_form="true", input_size="30")}
+ ${render_tagging_element(data, "dataset-tag-area", "edit_attributes.mako", use_toggle_link="false", in_form="true", input_size="30")}
%endif
%for name, spec in data.metadata.spec.items():
%if spec.visible:
diff -r 9d4945bbdcf5 -r f98643c26eb7 templates/history/view.mako
--- a/templates/history/view.mako Mon Nov 30 15:33:45 2009 -0500
+++ b/templates/history/view.mako Mon Nov 30 17:53:25 2009 -0500
@@ -327,7 +327,7 @@
%if trans.get_user() is not None:
<div id='history-tag-area' class="tag-element"></div>
- ${render_tagging_element(history, "history-tag-area", use_toggle_link='false', get_toggle_link_text_fn='get_toggle_link_text', editable=user_owns_history)}
+ ${render_tagging_element(history, "history-tag-area", "history/view.mako", use_toggle_link='false', get_toggle_link_text_fn='get_toggle_link_text', editable=user_owns_history)}
%endif
%if not datasets:
diff -r 9d4945bbdcf5 -r f98643c26eb7 templates/root/history.mako
--- a/templates/root/history.mako Mon Nov 30 15:33:45 2009 -0500
+++ b/templates/root/history.mako Mon Nov 30 17:53:25 2009 -0500
@@ -325,7 +325,7 @@
%if trans.get_user() is not None:
<div id='history-tag-area' class="tag-element"></div>
- ${render_tagging_element(history, "history-tag-area", get_toggle_link_text_fn='get_toggle_link_text')}
+ ${render_tagging_element( tagged_item=history, elt_id="history-tag-area", elt_context="history.mako", get_toggle_link_text_fn='get_toggle_link_text' )}
%endif
%if not datasets:
diff -r 9d4945bbdcf5 -r f98643c26eb7 templates/tagging_common.mako
--- a/templates/tagging_common.mako Mon Nov 30 15:33:45 2009 -0500
+++ b/templates/tagging_common.mako Mon Nov 30 17:53:25 2009 -0500
@@ -1,10 +1,10 @@
## Render a tagging element if there is a tagged_item.
%if tagged_item is not None and elt_id is not None:
- ${render_tagging_element(tagged_item, elt_id=elt_id, in_form=in_form, input_size=input_size, tag_click_fn=tag_click_fn)}
+ ${render_tagging_element(tagged_item=tagged_item, elt_id=elt_id, elt_context=elt_context, in_form=in_form, input_size=input_size, tag_click_fn=tag_click_fn)}
%endif
## Render the tags 'tags' as an autocomplete element.
-<%def name="render_tagging_element(tagged_item, elt_id, use_toggle_link='true', in_form='false', input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable='true')">
+<%def name="render_tagging_element(tagged_item, elt_id, elt_context, use_toggle_link='true', in_form='false', input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable='true')">
<script type="text/javascript">
//
// Set up autocomplete tagger.
@@ -75,8 +75,8 @@
tag_click_fn: ${tag_click_fn},
<% tagged_item_id = trans.security.encode_id(tagged_item.id) %>
ajax_autocomplete_tag_url: "${h.url_for( controller='tag', action='tag_autocomplete_data', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}",
- ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}",
- ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}",
+ ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}",
+ ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}",
delete_tag_img: "${h.url_for('/static/images/delete_tag_icon_gray.png')}",
delete_tag_img_rollover: "${h.url_for('/static/images/delete_tag_icon_white.png')}",
add_tag_img: "${h.url_for('/static/images/add_icon.png')}",
diff -r 9d4945bbdcf5 -r f98643c26eb7 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample Mon Nov 30 15:33:45 2009 -0500
+++ b/universe_wsgi.ini.sample Mon Nov 30 17:53:25 2009 -0500
@@ -144,6 +144,9 @@
# Log events
log_events = True
+# Log user actions
+log_actions = True
+
# Configuration for debugging middleware
debug = True
use_lint = False
1
0

02 Dec '09
details: http://www.bx.psu.edu/hg/galaxy/rev/92d6a9796b24
changeset: 3128:92d6a9796b24
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Mon Nov 30 14:55:30 2009 -0500
description:
When setting metadata externally, substitute a MetadataTempFile object for all populated metadata FileParameters. Fixes the problem with writting to metadata FileParameter files on cluster nodes with read-only database/files directory.
diffstat:
lib/galaxy/datatypes/metadata.py | 21 +++-
lib/galaxy/model/mapping.py | 1 +
lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py | 47 +++++++++
scripts/set_metadata.py | 23 ++++-
tools/regVariation/quality_filter.xml | 2 +-
5 files changed, 87 insertions(+), 7 deletions(-)
diffs (172 lines):
diff -r 9f7a2a3be0e7 -r 92d6a9796b24 lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py Mon Nov 30 11:59:54 2009 -0500
+++ b/lib/galaxy/datatypes/metadata.py Mon Nov 30 14:55:30 2009 -0500
@@ -429,7 +429,9 @@
if MetadataTempFile.is_JSONified_value( value ):
value = MetadataTempFile.from_JSON( value )
if isinstance( value, MetadataTempFile ):
- mf = self.new_file( dataset = parent, **value.kwds )
+ mf = parent.metadata.get( self.spec.name, None)
+ if mf is None:
+ mf = self.new_file( dataset = parent, **value.kwds )
shutil.move( value.file_name, mf.file_name )
value = mf.id
return value
@@ -521,7 +523,7 @@
if dataset_path.false_path and dataset_path.real_path == metadata_files.dataset.file_name:
return dataset_path.false_path
return ""
- return "%s,%s,%s,%s,%s" % ( metadata_files.filename_in, metadata_files.filename_kwds, metadata_files.filename_out, metadata_files.filename_results_code, __get_filename_override() )
+ return "%s,%s,%s,%s,%s,%s" % ( metadata_files.filename_in, metadata_files.filename_kwds, metadata_files.filename_out, metadata_files.filename_results_code, __get_filename_override(), metadata_files.filename_override_metadata )
if not isinstance( datasets, list ):
datasets = [ datasets ]
if exec_dir is None:
@@ -558,11 +560,22 @@
open( metadata_files.filename_out, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
#file to store a 'return code' indicating the results of the set_meta() call
#results code is like (True/False - if setting metadata was successful/failed , exception or string of reason of success/failure )
- metadata_files.filename_results_code = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_out_%s_" % key ).name )
+ metadata_files.filename_results_code = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_results_%s_" % key ).name )
simplejson.dump( ( False, 'External set_meta() not called' ), open( metadata_files.filename_results_code, 'wb+' ) ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
#file to store kwds passed to set_meta()
metadata_files.filename_kwds = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_kwds_%s_" % key ).name )
simplejson.dump( kwds, open( metadata_files.filename_kwds, 'wb+' ), ensure_ascii=True )
+ #existing metadata file parameters need to be overridden with cluster-writable file locations
+ metadata_files.filename_override_metadata = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_override_%s_" % key ).name )
+ open( metadata_files.filename_override_metadata, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
+ override_metadata = []
+ for meta_key, spec_value in dataset.metadata.spec.iteritems():
+ if isinstance( spec_value.param, FileParameter ) and dataset.metadata.get( meta_key, None ) is not None:
+ metadata_temp = MetadataTempFile()
+ shutil.copy( dataset.metadata.get( meta_key, None ).file_name, metadata_temp.file_name )
+ override_metadata.append( ( meta_key, metadata_temp.to_JSON() ) )
+ simplejson.dump( override_metadata, open( metadata_files.filename_override_metadata, 'wb+' ) )
+ #add to session and flush
sa_session.add( metadata_files )
sa_session.flush()
metadata_files_list.append( metadata_files )
@@ -585,7 +598,7 @@
#can occur if the job was stopped before completion, but a MetadataTempFile is used in the set_meta
MetadataTempFile.cleanup_from_JSON_dict_filename( metadata_files.filename_out )
dataset_key = self.get_dataset_metadata_key( metadata_files.dataset )
- for key, fname in [ ( 'filename_in', metadata_files.filename_in ), ( 'filename_out', metadata_files.filename_out ), ( 'filename_results_code', metadata_files.filename_results_code ), ( 'filename_kwds', metadata_files.filename_kwds ) ]:
+ for key, fname in [ ( 'filename_in', metadata_files.filename_in ), ( 'filename_out', metadata_files.filename_out ), ( 'filename_results_code', metadata_files.filename_results_code ), ( 'filename_kwds', metadata_files.filename_kwds ), ( 'filename_override_metadata', metadata_files.filename_override_metadata ) ]:
try:
os.remove( fname )
except Exception, e:
diff -r 9f7a2a3be0e7 -r 92d6a9796b24 lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py Mon Nov 30 11:59:54 2009 -0500
+++ b/lib/galaxy/model/mapping.py Mon Nov 30 14:55:30 2009 -0500
@@ -358,6 +358,7 @@
Column( "filename_out", String( 255 ) ),
Column( "filename_results_code", String( 255 ) ),
Column( "filename_kwds", String( 255 ) ),
+ Column( "filename_override_metadata", String( 255 ) ),
Column( "job_runner_external_pid", String( 255 ) ) )
Event.table = Table( "event", metadata,
diff -r 9f7a2a3be0e7 -r 92d6a9796b24 lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py Mon Nov 30 14:55:30 2009 -0500
@@ -0,0 +1,47 @@
+"""
+This script adds the filename_override_metadata column to the JobExternalOutputMetadata table,
+allowing existing metadata files to be written when using external metadata and a cluster
+set up with read-only access to database/files
+"""
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from sqlalchemy.exceptions import *
+from migrate import *
+from migrate.changeset import *
+import datetime
+now = datetime.datetime.utcnow
+import sys, logging
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def display_migration_details():
+ print "========================================"
+ print "This script adds the filename_override_metadata column to the JobExternalOutputMetadata table,"
+ print" allowing existing metadata files to be written when using external metadata and a cluster"
+ print "set up with read-only access to database/files"
+ print "========================================"
+def upgrade():
+ display_migration_details()
+ # Load existing tables
+ metadata.reflect()
+ try:
+ job_external_output_metadata = Table( "job_external_output_metadata", metadata, autoload=True )
+ col = Column( "filename_override_metadata", String( 255 ) )
+ col.create( job_external_output_metadata )
+ assert col is job_external_output_metadata.c.filename_override_metadata
+ except Exception, e:
+ log.debug( "Adding column 'filename_override_metadata' to job_external_output_metadata table failed: %s" % ( str( e ) ) )
+
+def downgrade():
+ pass
diff -r 9f7a2a3be0e7 -r 92d6a9796b24 scripts/set_metadata.py
--- a/scripts/set_metadata.py Mon Nov 30 11:59:54 2009 -0500
+++ b/scripts/set_metadata.py Mon Nov 30 14:55:30 2009 -0500
@@ -50,17 +50,36 @@
except:
continue
for filenames in sys.argv[1:]:
- filename_in, filename_kwds, filename_out, filename_results_code, dataset_filename_override = filenames.split( ',' )
+ fields = filenames.split( ',' )
+ filename_in = fields.pop( 0 )
+ filename_kwds = fields.pop( 0 )
+ filename_out = fields.pop( 0 )
+ filename_results_code = fields.pop( 0 )
+ dataset_filename_override = fields.pop( 0 )
+ #Need to be careful with the way that these parameters are populated from the filename splitting,
+ #because if a job is running when the server is updated, any existing external metadata command-lines
+ #will not have info about the newly added override_metadata file
+ if fields:
+ override_metadata = fields.pop( 0 )
+ else:
+ override_metadata = None
try:
dataset = cPickle.load( open( filename_in ) ) #load DatasetInstance
if dataset_filename_override:
dataset.dataset.external_filename = dataset_filename_override
if ext_override.get( dataset.dataset.id, None ):
dataset.extension = ext_override[ dataset.dataset.id ]
+ #Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
+ if override_metadata:
+ override_metadata = simplejson.load( open( override_metadata ) )
+ for metadata_name, metadata_file_override in override_metadata:
+ if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value( metadata_file_override ):
+ metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON( metadata_file_override )
+ setattr( dataset.metadata, metadata_name, metadata_file_override )
kwds = stringify_dictionary_keys( simplejson.load( open( filename_kwds ) ) )#load kwds; need to ensure our keywords are not unicode
dataset.datatype.set_meta( dataset, **kwds )
dataset.metadata.to_JSON_dict( filename_out ) # write out results of set_meta
- simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) #setting metadata has suceeded
+ simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) #setting metadata has succeeded
except Exception, e:
simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) #setting metadata has failed somehow
clear_mappers()
diff -r 9f7a2a3be0e7 -r 92d6a9796b24 tools/regVariation/quality_filter.xml
--- a/tools/regVariation/quality_filter.xml Mon Nov 30 11:59:54 2009 -0500
+++ b/tools/regVariation/quality_filter.xml Mon Nov 30 14:55:30 2009 -0500
@@ -61,7 +61,7 @@
</conditional>
</inputs>
<outputs>
- <data format="maf" name="out_file1"/>
+ <data format="maf" name="out_file1" metadata_source="input"/>
</outputs>
<requirements>
<requirement type="python-module">numpy</requirement>
1
0

02 Dec '09
details: http://www.bx.psu.edu/hg/galaxy/rev/9d4945bbdcf5
changeset: 3129:9d4945bbdcf5
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Mon Nov 30 15:33:45 2009 -0500
description:
Fix MAF to BED tool. This tool should be rewritten to not use a code file, but instead use one of the standard ways to create additional outputs, similar to how maf_to_interval functions.
diffstat:
tools/maf/maf_to_bed.py | 3 +--
tools/maf/maf_to_bed.xml | 4 ++--
tools/maf/maf_to_bed_code.py | 1 +
3 files changed, 4 insertions(+), 4 deletions(-)
diffs (36 lines):
diff -r 92d6a9796b24 -r 9d4945bbdcf5 tools/maf/maf_to_bed.py
--- a/tools/maf/maf_to_bed.py Mon Nov 30 14:55:30 2009 -0500
+++ b/tools/maf/maf_to_bed.py Mon Nov 30 15:33:45 2009 -0500
@@ -15,8 +15,7 @@
input_filename = sys.argv[1]
output_filename = sys.argv[2]
#where to store files that become additional output
- database_tmp_dir = './database/tmp' #os.path.join(os.path.split(os.path.split(os.path.realpath(output_filename))[0])[0],'tmp') #database/tmp
-
+ database_tmp_dir = sys.argv[5]
species = sys.argv[3].split(',')
partial = sys.argv[4]
diff -r 92d6a9796b24 -r 9d4945bbdcf5 tools/maf/maf_to_bed.xml
--- a/tools/maf/maf_to_bed.xml Mon Nov 30 14:55:30 2009 -0500
+++ b/tools/maf/maf_to_bed.xml Mon Nov 30 15:33:45 2009 -0500
@@ -1,6 +1,6 @@
-<tool id="MAF_To_BED1" name="Maf to BED">
+<tool id="MAF_To_BED1" name="Maf to BED" force_history_refresh="True">
<description>Converts a MAF formated file to the BED format</description>
- <command interpreter="python">maf_to_bed.py $input1 $out_file1 $species $complete_blocks</command>
+ <command interpreter="python">maf_to_bed.py $input1 $out_file1 $species $complete_blocks $__new_file_path__</command>
<inputs>
<param format="maf" name="input1" type="data" label="MAF file to convert"/>
<param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="a separate history item will be created for each checked species">
diff -r 92d6a9796b24 -r 9d4945bbdcf5 tools/maf/maf_to_bed_code.py
--- a/tools/maf/maf_to_bed_code.py Mon Nov 30 14:55:30 2009 -0500
+++ b/tools/maf/maf_to_bed_code.py Mon Nov 30 15:33:45 2009 -0500
@@ -46,6 +46,7 @@
newdata.state = newdata.states.ERROR
newdata.dbkey = dbkey
newdata.init_meta()
+ newdata.set_meta()
newdata.set_peek()
app.model.context.flush()
output_data_list.append(newdata)
1
0

02 Dec '09
details: http://www.bx.psu.edu/hg/galaxy/rev/9f7a2a3be0e7
changeset: 3127:9f7a2a3be0e7
user: guru
date: Mon Nov 30 11:59:54 2009 -0500
description:
Fixed a bug in 'fetch closest features' tool.
diffstat:
tools/new_operations/flanking_features.py | 5 ++---
1 files changed, 2 insertions(+), 3 deletions(-)
diffs (22 lines):
diff -r 71b779fde315 -r 9f7a2a3be0e7 tools/new_operations/flanking_features.py
--- a/tools/new_operations/flanking_features.py Mon Nov 30 11:56:58 2009 -0500
+++ b/tools/new_operations/flanking_features.py Mon Nov 30 11:59:54 2009 -0500
@@ -121,7 +121,7 @@
map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval
yield outfields
- if either:
+ if either and (result_up or result_down):
if result_up and result_down:
if abs(start - int(result_up[res_ind].end)) <= abs(end - int(result_down[-1].start)):
map(outfields.append, result_up[res_ind].other)
@@ -131,8 +131,7 @@
map(outfields.append, result_up[res_ind].other)
elif result_down:
map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval
- yield outfields
-
+ yield outfields
def main():
options, args = doc_optparse.parse( __doc__ )
1
0

02 Dec '09
details: http://www.bx.psu.edu/hg/galaxy/rev/efdb6fb5de34
changeset: 3123:efdb6fb5de34
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Fri Nov 27 10:53:50 2009 -0500
description:
First pass of the lastz tool wrapper that includes job splitting - works but needs polishing.
diffstat:
test-data/B1.fa | 1000 ----------------------------------------
test-data/b1.fasta | 1000 ++++++++++++++++++++++++++++++++++++++++
test-data/lastz_wrapper_out1.sam | 494 +++++++++++++++++++
test-data/lastz_wrapper_out3.tabular | 26 +
test-data/phiX.fa | 79 ---
test-data/phiX.fasta | 79 +++
tool-data/lastz_seqs.loc | 2 +
tool_conf.xml.sample | 2 +-
tools/sr_mapping/bwa_wrapper.xml | 2 +-
tools/sr_mapping/lastz_wrapper.py | 133 +++++
tools/sr_mapping/lastz_wrapper.xml | 300 +++++++----
11 files changed, 1913 insertions(+), 1204 deletions(-)
diffs (truncated from 3185 to 3000 lines):
diff -r 8d149264b777 -r efdb6fb5de34 test-data/B1.fa
--- a/test-data/B1.fa Wed Nov 25 14:06:28 2009 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1000 +0,0 @@
->HWI-EAS91_1_306UPAAXX:6:1:1503:1160
-GGTGGTCTATAGTGTTATTAATATCAAGTTGGGGGG
->HWI-EAS91_1_306UPAAXX:6:1:1564:1179
-GCGAGCAGTAGACTCCTTCTGTTGATAAGCAAGCAT
->HWI-EAS91_1_306UPAAXX:6:1:1704:1082
-GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC
->HWI-EAS91_1_306UPAAXX:6:1:1588:1797
-GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT
->HWI-EAS91_1_306UPAAXX:6:1:1304:1526
-GTAGTTGAAATGGTAATAAGACGACCAATCTGACCT
->HWI-EAS91_1_306UPAAXX:6:1:1490:1582
-GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC
->HWI-EAS91_1_306UPAAXX:6:1:1356:1339
-GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC
->HWI-EAS91_1_306UPAAXX:6:1:1311:853
-GGTTGGTTTATCGTTTTTGACACTCTCACGTTGTCT
->HWI-EAS91_1_306UPAAXX:6:1:1257:1552
-GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC
->HWI-EAS91_1_306UPAAXX:6:1:1486:1402
-GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC
->HWI-EAS91_1_306UPAAXX:6:1:1028:1081
-GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT
->HWI-EAS91_1_306UPAAXX:6:1:1167:752
-GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC
->HWI-EAS91_1_306UPAAXX:6:1:1507:1113
-GTCAACGTTATATTTTGATAGTTTGACGGTTAATTC
->HWI-EAS91_1_306UPAAXX:6:1:1654:1311
-GGATGAAAATGCTCACAATGACAAATCTGTCCACGG
->HWI-EAS91_1_306UPAAXX:6:1:1386:1060
-GTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTT
->HWI-EAS91_1_306UPAAXX:6:1:1070:1356
-GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG
->HWI-EAS91_1_306UPAAXX:6:1:787:1032
-GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA
->HWI-EAS91_1_306UPAAXX:6:1:834:1017
-GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT
->HWI-EAS91_1_306UPAAXX:6:1:1703:1155
-GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT
->HWI-EAS91_1_306UPAAXX:6:1:1406:593
-GTTGAGTTCGATAATGGTGATATGTATGTTTACGGC
->HWI-EAS91_1_306UPAAXX:6:1:1411:886
-GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT
->HWI-EAS91_1_306UPAAXX:6:1:923:972
-GCATGACAAGTAAAGGACGGTTGTCAGCGTCATAAG
->HWI-EAS91_1_306UPAAXX:6:1:1279:1004
-GCCATAGCACCAGAAACAAAACTAGGGGCGGCCTCT
->HWI-EAS91_1_306UPAAXX:6:1:1070:840
-GGTTGTCAGCGTCATAAGAGGTTTTACCTCCAAATG
->HWI-EAS91_1_306UPAAXX:6:1:1595:1040
-GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT
->HWI-EAS91_1_306UPAAXX:6:1:1002:559
-GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG
->HWI-EAS91_1_306UPAAXX:6:1:999:974
-GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC
->HWI-EAS91_1_306UPAAXX:6:1:896:982
-GTGGCTGGAGACAAATAATCTCTTTAATAACCTTAT
->HWI-EAS91_1_306UPAAXX:6:1:1366:741
-GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC
->HWI-EAS91_1_306UPAAXX:6:1:749:1469
-GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT
->HWI-EAS91_1_306UPAAXX:6:1:1010:592
-GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT
->HWI-EAS91_1_306UPAAXX:6:1:1393:650
-GTGACTCATATCTAAACCAGTCCTTGACGAACGTGC
->HWI-EAS91_1_306UPAAXX:6:1:1238:1731
-GAGAAATAAAAGTCTGAAACATGATTAAACTCCTAA
->HWI-EAS91_1_306UPAAXX:6:1:1629:908
-GATGCGGTTATCCATCTGCTTATGGAAGCCAAGCAT
->HWI-EAS91_1_306UPAAXX:6:1:1560:849
-GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG
->HWI-EAS91_1_306UPAAXX:6:1:1029:783
-GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT
->HWI-EAS91_1_306UPAAXX:6:1:1152:1324
-GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG
->HWI-EAS91_1_306UPAAXX:6:1:1614:2042
-GAAATGCCACAAGCCTCAATAGCAGGTTTAAGAGCC
->HWI-EAS91_1_306UPAAXX:6:1:1398:439
-GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG
->HWI-EAS91_1_306UPAAXX:6:1:955:616
-GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC
->HWI-EAS91_1_306UPAAXX:6:1:1672:753
-GAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCT
->HWI-EAS91_1_306UPAAXX:6:1:1195:1293
-GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC
->HWI-EAS91_1_306UPAAXX:6:1:1074:755
-GCAAGAGTAAACATAGTGCCATGCTCAGGAACAAAG
->HWI-EAS91_1_306UPAAXX:6:1:984:499
-GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT
->HWI-EAS91_1_306UPAAXX:6:1:1452:1833
-GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT
->HWI-EAS91_1_306UPAAXX:6:1:863:710
-GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT
->HWI-EAS91_1_306UPAAXX:6:1:885:649
-GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC
->HWI-EAS91_1_306UPAAXX:6:1:917:1214
-GACAGATGTATCCATCTGAATGCAATGAAGAAAACC
->HWI-EAS91_1_306UPAAXX:6:1:892:1254
-GCTCAGGAAATGCAGCAGCAAGATAATCACGAGTAT
->HWI-EAS91_1_306UPAAXX:6:1:1555:1005
-GCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCT
->HWI-EAS91_1_306UPAAXX:6:1:1637:1413
-GATGCTGTTCAACCACTAATAGGTAAGAAATCATGT
->HWI-EAS91_1_306UPAAXX:6:1:1102:1567
-GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA
->HWI-EAS91_1_306UPAAXX:6:1:799:1337
-GTATATGCACAAAATGAGATGCTTGCTTATCAACAG
->HWI-EAS91_1_306UPAAXX:6:1:1353:1843
-GCAGACCCATAATGTCAATAGATGTGGTAGAAGTCG
->HWI-EAS91_1_306UPAAXX:6:1:1196:789
-GCGGCATACGCTCGGCGCCAGTTTGAATATTAGACA
->HWI-EAS91_1_306UPAAXX:6:1:1056:1676
-GTAAAATACTGACCAGCCGTTTGAGCTTGAGTAAGC
->HWI-EAS91_1_306UPAAXX:6:1:1349:1836
-GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC
->HWI-EAS91_1_306UPAAXX:6:1:1027:788
-GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT
->HWI-EAS91_1_306UPAAXX:6:1:990:1283
-GCTTAGGGATTTTATTGGTATCAGGGTTAATCGTGC
->HWI-EAS91_1_306UPAAXX:6:1:904:939
-GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT
->HWI-EAS91_1_306UPAAXX:6:1:1732:793
-GTCAACATACATATCACCATTATCGAACTCAACGCC
->HWI-EAS91_1_306UPAAXX:6:1:1355:2003
-GTTAGACCAAACCATGAAACCAACATAAACATTATT
->HWI-EAS91_1_306UPAAXX:6:1:1337:977
-GCACCAGAAACAAAACTAGGGGCGGCCTCATCAGGG
->HWI-EAS91_1_306UPAAXX:6:1:1605:1175
-GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT
->HWI-EAS91_1_306UPAAXX:6:1:1763:1192
-GACAGGCCGTTTGAATGTTGACGGGATGAACATAAT
->HWI-EAS91_1_306UPAAXX:6:1:722:483
-GTTATTATACCGTCAAGGACTGTGTGACTATTGACT
->HWI-EAS91_1_306UPAAXX:6:1:1760:1136
-GCAAAGCATTGGGATTATCATAAAACGCCTCTAATC
->HWI-EAS91_1_306UPAAXX:6:1:1088:798
-GGAAACCTGCTGTTGCTTGGAAAGATTGGTGTTTTC
->HWI-EAS91_1_306UPAAXX:6:1:633:1076
-GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG
->HWI-EAS91_1_306UPAAXX:6:1:673:754
-GTCATGGAAGCGATAAAACTCTGCAGGTTGGATATT
->HWI-EAS91_1_306UPAAXX:6:1:1759:2019
-GTAAAGGACGGTTGTCAGCGTCATAAGAGGTTTTAC
->HWI-EAS91_1_306UPAAXX:6:1:1064:1797
-GCGGTTATCCATCTGCTTATGGAAGCCAAGCATTGG
->HWI-EAS91_1_306UPAAXX:6:1:1112:1669
-GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT
->HWI-EAS91_1_306UPAAXX:6:1:510:1447
-GCATTAAGCTCAGGAAATGCAGCAGCAAGATAATCA
->HWI-EAS91_1_306UPAAXX:6:1:877:1573
-GTGCTATTGCTGGCGGTATTTCTTCTTCTTTTTTTT
->HWI-EAS91_1_306UPAAXX:6:1:870:542
-GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC
->HWI-EAS91_1_306UPAAXX:6:1:966:384
-GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA
->HWI-EAS91_1_306UPAAXX:6:1:1186:1903
-GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG
->HWI-EAS91_1_306UPAAXX:6:1:1632:1742
-GCATCACCCATGCCTACAGTATTGTTATCGGTAGCC
->HWI-EAS91_1_306UPAAXX:6:1:1521:559
-GAGAGCGCCAACGGCGTCCATCTCGAAGGAGTCGCC
->HWI-EAS91_1_306UPAAXX:6:1:683:454
-GCTTATTATGTTCATCCCGTCAACATTCAAACGTCC
->HWI-EAS91_1_306UPAAXX:6:1:112:1280
-GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGTC
->HWI-EAS91_1_306UPAAXX:6:1:891:381
-GACCAGGGCGAGCGCCAGAACGTTTTTTACCTTTAG
->HWI-EAS91_1_306UPAAXX:6:1:1348:958
-GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT
->HWI-EAS91_1_306UPAAXX:6:1:1785:1915
-GCCCCGAAGGGGACNANAAATGGTTTTTAGAGAACG
->HWI-EAS91_1_306UPAAXX:6:1:1418:42
-GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT
->HWI-EAS91_1_306UPAAXX:6:1:1421:743
-GGTCAACGCTACCTGTAGGAAGTGTCCGCATAAAAT
->HWI-EAS91_1_306UPAAXX:6:1:1079:790
-GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT
->HWI-EAS91_1_306UPAAXX:6:1:663:740
-GGTATTAAGGATGAGTGTTCAAGATTGCTGGATGCC
->HWI-EAS91_1_306UPAAXX:6:1:1245:413
-GTTTGAATGTTGACGGGATGAACATAATAAGCAATG
->HWI-EAS91_1_306UPAAXX:6:1:1378:1035
-GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGG
->HWI-EAS91_1_306UPAAXX:6:1:903:1746
-GTACGGGGAAGGACGTCAATAGTCACACAGTCCTTG
->HWI-EAS91_1_306UPAAXX:6:1:1713:1134
-GGCGTACGGGGAAGGACGTCAATAGTCACACAGTCC
->HWI-EAS91_1_306UPAAXX:6:1:1246:1887
-GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG
->HWI-EAS91_1_306UPAAXX:6:1:872:1731
-GGGCGGCCTCATCAGGGTTAGGAACATTAGAGCCTT
->HWI-EAS91_1_306UPAAXX:6:1:1714:1582
-GCTTTCCTGCTCCTGTTGAGTTTATTGCTTCCGTCT
->HWI-EAS91_1_306UPAAXX:6:1:1785:763
-GNCGAGAAATAAAANNNTGAAACATGATTAAANTCC
->HWI-EAS91_1_306UPAAXX:6:1:1684:542
-GAAAAGACAGAATCTCTTCCAAGAGCTTGATGCGGT
->HWI-EAS91_1_306UPAAXX:6:1:1581:1665
-GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT
->HWI-EAS91_1_306UPAAXX:6:1:901:1581
-GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT
->HWI-EAS91_1_306UPAAXX:6:1:1128:239
-GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC
->HWI-EAS91_1_306UPAAXX:6:1:969:441
-GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG
->HWI-EAS91_1_306UPAAXX:6:1:630:1087
-GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC
->HWI-EAS91_1_306UPAAXX:6:1:606:1852
-GGAGACAAATAATCTCTTTAATAACCTGATTCAGCG
->HWI-EAS91_1_306UPAAXX:6:1:489:1315
-GAAAGCTCAGTCTCAGGAGGAAGCGGAGCAGTCCAC
->HWI-EAS91_1_306UPAAXX:6:1:465:1983
-GAGCCAATACCATCAGCTTTACCGTCTTTCCAGAAA
->HWI-EAS91_1_306UPAAXX:6:1:559:1028
-GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC
->HWI-EAS91_1_306UPAAXX:6:1:1655:1413
-GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG
->HWI-EAS91_1_306UPAAXX:6:1:980:605
-GCCGTTTGAATGTTGACGGGATGAACATAATAAGCA
->HWI-EAS91_1_306UPAAXX:6:1:1629:1865
-GAAAAGCGGCATGGTCAATATAACCAGTAGTGTTAT
->HWI-EAS91_1_306UPAAXX:6:1:1180:1920
-GCACTCCGTGGACAGATTTGTCATTGTGAGCATTTT
->HWI-EAS91_1_306UPAAXX:6:1:1116:383
-GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG
->HWI-EAS91_1_306UPAAXX:6:1:906:2041
-GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA
->HWI-EAS91_1_306UPAAXX:6:1:1514:157
-GTCAATAGATGTGGTAGAAGTCGTCATTTGGCGTGG
->HWI-EAS91_1_306UPAAXX:6:1:1032:1857
-GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT
->HWI-EAS91_1_306UPAAXX:6:1:638:609
-GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAT
->HWI-EAS91_1_306UPAAXX:6:1:74:750
-GATAATCACGAGTATCCTTTCCTTTATCATCTTCAT
->HWI-EAS91_1_306UPAAXX:6:1:486:822
-GTTGACGATGTAGCTTTAGGTGTCTTTAAAACAGGT
->HWI-EAS91_1_306UPAAXX:6:1:899:473
-GAACAGCATCGGACTCAGATAGTAATCCACGCTCTT
->HWI-EAS91_1_306UPAAXX:6:1:1613:197
-GTGACATTCAGAAGGGTAATAAGAACGAACCATAAA
->HWI-EAS91_1_306UPAAXX:6:1:326:1747
-GTTGAGGCTTTCGTTTATTGTACGCTTTGCTTTTTT
->HWI-EAS91_1_306UPAAXX:6:1:1487:526
-GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
->HWI-EAS91_1_306UPAAXX:6:1:629:665
-GAAATGCAGCAGCAAGATAATCACGAGTATCCTTTC
->HWI-EAS91_1_306UPAAXX:6:1:766:744
-GGCCGTCAACATACATATCACCATTATCGAACTCAA
->HWI-EAS91_1_306UPAAXX:6:1:391:1771
-GTGGTTGATATTTTTCATGGTATTGATAAATCTTTT
->HWI-EAS91_1_306UPAAXX:6:1:591:1102
-GCTTTGCGTGACTATTTTCGTGATATTGTTCGTTTG
->HWI-EAS91_1_306UPAAXX:6:1:917:664
-GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG
->HWI-EAS91_1_306UPAAXX:6:1:217:737
-GTTCAGTTGTTGCATTGGAATATTCAGTTTAAATTT
->HWI-EAS91_1_306UPAAXX:6:1:1047:839
-GACCATTCAAAGGATAAACATCATAGGCAGTCGGGG
->HWI-EAS91_1_306UPAAXX:6:1:558:1040
-GCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAAT
->HWI-EAS91_1_306UPAAXX:6:1:1207:524
-GCCAATACCATCAGCTTTACCGTCTTTCCAGAAATT
->HWI-EAS91_1_306UPAAXX:6:1:708:1634
-GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG
->HWI-EAS91_1_306UPAAXX:6:1:576:1851
-GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG
->HWI-EAS91_1_306UPAAXX:6:1:906:460
-GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC
->HWI-EAS91_1_306UPAAXX:6:1:693:1260
-GCGAAAGGTCGCAAAGTAAGAGCTTCTCGAGCTGCG
->HWI-EAS91_1_306UPAAXX:6:1:1373:286
-GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG
->HWI-EAS91_1_306UPAAXX:6:1:762:41
-GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT
->HWI-EAS91_1_306UPAAXX:6:1:475:1091
-GTCACACAGTCCTTGACGGTATAATAACCACCATCT
->HWI-EAS91_1_306UPAAXX:6:1:791:627
-GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC
->HWI-EAS91_1_306UPAAXX:6:1:336:1791
-GAAGGAGTCGCCAGCGATAACCGGAGTAGTTGAAAT
->HWI-EAS91_1_306UPAAXX:6:1:1483:943
-GCACGTAATTTTTGACGCACGTTTTCTTCTGCGTCT
->HWI-EAS91_1_306UPAAXX:6:1:641:1071
-GATGGGCATACTGTAACCATAAGGCCACGTATTTTG
->HWI-EAS91_1_306UPAAXX:6:1:196:755
-GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT
->HWI-EAS91_1_306UPAAXX:6:1:463:1398
-GTCATAAGAGGTTTTACCTCCAAATGAAGAAATAAC
->HWI-EAS91_1_306UPAAXX:6:1:1559:460
-GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT
->HWI-EAS91_1_306UPAAXX:6:1:1625:1561
-GAGGAGTGGCATTAACACCATCCTTCATGAACTTAC
->HWI-EAS91_1_306UPAAXX:6:1:1729:1588
-GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT
->HWI-EAS91_1_306UPAAXX:6:1:945:393
-GGCCTCATCAGGGTTAGGAACATTAGAGCCTTGAAT
->HWI-EAS91_1_306UPAAXX:6:1:298:1391
-GTAAAGTTAGACCAAACCATGAAACCAACATAAACA
->HWI-EAS91_1_306UPAAXX:6:1:1270:1500
-GAATTACTACTGCTTGTTTACGAATTAAATATATGT
->HWI-EAS91_1_306UPAAXX:6:1:481:1546
-GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG
->HWI-EAS91_1_306UPAAXX:6:1:473:1729
-GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAT
->HWI-EAS91_1_306UPAAXX:6:1:801:1831
-GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT
->HWI-EAS91_1_306UPAAXX:6:1:536:639
-GCCGACCCTAAATTTTTTGCCTGTTTGGTTCTCTTT
->HWI-EAS91_1_306UPAAXX:6:1:259:938
-GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG
->HWI-EAS91_1_306UPAAXX:6:1:907:1513
-GGCATGGGTGATGCTGGTATTAAATCTGCCATTCAC
->HWI-EAS91_1_306UPAAXX:6:1:372:1409
-GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG
->HWI-EAS91_1_306UPAAXX:6:1:485:1626
-GATGGCAGCAACGGAAACCATAACGAGCATCATCTT
->HWI-EAS91_1_306UPAAXX:6:1:583:1679
-GCTCAAAGTCAAAATAATCAGCGTGACATTCAGAAG
->HWI-EAS91_1_306UPAAXX:6:1:690:1610
-GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT
->HWI-EAS91_1_306UPAAXX:6:1:257:918
-GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTTCT
->HWI-EAS91_1_306UPAAXX:6:1:818:33
-GTGTTAATGCCACTCCTCTCCCGACTGTTAACTCTG
->HWI-EAS91_1_306UPAAXX:6:1:541:1242
-GGGATTATCATAAAACGCCTCTAATCGGTCGTCAGC
->HWI-EAS91_1_306UPAAXX:6:1:1014:279
-GTAAAAATGTCTACAGTAGAGTCAATAGCAAGGCCC
->HWI-EAS91_1_306UPAAXX:6:1:672:1790
-GGCCGTTTGAATGTTGACGGGATGAACATAATAAGC
->HWI-EAS91_1_306UPAAXX:6:1:708:464
-GGAGACAAATAATCTCTTTAATAACCTGATTCAGCG
->HWI-EAS91_1_306UPAAXX:6:1:633:1486
-GGGAAAGGTCATGCGGCATACGCTCGGCGCCAGTTT
->HWI-EAS91_1_306UPAAXX:6:1:328:696
-GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT
->HWI-EAS91_1_306UPAAXX:6:1:259:1389
-GCGTACTTATTCGCCACCATGATTATTACCAGTGTT
->HWI-EAS91_1_306UPAAXX:6:1:1315:41
-GCTTTCCGTGATGTCACAGCCTGCTTTGATGTGTCG
->HWI-EAS91_1_306UPAAXX:6:1:1647:549
-GCTTAATCCAACTTACCAAGCTGGGTTACGACGCGC
->HWI-EAS91_1_306UPAAXX:6:1:300:886
-GTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTT
->HWI-EAS91_1_306UPAAXX:6:1:317:1411
-GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCTT
->HWI-EAS91_1_306UPAAXX:6:1:321:1819
-GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT
->HWI-EAS91_1_306UPAAXX:6:1:631:70
-GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC
->HWI-EAS91_1_306UPAAXX:6:1:624:1040
-GCTGGCGACTCCTTCGAGATGGACGCCGTTTGCGCT
->HWI-EAS91_1_306UPAAXX:6:1:662:1187
-GGGAGAGGAGTGGCATTAACACCATCCTTCATGACC
->HWI-EAS91_1_306UPAAXX:6:1:1440:1959
-GAATCAGCGGTATGGCTCCTCTCCTATTTTTGCTTC
->HWI-EAS91_1_306UPAAXX:6:1:458:1629
-GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT
->HWI-EAS91_1_306UPAAXX:6:1:216:790
-GGGATGAAAATGCTCACAATGACAAATCTGTCCACG
->HWI-EAS91_1_306UPAAXX:6:1:1407:1174
-TTACCTATTAGTGGTTGAACAGCATCGGACTCAGAT
->HWI-EAS91_1_306UPAAXX:6:1:999:1790
-GTCCTGCGTGTAGCGAACTGCGATGGGCATACTGTC
->HWI-EAS91_1_306UPAAXX:6:1:141:1994
-GGCTTTTTTATGGTTCGTTCTTATTACCCTTCTTAT
->HWI-EAS91_1_306UPAAXX:6:1:225:465
-GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC
->HWI-EAS91_1_306UPAAXX:6:1:649:1760
-GACCCATAATGTCAATAGATGTGGTAGAAGTCGTCT
->HWI-EAS91_1_306UPAAXX:6:1:300:986
-GTTGAACACGACCAGAAAACTGGCCTAACGACGTTT
->HWI-EAS91_1_306UPAAXX:6:1:478:605
-GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC
->HWI-EAS91_1_306UPAAXX:6:1:622:395
-GGTAGCTTTAAGCGGCTCACCTTTAGCATCAACAGG
->HWI-EAS91_1_306UPAAXX:6:1:1701:574
-GTAAAGCCTCTACGCGATTTCATAGTGGAGGCCTCC
->HWI-EAS91_1_306UPAAXX:6:1:646:59
-GGAAGTGTCCGCATAAAATGCACCGCATGGAAATGT
->HWI-EAS91_1_306UPAAXX:6:1:284:2031
-GACAGAATCGTTAGTTGATGGCGAAAGGTCGCAAAG
->HWI-EAS91_1_306UPAAXX:6:1:22:1009
-GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT
->HWI-EAS91_1_306UPAAXX:6:1:47:1826
-GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG
->HWI-EAS91_1_306UPAAXX:6:1:1025:1236
-TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT
->HWI-EAS91_1_306UPAAXX:6:1:773:591
-GAGCAGGAAAGCGAGGGTATCCCACAAAGTCCAGCG
->HWI-EAS91_1_306UPAAXX:6:1:1753:527
-GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC
->HWI-EAS91_1_306UPAAXX:6:1:426:1717
-GTAGCGCCAATATGAGAAGAGCCATACCGCTGATTC
->HWI-EAS91_1_306UPAAXX:6:1:959:818
-TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC
->HWI-EAS91_1_306UPAAXX:6:1:459:1344
-GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT
->HWI-EAS91_1_306UPAAXX:6:1:973:1367
-TTCGTGATGAGTTTGTATCTGTTACTGATAAGTTAT
->HWI-EAS91_1_306UPAAXX:6:1:201:871
-GATTAGAGGCGTTTTATGATAATCCCAATGCTTTTC
->HWI-EAS91_1_306UPAAXX:6:1:713:1672
-GGCGTACGGGGAAGGACGTCAATAGTCACACAGTCC
->HWI-EAS91_1_306UPAAXX:6:1:444:1435
-TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGTG
->HWI-EAS91_1_306UPAAXX:6:1:288:1136
-GCCTTCCATGATGAGACAGGCCGTTTTAATTTTTTC
->HWI-EAS91_1_306UPAAXX:6:1:1653:225
-GCAAGGCCACGACGCAATGGAGAAAGACGGAGAGCG
->HWI-EAS91_1_306UPAAXX:6:1:537:1764
-GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA
->HWI-EAS91_1_306UPAAXX:6:1:196:1854
-GTATCGAGGCTCTTAAACCTGCTATTTAGGCTTTTT
->HWI-EAS91_1_306UPAAXX:6:1:312:1707
-GCGTCATAAGAGGTTTTACCTCCAAATGAAGAAATA
->HWI-EAS91_1_306UPAAXX:6:1:651:183
-GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT
->HWI-EAS91_1_306UPAAXX:6:1:295:694
-GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT
->HWI-EAS91_1_306UPAAXX:6:1:330:1895
-GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG
->HWI-EAS91_1_306UPAAXX:6:1:590:331
-GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT
->HWI-EAS91_1_306UPAAXX:6:1:481:1687
-GCAGATTGCGATAAACGGTCACATTAAATTTAACCT
->HWI-EAS91_1_306UPAAXX:6:1:1112:1279
-TGTGCATATACCTGGTCTTTCGTATTCTGTCGTGAT
->HWI-EAS91_1_306UPAAXX:6:1:1099:1216
-TTAGAGCGCATGACAAGTAAAGGACGGTTGTCAGCG
->HWI-EAS91_1_306UPAAXX:6:1:221:1238
-GTATCCTTTCCTTTATCATCGGCAGACTTTTCACCT
->HWI-EAS91_1_306UPAAXX:6:1:1015:364
-GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG
->HWI-EAS91_1_306UPAAXX:6:1:735:1806
-TGTTATTAATATCAAGTTGGGGGAGCACATTGTAGC
->HWI-EAS91_1_306UPAAXX:6:1:320:411
-GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGTG
->HWI-EAS91_1_306UPAAXX:6:1:1273:1031
-TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA
->HWI-EAS91_1_306UPAAXX:6:1:1456:1088
-AATAATCAGCGTGACATTCAGAAGGGTAATAAGAAC
->HWI-EAS91_1_306UPAAXX:6:1:1365:307
-GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG
->HWI-EAS91_1_306UPAAXX:6:1:478:252
-GATGCGGTTATCCATCTGCTTATTGAAGCCAAGCAT
->HWI-EAS91_1_306UPAAXX:6:1:915:1232
-TATTAATAACACTATAGACCACCGCCCCGAAGGGGC
->HWI-EAS91_1_306UPAAXX:6:1:680:1357
-TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGC
->HWI-EAS91_1_306UPAAXX:6:1:238:1279
-GCCGAAGCCCCTGCAATTAAAATTGTTGACCACCTA
->HWI-EAS91_1_306UPAAXX:6:1:1583:35
-GCAAATTAGCATAAGCAGCTTGCAGACCCATAATGT
->HWI-EAS91_1_306UPAAXX:6:1:502:283
-GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT
->HWI-EAS91_1_306UPAAXX:6:1:418:1730
-GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT
->HWI-EAS91_1_306UPAAXX:6:1:596:647
-GCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTA
->HWI-EAS91_1_306UPAAXX:6:1:92:1591
-GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC
->HWI-EAS91_1_306UPAAXX:6:1:430:1938
-GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGTCC
->HWI-EAS91_1_306UPAAXX:6:1:212:527
-GGTATTGATAAAGCTGTTGCCGATACTTGTAACAAT
->HWI-EAS91_1_306UPAAXX:6:1:594:942
-GACGACATTAGAAATATCCTTTGCAGTAGCGCCAAT
->HWI-EAS91_1_306UPAAXX:6:1:169:1774
-GCCTTCCATGATGAGACAGGCCGTTTTAATTTTTAC
->HWI-EAS91_1_306UPAAXX:6:1:1090:210
-GGAGAGCGCCAACGGCGTCCATCTCGAAGGAGTCGC
->HWI-EAS91_1_306UPAAXX:6:1:589:96
-GGCGGCCCCATCAGGGTTAGGAACATTAGAGCCTTG
->HWI-EAS91_1_306UPAAXX:6:1:1477:1231
-TAGGAACATTAGAGCCTTGAATGGCAGATTTAATAC
->HWI-EAS91_1_306UPAAXX:6:1:707:1076
-TCTGACGTTCGTGATGAGTTTGTATCTTTTTCTTTG
->HWI-EAS91_1_306UPAAXX:6:1:749:1715
-GAACATAATAAGCAATGACGGCAGCAATAAACTCAA
->HWI-EAS91_1_306UPAAXX:6:1:1738:1884
-GCTCACCTTTAGCATCAACAGGCCACAACCAACCAG
->HWI-EAS91_1_306UPAAXX:6:1:1160:1088
-TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC
->HWI-EAS91_1_306UPAAXX:6:1:517:119
-GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT
->HWI-EAS91_1_306UPAAXX:6:1:1472:716
-TGGTAATGGTGGTTTTCTTCATTTCATTCAGTTTTT
->HWI-EAS91_1_306UPAAXX:6:1:281:441
-GAGCAGTAGACTCCTTCTGTTGATAAGCAAGCATCT
->HWI-EAS91_1_306UPAAXX:6:1:1101:324
-AATACCATCAGCTTTACCGTCTTTCCAGAAATTGTT
->HWI-EAS91_1_306UPAAXX:6:1:1225:1494
-TTCTCAAATCCGGCGTCAACCATACCAGCAGAGGAA
->HWI-EAS91_1_306UPAAXX:6:1:1509:1025
-TTCTTGCTGCCGAGGGTCGCAAGGCTATTGTTTCAC
->HWI-EAS91_1_306UPAAXX:6:1:592:510
-GATACCAATAAAATCCCTAAGCATTTGTTTCTGGTT
->HWI-EAS91_1_306UPAAXX:6:1:324:1729
-GAACAAAGAAACGCGGCACAGAATGTTTATAGGTCT
->HWI-EAS91_1_306UPAAXX:6:1:128:1925
-GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC
->HWI-EAS91_1_306UPAAXX:6:1:786:893
-TACGGGGAAGGACGTCAATAGTCACACAGTCCTTGC
->HWI-EAS91_1_306UPAAXX:6:1:248:955
-GCTACAATGTGCTCCCCCAACTTGATATTAATAACA
->HWI-EAS91_1_306UPAAXX:6:1:388:1127
-GATATTGGTCGTATGGTTCTTGCTGCCTAGTGTCTC
->HWI-EAS91_1_306UPAAXX:6:1:721:1156
-TCTGGTTGGTTGTGGCCTTTTTATGCTAAATGTTAG
->HWI-EAS91_1_306UPAAXX:6:1:1564:1468
-TTACTTTTTATGTCCCTCATCGTCACGTTTATGTTG
->HWI-EAS91_1_306UPAAXX:6:1:750:77
-GGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTA
->HWI-EAS91_1_306UPAAXX:6:1:405:487
-GTTGGATTAAGCACTCCGTGGACAGATTTGTCATTT
->HWI-EAS91_1_306UPAAXX:6:1:836:1204
-TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT
->HWI-EAS91_1_306UPAAXX:6:1:224:1548
-GCTGCCGTCATTGCTTATTATGTTCATCCCTTCAAC
->HWI-EAS91_1_306UPAAXX:6:1:931:1015
-TTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGT
->HWI-EAS91_1_306UPAAXX:6:1:329:579
-GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT
->HWI-EAS91_1_306UPAAXX:6:1:260:1145
-GCTTGCGTTTATGGTACGCTGGACTTTTTGTGATAC
->HWI-EAS91_1_306UPAAXX:6:1:1523:1253
-TTGGTAAAATACTGACCAGCCGTTTGAGCTTGAGTA
->HWI-EAS91_1_306UPAAXX:6:1:326:1271
-GACCACTCGCGATTCAATCATGACTTCGTGATAAAT
->HWI-EAS91_1_306UPAAXX:6:1:213:622
-GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA
->HWI-EAS91_1_306UPAAXX:6:1:274:712
-GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG
->HWI-EAS91_1_306UPAAXX:6:1:1549:627
-TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGT
->HWI-EAS91_1_306UPAAXX:6:1:1714:737
-TCTTTCGTATTCTGGCGTGAAGTCGCCGACTGAATG
->HWI-EAS91_1_306UPAAXX:6:1:760:1217
-TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTT
->HWI-EAS91_1_306UPAAXX:6:1:174:768
-GTTGGCTGACGACCGATTAGAGGCGTTTTTTTATAT
->HWI-EAS91_1_306UPAAXX:6:1:172:1412
-GGTCGGCAGATTGCGATAAACGTTCACATTAAATTT
->HWI-EAS91_1_306UPAAXX:6:1:1393:869
-TTCATCCCGTCAACATTCAAACGGCCTGTCTCATCT
->HWI-EAS91_1_306UPAAXX:6:1:301:481
-GTTATAGATATTCAAATAACCCTGAAACAAATGCTT
->HWI-EAS91_1_306UPAAXX:6:1:648:1093
-TAACGCTGCATGAAGTAATCACGTTCTTGGTCAGTT
->HWI-EAS91_1_306UPAAXX:6:1:1233:591
-TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCT
->HWI-EAS91_1_306UPAAXX:6:1:540:1415
-TTATTAAAGAGATTATTTTTCTCCAGCCACTTATGT
->HWI-EAS91_1_306UPAAXX:6:1:151:1792
-GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA
->HWI-EAS91_1_306UPAAXX:6:1:748:1378
-TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT
->HWI-EAS91_1_306UPAAXX:6:1:1526:1479
-TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC
->HWI-EAS91_1_306UPAAXX:6:1:985:1093
-TAACCGTCTTCTCGTTCTCTAAAAACCATTTTTCTT
->HWI-EAS91_1_306UPAAXX:6:1:480:1378
-TCAACCTCAGCACTAACCTTGCGAGTCATTTCTTTG
->HWI-EAS91_1_306UPAAXX:6:1:903:753
-TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG
->HWI-EAS91_1_306UPAAXX:6:1:1697:1737
-GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT
->HWI-EAS91_1_306UPAAXX:6:1:803:1037
-TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCTACT
->HWI-EAS91_1_306UPAAXX:6:1:1727:1244
-TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT
->HWI-EAS91_1_306UPAAXX:6:1:253:1162
-GCATTTAGTAGCGGTAAAGTTTGACCAAACCATTAT
->HWI-EAS91_1_306UPAAXX:6:1:216:856
-GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT
->HWI-EAS91_1_306UPAAXX:6:1:825:886
-TCCCACAAAGTCCAGCGTACCATAAACGCAAGCCTC
->HWI-EAS91_1_306UPAAXX:6:1:1699:962
-TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT
->HWI-EAS91_1_306UPAAXX:6:1:1210:625
-TCAGATAGTAATCCACGCTCTTTTAAAATGTCAACA
->HWI-EAS91_1_306UPAAXX:6:1:538:616
-TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT
->HWI-EAS91_1_306UPAAXX:6:1:184:1849
-GCTCACCTTTAGCATCAACAGGCCACAACCAACCAG
->HWI-EAS91_1_306UPAAXX:6:1:1636:1103
-TATCTGACTTTTTGTTAACGTATTTAGCCACATAGA
->HWI-EAS91_1_306UPAAXX:6:1:605:223
-GGTTATTTGAATATCTATAACAACTATTTTAAATCG
->HWI-EAS91_1_306UPAAXX:6:1:256:1052
-GGTAAAGGACTTCTTGAAGGTACGTTGCAGTCTGGC
->HWI-EAS91_1_306UPAAXX:6:1:300:1515
-GCCATGATGGTGGTTATTATACCGTCAAGGACTTTT
->HWI-EAS91_1_306UPAAXX:6:1:1684:1320
-TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA
->HWI-EAS91_1_306UPAAXX:6:1:1186:895
-TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT
->HWI-EAS91_1_306UPAAXX:6:1:1463:754
-TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT
->HWI-EAS91_1_306UPAAXX:6:1:808:1053
-TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG
->HWI-EAS91_1_306UPAAXX:6:1:960:1218
-TTTCTAATGTCGTCACTGATGCTGCTTCTGTTGTTT
->HWI-EAS91_1_306UPAAXX:6:1:521:1646
-GGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCA
->HWI-EAS91_1_306UPAAXX:6:1:289:1885
-GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG
->HWI-EAS91_1_306UPAAXX:6:1:471:170
-GGTCAGTTCCATCAACATCATAGCCAGATGCCCAGA
->HWI-EAS91_1_306UPAAXX:6:1:828:754
-TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT
->HWI-EAS91_1_306UPAAXX:6:1:924:1679
-TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT
->HWI-EAS91_1_306UPAAXX:6:1:837:901
-TGCATTTTAGTAAGCTCTTTTTGATTCTCAAATCCG
->HWI-EAS91_1_306UPAAXX:6:1:543:16
-GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC
->HWI-EAS91_1_306UPAAXX:6:1:1482:578
-TCTTTAGCTCCTAGACCTTTAGCAGCAAGGTCCATA
->HWI-EAS91_1_306UPAAXX:6:1:1254:1668
-TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT
->HWI-EAS91_1_306UPAAXX:6:1:1402:898
-TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC
->HWI-EAS91_1_306UPAAXX:6:1:764:1534
-TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT
->HWI-EAS91_1_306UPAAXX:6:1:681:1079
-TGGCGAATAAGTACGCGTTCTTGCAAATCACCAGAA
->HWI-EAS91_1_306UPAAXX:6:1:672:1350
-TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT
->HWI-EAS91_1_306UPAAXX:6:1:1266:493
-TGACCAGCCGTTTGAGCTTGAGTAAGCATTTGGCGC
->HWI-EAS91_1_306UPAAXX:6:1:118:238
-GACGGTATAATAACCACCATCATGGCGACCATTCAA
->HWI-EAS91_1_306UPAAXX:6:1:699:433
-TTATTGCCCGGCGTACGGGGAAGGACGTCAATAGTC
->HWI-EAS91_1_306UPAAXX:6:1:708:1387
-TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC
->HWI-EAS91_1_306UPAAXX:6:1:498:1085
-TTATGATAATCCCAATGCTTTGCGTGACTATTTTCT
->HWI-EAS91_1_306UPAAXX:6:1:1101:1301
-TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAT
->HWI-EAS91_1_306UPAAXX:6:1:261:213
-GAATGGTCGCCATGATGGTGGTTATTATACCGTCAC
->HWI-EAS91_1_306UPAAXX:6:1:1287:1267
-TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGT
->HWI-EAS91_1_306UPAAXX:6:1:744:331
-TTAATGGATGAATTGGCACAATGCTACAATGTGCTC
->HWI-EAS91_1_306UPAAXX:6:1:614:814
-TGTCAGCGTCATAAGAGGTTTTACCTCCAAATGAAG
->HWI-EAS91_1_306UPAAXX:6:1:1362:1063
-TAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAG
->HWI-EAS91_1_306UPAAXX:6:1:1238:1508
-TCAACTAACGATTCTGTCAAAAACTGACGCGTTGGT
->HWI-EAS91_1_306UPAAXX:6:1:904:1130
-TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT
->HWI-EAS91_1_306UPAAXX:6:1:465:216
-GACCATGCCGCTTTTCTTGGCACGATTAACCCTTAT
->HWI-EAS91_1_306UPAAXX:6:1:844:628
-TAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGC
->HWI-EAS91_1_306UPAAXX:6:1:684:1444
-TATCCCACAAAGTCCAGCGTACCATAAACGCAAGCC
->HWI-EAS91_1_306UPAAXX:6:1:515:1373
-TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT
->HWI-EAS91_1_306UPAAXX:6:1:764:1667
-TTGAGTTCGATAATGGTGATATGTATGTTGACGTCC
->HWI-EAS91_1_306UPAAXX:6:1:1722:598
-TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCT
->HWI-EAS91_1_306UPAAXX:6:1:670:1188
-TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT
->HWI-EAS91_1_306UPAAXX:6:1:1682:1705
-TAGCCACATAGAAACCAACAGCCATATAACTGGTAG
->HWI-EAS91_1_306UPAAXX:6:1:1008:1616
-TCCTTTACTTGTCATGCGCTCTAATCTCTGTGCATC
->HWI-EAS91_1_306UPAAXX:6:1:490:1220
-TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCT
->HWI-EAS91_1_306UPAAXX:6:1:891:1437
-TAATGGTGATATGTATGTTTACGTCCATAAGGCTGT
->HWI-EAS91_1_306UPAAXX:6:1:1310:321
-TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGT
->HWI-EAS91_1_306UPAAXX:6:1:827:1597
-TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC
->HWI-EAS91_1_306UPAAXX:6:1:1062:1158
-TAGAGTCAATAGCAAGGCCACGACGCAATGGAGAAA
->HWI-EAS91_1_306UPAAXX:6:1:1419:208
-TGGCGCATAATCTCGGAAACCTGCTGTTGCTTGGAA
->HWI-EAS91_1_306UPAAXX:6:1:691:1018
-AAATATCAACCACACCAGAAGCAGCATCAGTGACGA
->HWI-EAS91_1_306UPAAXX:6:1:374:113
-GATAAAGCTGTTGCCGATACTTGGAACAATTTCTGT
->HWI-EAS91_1_306UPAAXX:6:1:1720:784
-TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC
->HWI-EAS91_1_306UPAAXX:6:1:1424:1394
-ATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTT
->HWI-EAS91_1_306UPAAXX:6:1:1063:1760
-TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT
->HWI-EAS91_1_306UPAAXX:6:1:1235:729
-TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA
->HWI-EAS91_1_306UPAAXX:6:1:167:1507
-TAGTGTTATTAATATCAAGTTTTTGGAGCACATTGT
->HWI-EAS91_1_306UPAAXX:6:1:717:1569
-TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT
->HWI-EAS91_1_306UPAAXX:6:1:610:765
-TTCAGCGCCTTCCATGATGAGACAGGCCGTTTGAAT
->HWI-EAS91_1_306UPAAXX:6:1:663:380
-TAAACATTCTGTGCCGCGTTTCTTTGTTCCTTATCT
->HWI-EAS91_1_306UPAAXX:6:1:790:1358
-TTATCACCTTATTGAAGGCTTATCATTCATTTAGGT
->HWI-EAS91_1_306UPAAXX:6:1:965:1633
-TAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGCT
->HWI-EAS91_1_306UPAAXX:6:1:673:319
-TTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAT
->HWI-EAS91_1_306UPAAXX:6:1:684:371
-TAGCGGTAAAGTTAGACCAAACCATGAAACCAACAT
->HWI-EAS91_1_306UPAAXX:6:1:1147:1444
-ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC
->HWI-EAS91_1_306UPAAXX:6:1:983:678
-ATACCTGGTCTTTCGTATTCTGGCGTGAAGTCGCCG
->HWI-EAS91_1_306UPAAXX:6:1:1608:1119
-TCACGCGGCGGCAAGTTGCCATACAAAACAGGGTCG
->HWI-EAS91_1_306UPAAXX:6:1:1048:1193
-TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAT
->HWI-EAS91_1_306UPAAXX:6:1:1265:1429
-ATATTTTTCATGGTATTGATAAAGCTGTTGCCGATT
->HWI-EAS91_1_306UPAAXX:6:1:1607:1677
-TGTTGCTTGGAAAGATTGGTGTTTTCCATAATAGAC
->HWI-EAS91_1_306UPAAXX:6:1:1087:1421
-ACGAACGTCAGAAGCAGCCTTATGGCCGTCAACATC
->HWI-EAS91_1_306UPAAXX:6:1:324:490
-GCACCAAACATAAATCACCTCACTTAAGTGGCTGGG
->HWI-EAS91_1_306UPAAXX:6:1:1596:614
-TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGT
->HWI-EAS91_1_306UPAAXX:6:1:343:83
-GTTACGCAGTTTTGCCGCAAGCTGGCTGCTGTACGC
->HWI-EAS91_1_306UPAAXX:6:1:203:667
-GCATGAATGTGCTTAATAGAGGCCAAGGCGGTCTAG
->HWI-EAS91_1_306UPAAXX:6:1:34:480
-GGCAAGTTGCCATACAAAACAGGGTCGCCAGCAATT
->HWI-EAS91_1_306UPAAXX:6:1:606:1743
-TAGCGACAGCTTGGTTTTTAGTGAGTTGTTCCATTC
->HWI-EAS91_1_306UPAAXX:6:1:254:1391
-TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG
->HWI-EAS91_1_306UPAAXX:6:1:1568:1750
-TAACCAGTAGTGTTAACAGTCGGGAGAGGAGTGGCT
->HWI-EAS91_1_306UPAAXX:6:1:1538:869
-TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA
->HWI-EAS91_1_306UPAAXX:6:1:255:38
-GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT
->HWI-EAS91_1_306UPAAXX:6:1:1543:1555
-TAAAACGCCTCTAATCGGTCGTCAGCCAACGTGAGG
->HWI-EAS91_1_306UPAAXX:6:1:1365:733
-AGAATCAGCGGTATGGCTCTTCTCCTTTTTTCGCTT
->HWI-EAS91_1_306UPAAXX:6:1:1604:943
-TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT
->HWI-EAS91_1_306UPAAXX:6:1:1574:1632
-TCAGTATGCAAATTAGCATAAGCAGCTTGCAGACCC
->HWI-EAS91_1_306UPAAXX:6:1:565:1799
-TCTTGGTCAGTATGCAAATTAGCATAAGCAGCTTGC
->HWI-EAS91_1_306UPAAXX:6:1:1004:380
-TATTGACTCTACTGTAGACATTTTTACTTTTTATTT
->HWI-EAS91_1_306UPAAXX:6:1:1345:965
-ATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGT
->HWI-EAS91_1_306UPAAXX:6:1:1704:756
-TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG
->HWI-EAS91_1_306UPAAXX:6:1:310:1346
-TATAACGTTGACGATGTAGCTTTAGTTTTCTTTAAA
->HWI-EAS91_1_306UPAAXX:6:1:900:1858
-TTTACCGCTTCGGCGTTATAACCTCACACTCAATCT
->HWI-EAS91_1_306UPAAXX:6:1:1250:1741
-TAAATCCAAAACGGCAGAAGCCTGAATGAGCTTAAT
->HWI-EAS91_1_306UPAAXX:6:1:1170:1317
-TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC
->HWI-EAS91_1_306UPAAXX:6:1:149:1896
-GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC
->HWI-EAS91_1_306UPAAXX:6:1:1504:494
-TGTCTACAGTAGAGTCAATAGCAAGGCCACGACGCC
->HWI-EAS91_1_306UPAAXX:6:1:395:256
-GTCCATATCTGACTTTTTGTTAACGTATTTATCCAC
->HWI-EAS91_1_306UPAAXX:6:1:1110:1109
-ACCGCTTCGGCGTTATAACCTCACACTCAATCTTTT
->HWI-EAS91_1_306UPAAXX:6:1:895:649
-TTCTGCACGTAATTTTTGACGCACGTTTTCTTCTGC
->HWI-EAS91_1_306UPAAXX:6:1:827:1378
-TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG
->HWI-EAS91_1_306UPAAXX:6:1:1051:1587
-TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG
->HWI-EAS91_1_306UPAAXX:6:1:1656:1549
-AACCTGCTGTTGCTTGGAAAGATTGGTGTTTTCCAT
->HWI-EAS91_1_306UPAAXX:6:1:366:150
-GGTCAGTAGCAATCCAAACTTTGTTACTCGTCAGAA
->HWI-EAS91_1_306UPAAXX:6:1:955:1792
-ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA
->HWI-EAS91_1_306UPAAXX:6:1:1340:1403
-ATAAAATGCACCGCATGGAAATGAAGACGGCCATTA
->HWI-EAS91_1_306UPAAXX:6:1:1693:1017
-TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGT
->HWI-EAS91_1_306UPAAXX:6:1:1099:1572
-AATTTTTACCGCTTCGGCGTTATAACCTCACACTCA
->HWI-EAS91_1_306UPAAXX:6:1:218:1148
-TATGCAAATTAGCATAAGCAGCTTGCAGACCCATAT
->HWI-EAS91_1_306UPAAXX:6:1:403:614
-TGGTGCTGATGCTTCCTCTGCTGGTATGGTTTACGC
->HWI-EAS91_1_306UPAAXX:6:1:1651:646
-TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC
->HWI-EAS91_1_306UPAAXX:6:1:1566:499
-TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG
->HWI-EAS91_1_306UPAAXX:6:1:825:951
-ACAGGCCGTTTGAATGTTTACGGGGTGTACATAATA
->HWI-EAS91_1_306UPAAXX:6:1:1745:1865
-TTAACTTCTGCGTCATGGAAGCGATAAAACTCTGCG
->HWI-EAS91_1_306UPAAXX:6:1:973:1992
-TAGTAATTCCTGCTTTATCAAGATAATTTTTCGACT
->HWI-EAS91_1_306UPAAXX:6:1:171:1653
-TAATAATGTTTTCCGTAAATTCAGCGCCTTCCATGT
->HWI-EAS91_1_306UPAAXX:6:1:397:363
-TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT
->HWI-EAS91_1_306UPAAXX:6:1:1336:1155
-ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG
->HWI-EAS91_1_306UPAAXX:6:1:685:629
-AGTATGCAAATTAGCATAAGCAGCTTGCAGACCCAT
->HWI-EAS91_1_306UPAAXX:6:1:1409:510
-ACATAATAAGCAATGACGGCAGCAATAAACTCAACA
->HWI-EAS91_1_306UPAAXX:6:1:1631:998
-AACCATCAGCATGAGCCTGTCGCATTGCATTCATCC
->HWI-EAS91_1_306UPAAXX:6:1:260:1698
-TTATTATGTTCATCCCGTCAACATTCAAACTGCCTT
->HWI-EAS91_1_306UPAAXX:6:1:578:971
-TTAACGCTACTAAATTCCGCGGATTGGTTTCGTTGT
->HWI-EAS91_1_306UPAAXX:6:1:1613:642
-ATAGAAATTTCACGCGGCGGCAAGTTGCCATACAAA
->HWI-EAS91_1_306UPAAXX:6:1:237:650
-GACGGTATAATAACCACCATCATGGCGACCATTCAA
->HWI-EAS91_1_306UPAAXX:6:1:1100:1875
-TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG
->HWI-EAS91_1_306UPAAXX:6:1:352:32
-GTACCATAAACGCAAGCCTCAACGCAGCGACGAGCC
->HWI-EAS91_1_306UPAAXX:6:1:443:229
-GCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAAC
->HWI-EAS91_1_306UPAAXX:6:1:1131:731
-AGCAGTCGGCGTGTGAATCATTAGCCTTGCGACCCT
->HWI-EAS91_1_306UPAAXX:6:1:133:1089
-AAGGTTAGTGCTGAGGTTGACTTAGTTCATCATCAA
->HWI-EAS91_1_306UPAAXX:6:1:65:1307
-TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT
->HWI-EAS91_1_306UPAAXX:6:1:905:1493
-TCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTT
->HWI-EAS91_1_306UPAAXX:6:1:733:540
-TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAT
->HWI-EAS91_1_306UPAAXX:6:1:161:1707
-TAATGTCGTCACTGATGCTGCTTCTGTTGTTGTTTT
->HWI-EAS91_1_306UPAAXX:6:1:380:1861
-TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC
->HWI-EAS91_1_306UPAAXX:6:1:1761:566
-TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAT
->HWI-EAS91_1_306UPAAXX:6:1:1486:651
-TGGCGGTATTTCTTCTTCTCTTTCTTGTTGCGCCCT
->HWI-EAS91_1_306UPAAXX:6:1:508:1380
-TCCATCAACATCATAGCCAGATGCCCAGAGATTAGA
->HWI-EAS91_1_306UPAAXX:6:1:1763:855
-TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC
->HWI-EAS91_1_306UPAAXX:6:1:1553:553
-TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA
->HWI-EAS91_1_306UPAAXX:6:1:1424:507
-TCCACTGCAACAACTGAACGGACTGGAAACACTGGT
->HWI-EAS91_1_306UPAAXX:6:1:988:135
-TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC
->HWI-EAS91_1_306UPAAXX:6:1:810:1918
-TTTTCATCCCGAAGTTGCGGCTCATTCTGATTCTGT
->HWI-EAS91_1_306UPAAXX:6:1:588:559
-TCTGGTTGAACGGCGTCGCGTCGTAACCCAGCTTGG
->HWI-EAS91_1_306UPAAXX:6:1:1264:1214
-ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC
->HWI-EAS91_1_306UPAAXX:6:1:1000:1475
-TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG
->HWI-EAS91_1_306UPAAXX:6:1:1389:160
-TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT
->HWI-EAS91_1_306UPAAXX:6:1:422:1296
-TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGT
->HWI-EAS91_1_306UPAAXX:6:1:1273:856
-TAGCCATAGCACCAGAAACAAAACTAGGGGCGGCCT
->HWI-EAS91_1_306UPAAXX:6:1:450:969
-TGTTTTCCATAATAGACGCAACGCGAGCAGTAGACT
->HWI-EAS91_1_306UPAAXX:6:1:1202:828
-ATCGTCAACGTTATATTTTGATAGTTTGACGTTTAT
->HWI-EAS91_1_306UPAAXX:6:1:1721:1800
-GGGTTAGGGACATTAGAGCCTTGACTGACTGAGTTT
->HWI-EAS91_1_306UPAAXX:6:1:228:2019
-TTGAGTAAGCATTTGGCGCATAATCTCGGAAACCTG
->HWI-EAS91_1_306UPAAXX:6:1:1579:1214
-ACGTTTGGTCAGTTCCATCAACATCATAGCCAGATG
->HWI-EAS91_1_306UPAAXX:6:1:429:1055
-TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCTTT
->HWI-EAS91_1_306UPAAXX:6:1:1359:1689
-AAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAA
->HWI-EAS91_1_306UPAAXX:6:1:1474:1056
-TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC
->HWI-EAS91_1_306UPAAXX:6:1:105:1818
-TTGGGGATTGAGAAAGAGTAGAAATGCCACAAGCCT
->HWI-EAS91_1_306UPAAXX:6:1:208:1538
-TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
->HWI-EAS91_1_306UPAAXX:6:1:1361:1623
-AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA
->HWI-EAS91_1_306UPAAXX:6:1:595:1670
-TGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACA
->HWI-EAS91_1_306UPAAXX:6:1:6:1885
-TCTAATGTCGTCACTGATGCTGCTTCTGGTGTGTTT
->HWI-EAS91_1_306UPAAXX:6:1:706:1085
-TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG
->HWI-EAS91_1_306UPAAXX:6:1:1307:825
-AGCGGTAAAGTTAGACCAAACCATGAAACCAACATA
->HWI-EAS91_1_306UPAAXX:6:1:762:802
-TGGCATTAACACCATCCTTCATGAACTTAATCCACT
->HWI-EAS91_1_306UPAAXX:6:1:1657:506
-TTGCGACCCTCGGCAGCAAGAACCATACGACCAATT
->HWI-EAS91_1_306UPAAXX:6:1:184:811
-TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC
->HWI-EAS91_1_306UPAAXX:6:1:1469:1718
-TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTT
->HWI-EAS91_1_306UPAAXX:6:1:815:1640
-TGGCGGCGATTGCGTACCCGACGACCCAAATTAGGG
->HWI-EAS91_1_306UPAAXX:6:1:1580:1388
-AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG
->HWI-EAS91_1_306UPAAXX:6:1:1617:1554
-TACGGGGAAGGACGTCAATAGTCACACAGTCCTTGA
->HWI-EAS91_1_306UPAAXX:6:1:1544:431
-TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA
->HWI-EAS91_1_306UPAAXX:6:1:1604:1541
-TCAGTGACGACATTAGAAATATCCTTTGCAGTAGCG
->HWI-EAS91_1_306UPAAXX:6:1:1485:741
-ATCAAACGCTGAATAGTAAAGCCTCTACGCGATTTC
->HWI-EAS91_1_306UPAAXX:6:1:1226:393
-TGCCACAAGCCTCAATAGCAGGTTTAAGAGCCTCGA
->HWI-EAS91_1_306UPAAXX:6:1:1506:973
-ATTAGGGTCAACGCTACCTGTAGGAAGTGTCCGCAT
->HWI-EAS91_1_306UPAAXX:6:1:890:1838
-TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC
->HWI-EAS91_1_306UPAAXX:6:1:453:1527
-TAAGAGGGCGTTCAGCAGCCAGCTTGCGGCAAAACT
->HWI-EAS91_1_306UPAAXX:6:1:1056:570
-ACATTGTAGCATTGTGCCAATTCATCCATTAACTTC
->HWI-EAS91_1_306UPAAXX:6:1:1736:74
-TATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGT
->HWI-EAS91_1_306UPAAXX:6:1:169:1896
-GTATGCAAATTAGCATAAGCAGCTTGCAGACCCATA
->HWI-EAS91_1_306UPAAXX:6:1:259:949
-TGAGGATAAATTATGTCTAATATTCAAACTTGCTCC
->HWI-EAS91_1_306UPAAXX:6:1:1205:893
-ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT
->HWI-EAS91_1_306UPAAXX:6:1:732:1335
-TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT
->HWI-EAS91_1_306UPAAXX:6:1:667:664
-TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG
->HWI-EAS91_1_306UPAAXX:6:1:535:587
-TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT
->HWI-EAS91_1_306UPAAXX:6:1:412:446
-GTGTGGTTGATATTTTTCATGGTATTGATAAAGCTT
->HWI-EAS91_1_306UPAAXX:6:1:507:1599
-TTGCTGGCGGTTTTTCTTTTTTTTTTTTTTTTTTTT
->HWI-EAS91_1_306UPAAXX:6:1:575:1818
-TAAAATGCACCGCATGGAAATGAAGACGGCCATTAG
->HWI-EAS91_1_306UPAAXX:6:1:1568:1428
-ACCAGTTATATGGCTGGTTGTTTTTTTTTTTTTTTT
->HWI-EAS91_1_306UPAAXX:6:1:1417:982
-AACAAGAGAATCTCTACCATGAACAAAATGTGACTC
->HWI-EAS91_1_306UPAAXX:6:1:280:1340
-GGCCAAACCAGTGGCGATGGCCGCGCTGGAGGTTTT
->HWI-EAS91_1_306UPAAXX:6:1:966:144
-TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT
->HWI-EAS91_1_306UPAAXX:6:1:1391:1987
-TAATAATGTTTTCCGTAAATTCAGCGCCTTCCATGT
->HWI-EAS91_1_306UPAAXX:6:1:1280:278
-ATGGAAATGAAGACGGCCATTAGCTGTACCATACTC
->HWI-EAS91_1_306UPAAXX:6:1:631:858
-TGATATTGGTCGTATGGTTCTTGCTTCCGTGGGTCT
->HWI-EAS91_1_306UPAAXX:6:1:518:573
-TTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGT
->HWI-EAS91_1_306UPAAXX:6:1:54:981
-TTGACATTTTAAAAGAGCGTGGATTACTATCTGATT
->HWI-EAS91_1_306UPAAXX:6:1:218:1165
-TATTGACTCTACTGTAGACATTTTTACTTTTTATTT
->HWI-EAS91_1_306UPAAXX:6:1:1727:1530
-TCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCA
->HWI-EAS91_1_306UPAAXX:6:1:519:657
-TGAACAGCATCGGACTCAGATAGTAATCCACGCTCT
->HWI-EAS91_1_306UPAAXX:6:1:939:967
-ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC
->HWI-EAS91_1_306UPAAXX:6:1:299:1060
-TATAACTGGTAGCTTTAAGCGGCTCACCTTTAGCAT
->HWI-EAS91_1_306UPAAXX:6:1:438:665
-TAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTAT
->HWI-EAS91_1_306UPAAXX:6:1:1303:1971
-AGCATTGTGCCAATTCATCCATTAACTTCTCAGTAA
->HWI-EAS91_1_306UPAAXX:6:1:214:1264
-TCAGCACCAACAGAAACAACCTGATTAGCGGCGTTG
->HWI-EAS91_1_306UPAAXX:6:1:1454:1423
-AACGGAAAACATCCTTCATAGAAATTTCACGCGGCG
->HWI-EAS91_1_306UPAAXX:6:1:1633:340
-TTCCATAATAGACGCAACGCGAGCAGTAGACTCCTT
->HWI-EAS91_1_306UPAAXX:6:1:671:1196
-ATACGAAAAGACAGAATCTCTTCCAAGAGCTTGATG
diff -r 8d149264b777 -r efdb6fb5de34 test-data/b1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b1.fasta Fri Nov 27 10:53:50 2009 -0500
@@ -0,0 +1,1000 @@
+>HWI-EAS91_1_306UPAAXX:6:1:1503:1160
+GGTGGTCTATAGTGTTATTAATATCAAGTTGGGGGG
+>HWI-EAS91_1_306UPAAXX:6:1:1564:1179
+GCGAGCAGTAGACTCCTTCTGTTGATAAGCAAGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1704:1082
+GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1588:1797
+GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1304:1526
+GTAGTTGAAATGGTAATAAGACGACCAATCTGACCT
+>HWI-EAS91_1_306UPAAXX:6:1:1490:1582
+GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC
+>HWI-EAS91_1_306UPAAXX:6:1:1356:1339
+GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC
+>HWI-EAS91_1_306UPAAXX:6:1:1311:853
+GGTTGGTTTATCGTTTTTGACACTCTCACGTTGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:1257:1552
+GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC
+>HWI-EAS91_1_306UPAAXX:6:1:1486:1402
+GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC
+>HWI-EAS91_1_306UPAAXX:6:1:1028:1081
+GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT
+>HWI-EAS91_1_306UPAAXX:6:1:1167:752
+GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC
+>HWI-EAS91_1_306UPAAXX:6:1:1507:1113
+GTCAACGTTATATTTTGATAGTTTGACGGTTAATTC
+>HWI-EAS91_1_306UPAAXX:6:1:1654:1311
+GGATGAAAATGCTCACAATGACAAATCTGTCCACGG
+>HWI-EAS91_1_306UPAAXX:6:1:1386:1060
+GTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1070:1356
+GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG
+>HWI-EAS91_1_306UPAAXX:6:1:787:1032
+GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA
+>HWI-EAS91_1_306UPAAXX:6:1:834:1017
+GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1703:1155
+GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT
+>HWI-EAS91_1_306UPAAXX:6:1:1406:593
+GTTGAGTTCGATAATGGTGATATGTATGTTTACGGC
+>HWI-EAS91_1_306UPAAXX:6:1:1411:886
+GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:923:972
+GCATGACAAGTAAAGGACGGTTGTCAGCGTCATAAG
+>HWI-EAS91_1_306UPAAXX:6:1:1279:1004
+GCCATAGCACCAGAAACAAAACTAGGGGCGGCCTCT
+>HWI-EAS91_1_306UPAAXX:6:1:1070:840
+GGTTGTCAGCGTCATAAGAGGTTTTACCTCCAAATG
+>HWI-EAS91_1_306UPAAXX:6:1:1595:1040
+GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1002:559
+GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG
+>HWI-EAS91_1_306UPAAXX:6:1:999:974
+GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC
+>HWI-EAS91_1_306UPAAXX:6:1:896:982
+GTGGCTGGAGACAAATAATCTCTTTAATAACCTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1366:741
+GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC
+>HWI-EAS91_1_306UPAAXX:6:1:749:1469
+GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT
+>HWI-EAS91_1_306UPAAXX:6:1:1010:592
+GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1393:650
+GTGACTCATATCTAAACCAGTCCTTGACGAACGTGC
+>HWI-EAS91_1_306UPAAXX:6:1:1238:1731
+GAGAAATAAAAGTCTGAAACATGATTAAACTCCTAA
+>HWI-EAS91_1_306UPAAXX:6:1:1629:908
+GATGCGGTTATCCATCTGCTTATGGAAGCCAAGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1560:849
+GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG
+>HWI-EAS91_1_306UPAAXX:6:1:1029:783
+GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1152:1324
+GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG
+>HWI-EAS91_1_306UPAAXX:6:1:1614:2042
+GAAATGCCACAAGCCTCAATAGCAGGTTTAAGAGCC
+>HWI-EAS91_1_306UPAAXX:6:1:1398:439
+GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG
+>HWI-EAS91_1_306UPAAXX:6:1:955:616
+GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC
+>HWI-EAS91_1_306UPAAXX:6:1:1672:753
+GAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCT
+>HWI-EAS91_1_306UPAAXX:6:1:1195:1293
+GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC
+>HWI-EAS91_1_306UPAAXX:6:1:1074:755
+GCAAGAGTAAACATAGTGCCATGCTCAGGAACAAAG
+>HWI-EAS91_1_306UPAAXX:6:1:984:499
+GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1452:1833
+GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT
+>HWI-EAS91_1_306UPAAXX:6:1:863:710
+GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT
+>HWI-EAS91_1_306UPAAXX:6:1:885:649
+GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC
+>HWI-EAS91_1_306UPAAXX:6:1:917:1214
+GACAGATGTATCCATCTGAATGCAATGAAGAAAACC
+>HWI-EAS91_1_306UPAAXX:6:1:892:1254
+GCTCAGGAAATGCAGCAGCAAGATAATCACGAGTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1555:1005
+GCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCT
+>HWI-EAS91_1_306UPAAXX:6:1:1637:1413
+GATGCTGTTCAACCACTAATAGGTAAGAAATCATGT
+>HWI-EAS91_1_306UPAAXX:6:1:1102:1567
+GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA
+>HWI-EAS91_1_306UPAAXX:6:1:799:1337
+GTATATGCACAAAATGAGATGCTTGCTTATCAACAG
+>HWI-EAS91_1_306UPAAXX:6:1:1353:1843
+GCAGACCCATAATGTCAATAGATGTGGTAGAAGTCG
+>HWI-EAS91_1_306UPAAXX:6:1:1196:789
+GCGGCATACGCTCGGCGCCAGTTTGAATATTAGACA
+>HWI-EAS91_1_306UPAAXX:6:1:1056:1676
+GTAAAATACTGACCAGCCGTTTGAGCTTGAGTAAGC
+>HWI-EAS91_1_306UPAAXX:6:1:1349:1836
+GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1027:788
+GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT
+>HWI-EAS91_1_306UPAAXX:6:1:990:1283
+GCTTAGGGATTTTATTGGTATCAGGGTTAATCGTGC
+>HWI-EAS91_1_306UPAAXX:6:1:904:939
+GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1732:793
+GTCAACATACATATCACCATTATCGAACTCAACGCC
+>HWI-EAS91_1_306UPAAXX:6:1:1355:2003
+GTTAGACCAAACCATGAAACCAACATAAACATTATT
+>HWI-EAS91_1_306UPAAXX:6:1:1337:977
+GCACCAGAAACAAAACTAGGGGCGGCCTCATCAGGG
+>HWI-EAS91_1_306UPAAXX:6:1:1605:1175
+GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT
+>HWI-EAS91_1_306UPAAXX:6:1:1763:1192
+GACAGGCCGTTTGAATGTTGACGGGATGAACATAAT
+>HWI-EAS91_1_306UPAAXX:6:1:722:483
+GTTATTATACCGTCAAGGACTGTGTGACTATTGACT
+>HWI-EAS91_1_306UPAAXX:6:1:1760:1136
+GCAAAGCATTGGGATTATCATAAAACGCCTCTAATC
+>HWI-EAS91_1_306UPAAXX:6:1:1088:798
+GGAAACCTGCTGTTGCTTGGAAAGATTGGTGTTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:633:1076
+GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG
+>HWI-EAS91_1_306UPAAXX:6:1:673:754
+GTCATGGAAGCGATAAAACTCTGCAGGTTGGATATT
+>HWI-EAS91_1_306UPAAXX:6:1:1759:2019
+GTAAAGGACGGTTGTCAGCGTCATAAGAGGTTTTAC
+>HWI-EAS91_1_306UPAAXX:6:1:1064:1797
+GCGGTTATCCATCTGCTTATGGAAGCCAAGCATTGG
+>HWI-EAS91_1_306UPAAXX:6:1:1112:1669
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT
+>HWI-EAS91_1_306UPAAXX:6:1:510:1447
+GCATTAAGCTCAGGAAATGCAGCAGCAAGATAATCA
+>HWI-EAS91_1_306UPAAXX:6:1:877:1573
+GTGCTATTGCTGGCGGTATTTCTTCTTCTTTTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:870:542
+GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC
+>HWI-EAS91_1_306UPAAXX:6:1:966:384
+GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA
+>HWI-EAS91_1_306UPAAXX:6:1:1186:1903
+GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG
+>HWI-EAS91_1_306UPAAXX:6:1:1632:1742
+GCATCACCCATGCCTACAGTATTGTTATCGGTAGCC
+>HWI-EAS91_1_306UPAAXX:6:1:1521:559
+GAGAGCGCCAACGGCGTCCATCTCGAAGGAGTCGCC
+>HWI-EAS91_1_306UPAAXX:6:1:683:454
+GCTTATTATGTTCATCCCGTCAACATTCAAACGTCC
+>HWI-EAS91_1_306UPAAXX:6:1:112:1280
+GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGTC
+>HWI-EAS91_1_306UPAAXX:6:1:891:381
+GACCAGGGCGAGCGCCAGAACGTTTTTTACCTTTAG
+>HWI-EAS91_1_306UPAAXX:6:1:1348:958
+GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1785:1915
+GCCCCGAAGGGGACNANAAATGGTTTTTAGAGAACG
+>HWI-EAS91_1_306UPAAXX:6:1:1418:42
+GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1421:743
+GGTCAACGCTACCTGTAGGAAGTGTCCGCATAAAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1079:790
+GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT
+>HWI-EAS91_1_306UPAAXX:6:1:663:740
+GGTATTAAGGATGAGTGTTCAAGATTGCTGGATGCC
+>HWI-EAS91_1_306UPAAXX:6:1:1245:413
+GTTTGAATGTTGACGGGATGAACATAATAAGCAATG
+>HWI-EAS91_1_306UPAAXX:6:1:1378:1035
+GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGG
+>HWI-EAS91_1_306UPAAXX:6:1:903:1746
+GTACGGGGAAGGACGTCAATAGTCACACAGTCCTTG
+>HWI-EAS91_1_306UPAAXX:6:1:1713:1134
+GGCGTACGGGGAAGGACGTCAATAGTCACACAGTCC
+>HWI-EAS91_1_306UPAAXX:6:1:1246:1887
+GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG
+>HWI-EAS91_1_306UPAAXX:6:1:872:1731
+GGGCGGCCTCATCAGGGTTAGGAACATTAGAGCCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1714:1582
+GCTTTCCTGCTCCTGTTGAGTTTATTGCTTCCGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:1785:763
+GNCGAGAAATAAAANNNTGAAACATGATTAAANTCC
+>HWI-EAS91_1_306UPAAXX:6:1:1684:542
+GAAAAGACAGAATCTCTTCCAAGAGCTTGATGCGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1581:1665
+GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT
+>HWI-EAS91_1_306UPAAXX:6:1:901:1581
+GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1128:239
+GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC
+>HWI-EAS91_1_306UPAAXX:6:1:969:441
+GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG
+>HWI-EAS91_1_306UPAAXX:6:1:630:1087
+GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC
+>HWI-EAS91_1_306UPAAXX:6:1:606:1852
+GGAGACAAATAATCTCTTTAATAACCTGATTCAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:489:1315
+GAAAGCTCAGTCTCAGGAGGAAGCGGAGCAGTCCAC
+>HWI-EAS91_1_306UPAAXX:6:1:465:1983
+GAGCCAATACCATCAGCTTTACCGTCTTTCCAGAAA
+>HWI-EAS91_1_306UPAAXX:6:1:559:1028
+GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC
+>HWI-EAS91_1_306UPAAXX:6:1:1655:1413
+GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG
+>HWI-EAS91_1_306UPAAXX:6:1:980:605
+GCCGTTTGAATGTTGACGGGATGAACATAATAAGCA
+>HWI-EAS91_1_306UPAAXX:6:1:1629:1865
+GAAAAGCGGCATGGTCAATATAACCAGTAGTGTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1180:1920
+GCACTCCGTGGACAGATTTGTCATTGTGAGCATTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1116:383
+GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG
+>HWI-EAS91_1_306UPAAXX:6:1:906:2041
+GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA
+>HWI-EAS91_1_306UPAAXX:6:1:1514:157
+GTCAATAGATGTGGTAGAAGTCGTCATTTGGCGTGG
+>HWI-EAS91_1_306UPAAXX:6:1:1032:1857
+GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT
+>HWI-EAS91_1_306UPAAXX:6:1:638:609
+GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAT
+>HWI-EAS91_1_306UPAAXX:6:1:74:750
+GATAATCACGAGTATCCTTTCCTTTATCATCTTCAT
+>HWI-EAS91_1_306UPAAXX:6:1:486:822
+GTTGACGATGTAGCTTTAGGTGTCTTTAAAACAGGT
+>HWI-EAS91_1_306UPAAXX:6:1:899:473
+GAACAGCATCGGACTCAGATAGTAATCCACGCTCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1613:197
+GTGACATTCAGAAGGGTAATAAGAACGAACCATAAA
+>HWI-EAS91_1_306UPAAXX:6:1:326:1747
+GTTGAGGCTTTCGTTTATTGTACGCTTTGCTTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1487:526
+GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+>HWI-EAS91_1_306UPAAXX:6:1:629:665
+GAAATGCAGCAGCAAGATAATCACGAGTATCCTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:766:744
+GGCCGTCAACATACATATCACCATTATCGAACTCAA
+>HWI-EAS91_1_306UPAAXX:6:1:391:1771
+GTGGTTGATATTTTTCATGGTATTGATAAATCTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:591:1102
+GCTTTGCGTGACTATTTTCGTGATATTGTTCGTTTG
+>HWI-EAS91_1_306UPAAXX:6:1:917:664
+GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG
+>HWI-EAS91_1_306UPAAXX:6:1:217:737
+GTTCAGTTGTTGCATTGGAATATTCAGTTTAAATTT
+>HWI-EAS91_1_306UPAAXX:6:1:1047:839
+GACCATTCAAAGGATAAACATCATAGGCAGTCGGGG
+>HWI-EAS91_1_306UPAAXX:6:1:558:1040
+GCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1207:524
+GCCAATACCATCAGCTTTACCGTCTTTCCAGAAATT
+>HWI-EAS91_1_306UPAAXX:6:1:708:1634
+GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG
+>HWI-EAS91_1_306UPAAXX:6:1:576:1851
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG
+>HWI-EAS91_1_306UPAAXX:6:1:906:460
+GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC
+>HWI-EAS91_1_306UPAAXX:6:1:693:1260
+GCGAAAGGTCGCAAAGTAAGAGCTTCTCGAGCTGCG
+>HWI-EAS91_1_306UPAAXX:6:1:1373:286
+GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG
+>HWI-EAS91_1_306UPAAXX:6:1:762:41
+GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT
+>HWI-EAS91_1_306UPAAXX:6:1:475:1091
+GTCACACAGTCCTTGACGGTATAATAACCACCATCT
+>HWI-EAS91_1_306UPAAXX:6:1:791:627
+GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC
+>HWI-EAS91_1_306UPAAXX:6:1:336:1791
+GAAGGAGTCGCCAGCGATAACCGGAGTAGTTGAAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1483:943
+GCACGTAATTTTTGACGCACGTTTTCTTCTGCGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:641:1071
+GATGGGCATACTGTAACCATAAGGCCACGTATTTTG
+>HWI-EAS91_1_306UPAAXX:6:1:196:755
+GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT
+>HWI-EAS91_1_306UPAAXX:6:1:463:1398
+GTCATAAGAGGTTTTACCTCCAAATGAAGAAATAAC
+>HWI-EAS91_1_306UPAAXX:6:1:1559:460
+GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1625:1561
+GAGGAGTGGCATTAACACCATCCTTCATGAACTTAC
+>HWI-EAS91_1_306UPAAXX:6:1:1729:1588
+GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT
+>HWI-EAS91_1_306UPAAXX:6:1:945:393
+GGCCTCATCAGGGTTAGGAACATTAGAGCCTTGAAT
+>HWI-EAS91_1_306UPAAXX:6:1:298:1391
+GTAAAGTTAGACCAAACCATGAAACCAACATAAACA
+>HWI-EAS91_1_306UPAAXX:6:1:1270:1500
+GAATTACTACTGCTTGTTTACGAATTAAATATATGT
+>HWI-EAS91_1_306UPAAXX:6:1:481:1546
+GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG
+>HWI-EAS91_1_306UPAAXX:6:1:473:1729
+GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAT
+>HWI-EAS91_1_306UPAAXX:6:1:801:1831
+GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT
+>HWI-EAS91_1_306UPAAXX:6:1:536:639
+GCCGACCCTAAATTTTTTGCCTGTTTGGTTCTCTTT
+>HWI-EAS91_1_306UPAAXX:6:1:259:938
+GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG
+>HWI-EAS91_1_306UPAAXX:6:1:907:1513
+GGCATGGGTGATGCTGGTATTAAATCTGCCATTCAC
+>HWI-EAS91_1_306UPAAXX:6:1:372:1409
+GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG
+>HWI-EAS91_1_306UPAAXX:6:1:485:1626
+GATGGCAGCAACGGAAACCATAACGAGCATCATCTT
+>HWI-EAS91_1_306UPAAXX:6:1:583:1679
+GCTCAAAGTCAAAATAATCAGCGTGACATTCAGAAG
+>HWI-EAS91_1_306UPAAXX:6:1:690:1610
+GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:257:918
+GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTTCT
+>HWI-EAS91_1_306UPAAXX:6:1:818:33
+GTGTTAATGCCACTCCTCTCCCGACTGTTAACTCTG
+>HWI-EAS91_1_306UPAAXX:6:1:541:1242
+GGGATTATCATAAAACGCCTCTAATCGGTCGTCAGC
+>HWI-EAS91_1_306UPAAXX:6:1:1014:279
+GTAAAAATGTCTACAGTAGAGTCAATAGCAAGGCCC
+>HWI-EAS91_1_306UPAAXX:6:1:672:1790
+GGCCGTTTGAATGTTGACGGGATGAACATAATAAGC
+>HWI-EAS91_1_306UPAAXX:6:1:708:464
+GGAGACAAATAATCTCTTTAATAACCTGATTCAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:633:1486
+GGGAAAGGTCATGCGGCATACGCTCGGCGCCAGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:328:696
+GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:259:1389
+GCGTACTTATTCGCCACCATGATTATTACCAGTGTT
+>HWI-EAS91_1_306UPAAXX:6:1:1315:41
+GCTTTCCGTGATGTCACAGCCTGCTTTGATGTGTCG
+>HWI-EAS91_1_306UPAAXX:6:1:1647:549
+GCTTAATCCAACTTACCAAGCTGGGTTACGACGCGC
+>HWI-EAS91_1_306UPAAXX:6:1:300:886
+GTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:317:1411
+GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCTT
+>HWI-EAS91_1_306UPAAXX:6:1:321:1819
+GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:631:70
+GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC
+>HWI-EAS91_1_306UPAAXX:6:1:624:1040
+GCTGGCGACTCCTTCGAGATGGACGCCGTTTGCGCT
+>HWI-EAS91_1_306UPAAXX:6:1:662:1187
+GGGAGAGGAGTGGCATTAACACCATCCTTCATGACC
+>HWI-EAS91_1_306UPAAXX:6:1:1440:1959
+GAATCAGCGGTATGGCTCCTCTCCTATTTTTGCTTC
+>HWI-EAS91_1_306UPAAXX:6:1:458:1629
+GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT
+>HWI-EAS91_1_306UPAAXX:6:1:216:790
+GGGATGAAAATGCTCACAATGACAAATCTGTCCACG
+>HWI-EAS91_1_306UPAAXX:6:1:1407:1174
+TTACCTATTAGTGGTTGAACAGCATCGGACTCAGAT
+>HWI-EAS91_1_306UPAAXX:6:1:999:1790
+GTCCTGCGTGTAGCGAACTGCGATGGGCATACTGTC
+>HWI-EAS91_1_306UPAAXX:6:1:141:1994
+GGCTTTTTTATGGTTCGTTCTTATTACCCTTCTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:225:465
+GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC
+>HWI-EAS91_1_306UPAAXX:6:1:649:1760
+GACCCATAATGTCAATAGATGTGGTAGAAGTCGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:300:986
+GTTGAACACGACCAGAAAACTGGCCTAACGACGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:478:605
+GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC
+>HWI-EAS91_1_306UPAAXX:6:1:622:395
+GGTAGCTTTAAGCGGCTCACCTTTAGCATCAACAGG
+>HWI-EAS91_1_306UPAAXX:6:1:1701:574
+GTAAAGCCTCTACGCGATTTCATAGTGGAGGCCTCC
+>HWI-EAS91_1_306UPAAXX:6:1:646:59
+GGAAGTGTCCGCATAAAATGCACCGCATGGAAATGT
+>HWI-EAS91_1_306UPAAXX:6:1:284:2031
+GACAGAATCGTTAGTTGATGGCGAAAGGTCGCAAAG
+>HWI-EAS91_1_306UPAAXX:6:1:22:1009
+GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT
+>HWI-EAS91_1_306UPAAXX:6:1:47:1826
+GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG
+>HWI-EAS91_1_306UPAAXX:6:1:1025:1236
+TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT
+>HWI-EAS91_1_306UPAAXX:6:1:773:591
+GAGCAGGAAAGCGAGGGTATCCCACAAAGTCCAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:1753:527
+GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC
+>HWI-EAS91_1_306UPAAXX:6:1:426:1717
+GTAGCGCCAATATGAGAAGAGCCATACCGCTGATTC
+>HWI-EAS91_1_306UPAAXX:6:1:959:818
+TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC
+>HWI-EAS91_1_306UPAAXX:6:1:459:1344
+GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT
+>HWI-EAS91_1_306UPAAXX:6:1:973:1367
+TTCGTGATGAGTTTGTATCTGTTACTGATAAGTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:201:871
+GATTAGAGGCGTTTTATGATAATCCCAATGCTTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:713:1672
+GGCGTACGGGGAAGGACGTCAATAGTCACACAGTCC
+>HWI-EAS91_1_306UPAAXX:6:1:444:1435
+TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGTG
+>HWI-EAS91_1_306UPAAXX:6:1:288:1136
+GCCTTCCATGATGAGACAGGCCGTTTTAATTTTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1653:225
+GCAAGGCCACGACGCAATGGAGAAAGACGGAGAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:537:1764
+GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA
+>HWI-EAS91_1_306UPAAXX:6:1:196:1854
+GTATCGAGGCTCTTAAACCTGCTATTTAGGCTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:312:1707
+GCGTCATAAGAGGTTTTACCTCCAAATGAAGAAATA
+>HWI-EAS91_1_306UPAAXX:6:1:651:183
+GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:295:694
+GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT
+>HWI-EAS91_1_306UPAAXX:6:1:330:1895
+GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG
+>HWI-EAS91_1_306UPAAXX:6:1:590:331
+GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT
+>HWI-EAS91_1_306UPAAXX:6:1:481:1687
+GCAGATTGCGATAAACGGTCACATTAAATTTAACCT
+>HWI-EAS91_1_306UPAAXX:6:1:1112:1279
+TGTGCATATACCTGGTCTTTCGTATTCTGTCGTGAT
+>HWI-EAS91_1_306UPAAXX:6:1:1099:1216
+TTAGAGCGCATGACAAGTAAAGGACGGTTGTCAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:221:1238
+GTATCCTTTCCTTTATCATCGGCAGACTTTTCACCT
+>HWI-EAS91_1_306UPAAXX:6:1:1015:364
+GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG
+>HWI-EAS91_1_306UPAAXX:6:1:735:1806
+TGTTATTAATATCAAGTTGGGGGAGCACATTGTAGC
+>HWI-EAS91_1_306UPAAXX:6:1:320:411
+GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGTG
+>HWI-EAS91_1_306UPAAXX:6:1:1273:1031
+TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA
+>HWI-EAS91_1_306UPAAXX:6:1:1456:1088
+AATAATCAGCGTGACATTCAGAAGGGTAATAAGAAC
+>HWI-EAS91_1_306UPAAXX:6:1:1365:307
+GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG
+>HWI-EAS91_1_306UPAAXX:6:1:478:252
+GATGCGGTTATCCATCTGCTTATTGAAGCCAAGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:915:1232
+TATTAATAACACTATAGACCACCGCCCCGAAGGGGC
+>HWI-EAS91_1_306UPAAXX:6:1:680:1357
+TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGC
+>HWI-EAS91_1_306UPAAXX:6:1:238:1279
+GCCGAAGCCCCTGCAATTAAAATTGTTGACCACCTA
+>HWI-EAS91_1_306UPAAXX:6:1:1583:35
+GCAAATTAGCATAAGCAGCTTGCAGACCCATAATGT
+>HWI-EAS91_1_306UPAAXX:6:1:502:283
+GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:418:1730
+GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:596:647
+GCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTA
+>HWI-EAS91_1_306UPAAXX:6:1:92:1591
+GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC
+>HWI-EAS91_1_306UPAAXX:6:1:430:1938
+GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGTCC
+>HWI-EAS91_1_306UPAAXX:6:1:212:527
+GGTATTGATAAAGCTGTTGCCGATACTTGTAACAAT
+>HWI-EAS91_1_306UPAAXX:6:1:594:942
+GACGACATTAGAAATATCCTTTGCAGTAGCGCCAAT
+>HWI-EAS91_1_306UPAAXX:6:1:169:1774
+GCCTTCCATGATGAGACAGGCCGTTTTAATTTTTAC
+>HWI-EAS91_1_306UPAAXX:6:1:1090:210
+GGAGAGCGCCAACGGCGTCCATCTCGAAGGAGTCGC
+>HWI-EAS91_1_306UPAAXX:6:1:589:96
+GGCGGCCCCATCAGGGTTAGGAACATTAGAGCCTTG
+>HWI-EAS91_1_306UPAAXX:6:1:1477:1231
+TAGGAACATTAGAGCCTTGAATGGCAGATTTAATAC
+>HWI-EAS91_1_306UPAAXX:6:1:707:1076
+TCTGACGTTCGTGATGAGTTTGTATCTTTTTCTTTG
+>HWI-EAS91_1_306UPAAXX:6:1:749:1715
+GAACATAATAAGCAATGACGGCAGCAATAAACTCAA
+>HWI-EAS91_1_306UPAAXX:6:1:1738:1884
+GCTCACCTTTAGCATCAACAGGCCACAACCAACCAG
+>HWI-EAS91_1_306UPAAXX:6:1:1160:1088
+TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC
+>HWI-EAS91_1_306UPAAXX:6:1:517:119
+GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT
+>HWI-EAS91_1_306UPAAXX:6:1:1472:716
+TGGTAATGGTGGTTTTCTTCATTTCATTCAGTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:281:441
+GAGCAGTAGACTCCTTCTGTTGATAAGCAAGCATCT
+>HWI-EAS91_1_306UPAAXX:6:1:1101:324
+AATACCATCAGCTTTACCGTCTTTCCAGAAATTGTT
+>HWI-EAS91_1_306UPAAXX:6:1:1225:1494
+TTCTCAAATCCGGCGTCAACCATACCAGCAGAGGAA
+>HWI-EAS91_1_306UPAAXX:6:1:1509:1025
+TTCTTGCTGCCGAGGGTCGCAAGGCTATTGTTTCAC
+>HWI-EAS91_1_306UPAAXX:6:1:592:510
+GATACCAATAAAATCCCTAAGCATTTGTTTCTGGTT
+>HWI-EAS91_1_306UPAAXX:6:1:324:1729
+GAACAAAGAAACGCGGCACAGAATGTTTATAGGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:128:1925
+GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC
+>HWI-EAS91_1_306UPAAXX:6:1:786:893
+TACGGGGAAGGACGTCAATAGTCACACAGTCCTTGC
+>HWI-EAS91_1_306UPAAXX:6:1:248:955
+GCTACAATGTGCTCCCCCAACTTGATATTAATAACA
+>HWI-EAS91_1_306UPAAXX:6:1:388:1127
+GATATTGGTCGTATGGTTCTTGCTGCCTAGTGTCTC
+>HWI-EAS91_1_306UPAAXX:6:1:721:1156
+TCTGGTTGGTTGTGGCCTTTTTATGCTAAATGTTAG
+>HWI-EAS91_1_306UPAAXX:6:1:1564:1468
+TTACTTTTTATGTCCCTCATCGTCACGTTTATGTTG
+>HWI-EAS91_1_306UPAAXX:6:1:750:77
+GGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTA
+>HWI-EAS91_1_306UPAAXX:6:1:405:487
+GTTGGATTAAGCACTCCGTGGACAGATTTGTCATTT
+>HWI-EAS91_1_306UPAAXX:6:1:836:1204
+TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT
+>HWI-EAS91_1_306UPAAXX:6:1:224:1548
+GCTGCCGTCATTGCTTATTATGTTCATCCCTTCAAC
+>HWI-EAS91_1_306UPAAXX:6:1:931:1015
+TTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGT
+>HWI-EAS91_1_306UPAAXX:6:1:329:579
+GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT
+>HWI-EAS91_1_306UPAAXX:6:1:260:1145
+GCTTGCGTTTATGGTACGCTGGACTTTTTGTGATAC
+>HWI-EAS91_1_306UPAAXX:6:1:1523:1253
+TTGGTAAAATACTGACCAGCCGTTTGAGCTTGAGTA
+>HWI-EAS91_1_306UPAAXX:6:1:326:1271
+GACCACTCGCGATTCAATCATGACTTCGTGATAAAT
+>HWI-EAS91_1_306UPAAXX:6:1:213:622
+GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA
+>HWI-EAS91_1_306UPAAXX:6:1:274:712
+GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG
+>HWI-EAS91_1_306UPAAXX:6:1:1549:627
+TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGT
+>HWI-EAS91_1_306UPAAXX:6:1:1714:737
+TCTTTCGTATTCTGGCGTGAAGTCGCCGACTGAATG
+>HWI-EAS91_1_306UPAAXX:6:1:760:1217
+TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:174:768
+GTTGGCTGACGACCGATTAGAGGCGTTTTTTTATAT
+>HWI-EAS91_1_306UPAAXX:6:1:172:1412
+GGTCGGCAGATTGCGATAAACGTTCACATTAAATTT
+>HWI-EAS91_1_306UPAAXX:6:1:1393:869
+TTCATCCCGTCAACATTCAAACGGCCTGTCTCATCT
+>HWI-EAS91_1_306UPAAXX:6:1:301:481
+GTTATAGATATTCAAATAACCCTGAAACAAATGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:648:1093
+TAACGCTGCATGAAGTAATCACGTTCTTGGTCAGTT
+>HWI-EAS91_1_306UPAAXX:6:1:1233:591
+TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:540:1415
+TTATTAAAGAGATTATTTTTCTCCAGCCACTTATGT
+>HWI-EAS91_1_306UPAAXX:6:1:151:1792
+GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA
+>HWI-EAS91_1_306UPAAXX:6:1:748:1378
+TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT
+>HWI-EAS91_1_306UPAAXX:6:1:1526:1479
+TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC
+>HWI-EAS91_1_306UPAAXX:6:1:985:1093
+TAACCGTCTTCTCGTTCTCTAAAAACCATTTTTCTT
+>HWI-EAS91_1_306UPAAXX:6:1:480:1378
+TCAACCTCAGCACTAACCTTGCGAGTCATTTCTTTG
+>HWI-EAS91_1_306UPAAXX:6:1:903:753
+TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG
+>HWI-EAS91_1_306UPAAXX:6:1:1697:1737
+GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT
+>HWI-EAS91_1_306UPAAXX:6:1:803:1037
+TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCTACT
+>HWI-EAS91_1_306UPAAXX:6:1:1727:1244
+TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT
+>HWI-EAS91_1_306UPAAXX:6:1:253:1162
+GCATTTAGTAGCGGTAAAGTTTGACCAAACCATTAT
+>HWI-EAS91_1_306UPAAXX:6:1:216:856
+GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT
+>HWI-EAS91_1_306UPAAXX:6:1:825:886
+TCCCACAAAGTCCAGCGTACCATAAACGCAAGCCTC
+>HWI-EAS91_1_306UPAAXX:6:1:1699:962
+TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT
+>HWI-EAS91_1_306UPAAXX:6:1:1210:625
+TCAGATAGTAATCCACGCTCTTTTAAAATGTCAACA
+>HWI-EAS91_1_306UPAAXX:6:1:538:616
+TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT
+>HWI-EAS91_1_306UPAAXX:6:1:184:1849
+GCTCACCTTTAGCATCAACAGGCCACAACCAACCAG
+>HWI-EAS91_1_306UPAAXX:6:1:1636:1103
+TATCTGACTTTTTGTTAACGTATTTAGCCACATAGA
+>HWI-EAS91_1_306UPAAXX:6:1:605:223
+GGTTATTTGAATATCTATAACAACTATTTTAAATCG
+>HWI-EAS91_1_306UPAAXX:6:1:256:1052
+GGTAAAGGACTTCTTGAAGGTACGTTGCAGTCTGGC
+>HWI-EAS91_1_306UPAAXX:6:1:300:1515
+GCCATGATGGTGGTTATTATACCGTCAAGGACTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1684:1320
+TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA
+>HWI-EAS91_1_306UPAAXX:6:1:1186:895
+TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1463:754
+TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:808:1053
+TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG
+>HWI-EAS91_1_306UPAAXX:6:1:960:1218
+TTTCTAATGTCGTCACTGATGCTGCTTCTGTTGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:521:1646
+GGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCA
+>HWI-EAS91_1_306UPAAXX:6:1:289:1885
+GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAG
+>HWI-EAS91_1_306UPAAXX:6:1:471:170
+GGTCAGTTCCATCAACATCATAGCCAGATGCCCAGA
+>HWI-EAS91_1_306UPAAXX:6:1:828:754
+TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT
+>HWI-EAS91_1_306UPAAXX:6:1:924:1679
+TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT
+>HWI-EAS91_1_306UPAAXX:6:1:837:901
+TGCATTTTAGTAAGCTCTTTTTGATTCTCAAATCCG
+>HWI-EAS91_1_306UPAAXX:6:1:543:16
+GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1482:578
+TCTTTAGCTCCTAGACCTTTAGCAGCAAGGTCCATA
+>HWI-EAS91_1_306UPAAXX:6:1:1254:1668
+TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT
+>HWI-EAS91_1_306UPAAXX:6:1:1402:898
+TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC
+>HWI-EAS91_1_306UPAAXX:6:1:764:1534
+TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT
+>HWI-EAS91_1_306UPAAXX:6:1:681:1079
+TGGCGAATAAGTACGCGTTCTTGCAAATCACCAGAA
+>HWI-EAS91_1_306UPAAXX:6:1:672:1350
+TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1266:493
+TGACCAGCCGTTTGAGCTTGAGTAAGCATTTGGCGC
+>HWI-EAS91_1_306UPAAXX:6:1:118:238
+GACGGTATAATAACCACCATCATGGCGACCATTCAA
+>HWI-EAS91_1_306UPAAXX:6:1:699:433
+TTATTGCCCGGCGTACGGGGAAGGACGTCAATAGTC
+>HWI-EAS91_1_306UPAAXX:6:1:708:1387
+TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC
+>HWI-EAS91_1_306UPAAXX:6:1:498:1085
+TTATGATAATCCCAATGCTTTGCGTGACTATTTTCT
+>HWI-EAS91_1_306UPAAXX:6:1:1101:1301
+TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAT
+>HWI-EAS91_1_306UPAAXX:6:1:261:213
+GAATGGTCGCCATGATGGTGGTTATTATACCGTCAC
+>HWI-EAS91_1_306UPAAXX:6:1:1287:1267
+TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGT
+>HWI-EAS91_1_306UPAAXX:6:1:744:331
+TTAATGGATGAATTGGCACAATGCTACAATGTGCTC
+>HWI-EAS91_1_306UPAAXX:6:1:614:814
+TGTCAGCGTCATAAGAGGTTTTACCTCCAAATGAAG
+>HWI-EAS91_1_306UPAAXX:6:1:1362:1063
+TAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAG
+>HWI-EAS91_1_306UPAAXX:6:1:1238:1508
+TCAACTAACGATTCTGTCAAAAACTGACGCGTTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:904:1130
+TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT
+>HWI-EAS91_1_306UPAAXX:6:1:465:216
+GACCATGCCGCTTTTCTTGGCACGATTAACCCTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:844:628
+TAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGC
+>HWI-EAS91_1_306UPAAXX:6:1:684:1444
+TATCCCACAAAGTCCAGCGTACCATAAACGCAAGCC
+>HWI-EAS91_1_306UPAAXX:6:1:515:1373
+TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT
+>HWI-EAS91_1_306UPAAXX:6:1:764:1667
+TTGAGTTCGATAATGGTGATATGTATGTTGACGTCC
+>HWI-EAS91_1_306UPAAXX:6:1:1722:598
+TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCT
+>HWI-EAS91_1_306UPAAXX:6:1:670:1188
+TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT
+>HWI-EAS91_1_306UPAAXX:6:1:1682:1705
+TAGCCACATAGAAACCAACAGCCATATAACTGGTAG
+>HWI-EAS91_1_306UPAAXX:6:1:1008:1616
+TCCTTTACTTGTCATGCGCTCTAATCTCTGTGCATC
+>HWI-EAS91_1_306UPAAXX:6:1:490:1220
+TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCT
+>HWI-EAS91_1_306UPAAXX:6:1:891:1437
+TAATGGTGATATGTATGTTTACGTCCATAAGGCTGT
+>HWI-EAS91_1_306UPAAXX:6:1:1310:321
+TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGT
+>HWI-EAS91_1_306UPAAXX:6:1:827:1597
+TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC
+>HWI-EAS91_1_306UPAAXX:6:1:1062:1158
+TAGAGTCAATAGCAAGGCCACGACGCAATGGAGAAA
+>HWI-EAS91_1_306UPAAXX:6:1:1419:208
+TGGCGCATAATCTCGGAAACCTGCTGTTGCTTGGAA
+>HWI-EAS91_1_306UPAAXX:6:1:691:1018
+AAATATCAACCACACCAGAAGCAGCATCAGTGACGA
+>HWI-EAS91_1_306UPAAXX:6:1:374:113
+GATAAAGCTGTTGCCGATACTTGGAACAATTTCTGT
+>HWI-EAS91_1_306UPAAXX:6:1:1720:784
+TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC
+>HWI-EAS91_1_306UPAAXX:6:1:1424:1394
+ATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1063:1760
+TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT
+>HWI-EAS91_1_306UPAAXX:6:1:1235:729
+TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA
+>HWI-EAS91_1_306UPAAXX:6:1:167:1507
+TAGTGTTATTAATATCAAGTTTTTGGAGCACATTGT
+>HWI-EAS91_1_306UPAAXX:6:1:717:1569
+TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT
+>HWI-EAS91_1_306UPAAXX:6:1:610:765
+TTCAGCGCCTTCCATGATGAGACAGGCCGTTTGAAT
+>HWI-EAS91_1_306UPAAXX:6:1:663:380
+TAAACATTCTGTGCCGCGTTTCTTTGTTCCTTATCT
+>HWI-EAS91_1_306UPAAXX:6:1:790:1358
+TTATCACCTTATTGAAGGCTTATCATTCATTTAGGT
+>HWI-EAS91_1_306UPAAXX:6:1:965:1633
+TAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGCT
+>HWI-EAS91_1_306UPAAXX:6:1:673:319
+TTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAT
+>HWI-EAS91_1_306UPAAXX:6:1:684:371
+TAGCGGTAAAGTTAGACCAAACCATGAAACCAACAT
+>HWI-EAS91_1_306UPAAXX:6:1:1147:1444
+ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC
+>HWI-EAS91_1_306UPAAXX:6:1:983:678
+ATACCTGGTCTTTCGTATTCTGGCGTGAAGTCGCCG
+>HWI-EAS91_1_306UPAAXX:6:1:1608:1119
+TCACGCGGCGGCAAGTTGCCATACAAAACAGGGTCG
+>HWI-EAS91_1_306UPAAXX:6:1:1048:1193
+TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1265:1429
+ATATTTTTCATGGTATTGATAAAGCTGTTGCCGATT
+>HWI-EAS91_1_306UPAAXX:6:1:1607:1677
+TGTTGCTTGGAAAGATTGGTGTTTTCCATAATAGAC
+>HWI-EAS91_1_306UPAAXX:6:1:1087:1421
+ACGAACGTCAGAAGCAGCCTTATGGCCGTCAACATC
+>HWI-EAS91_1_306UPAAXX:6:1:324:490
+GCACCAAACATAAATCACCTCACTTAAGTGGCTGGG
+>HWI-EAS91_1_306UPAAXX:6:1:1596:614
+TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGT
+>HWI-EAS91_1_306UPAAXX:6:1:343:83
+GTTACGCAGTTTTGCCGCAAGCTGGCTGCTGTACGC
+>HWI-EAS91_1_306UPAAXX:6:1:203:667
+GCATGAATGTGCTTAATAGAGGCCAAGGCGGTCTAG
+>HWI-EAS91_1_306UPAAXX:6:1:34:480
+GGCAAGTTGCCATACAAAACAGGGTCGCCAGCAATT
+>HWI-EAS91_1_306UPAAXX:6:1:606:1743
+TAGCGACAGCTTGGTTTTTAGTGAGTTGTTCCATTC
+>HWI-EAS91_1_306UPAAXX:6:1:254:1391
+TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG
+>HWI-EAS91_1_306UPAAXX:6:1:1568:1750
+TAACCAGTAGTGTTAACAGTCGGGAGAGGAGTGGCT
+>HWI-EAS91_1_306UPAAXX:6:1:1538:869
+TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA
+>HWI-EAS91_1_306UPAAXX:6:1:255:38
+GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1543:1555
+TAAAACGCCTCTAATCGGTCGTCAGCCAACGTGAGG
+>HWI-EAS91_1_306UPAAXX:6:1:1365:733
+AGAATCAGCGGTATGGCTCTTCTCCTTTTTTCGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:1604:943
+TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT
+>HWI-EAS91_1_306UPAAXX:6:1:1574:1632
+TCAGTATGCAAATTAGCATAAGCAGCTTGCAGACCC
+>HWI-EAS91_1_306UPAAXX:6:1:565:1799
+TCTTGGTCAGTATGCAAATTAGCATAAGCAGCTTGC
+>HWI-EAS91_1_306UPAAXX:6:1:1004:380
+TATTGACTCTACTGTAGACATTTTTACTTTTTATTT
+>HWI-EAS91_1_306UPAAXX:6:1:1345:965
+ATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1704:756
+TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG
+>HWI-EAS91_1_306UPAAXX:6:1:310:1346
+TATAACGTTGACGATGTAGCTTTAGTTTTCTTTAAA
+>HWI-EAS91_1_306UPAAXX:6:1:900:1858
+TTTACCGCTTCGGCGTTATAACCTCACACTCAATCT
+>HWI-EAS91_1_306UPAAXX:6:1:1250:1741
+TAAATCCAAAACGGCAGAAGCCTGAATGAGCTTAAT
+>HWI-EAS91_1_306UPAAXX:6:1:1170:1317
+TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC
+>HWI-EAS91_1_306UPAAXX:6:1:149:1896
+GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC
+>HWI-EAS91_1_306UPAAXX:6:1:1504:494
+TGTCTACAGTAGAGTCAATAGCAAGGCCACGACGCC
+>HWI-EAS91_1_306UPAAXX:6:1:395:256
+GTCCATATCTGACTTTTTGTTAACGTATTTATCCAC
+>HWI-EAS91_1_306UPAAXX:6:1:1110:1109
+ACCGCTTCGGCGTTATAACCTCACACTCAATCTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:895:649
+TTCTGCACGTAATTTTTGACGCACGTTTTCTTCTGC
+>HWI-EAS91_1_306UPAAXX:6:1:827:1378
+TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG
+>HWI-EAS91_1_306UPAAXX:6:1:1051:1587
+TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG
+>HWI-EAS91_1_306UPAAXX:6:1:1656:1549
+AACCTGCTGTTGCTTGGAAAGATTGGTGTTTTCCAT
+>HWI-EAS91_1_306UPAAXX:6:1:366:150
+GGTCAGTAGCAATCCAAACTTTGTTACTCGTCAGAA
+>HWI-EAS91_1_306UPAAXX:6:1:955:1792
+ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA
+>HWI-EAS91_1_306UPAAXX:6:1:1340:1403
+ATAAAATGCACCGCATGGAAATGAAGACGGCCATTA
+>HWI-EAS91_1_306UPAAXX:6:1:1693:1017
+TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGT
+>HWI-EAS91_1_306UPAAXX:6:1:1099:1572
+AATTTTTACCGCTTCGGCGTTATAACCTCACACTCA
+>HWI-EAS91_1_306UPAAXX:6:1:218:1148
+TATGCAAATTAGCATAAGCAGCTTGCAGACCCATAT
+>HWI-EAS91_1_306UPAAXX:6:1:403:614
+TGGTGCTGATGCTTCCTCTGCTGGTATGGTTTACGC
+>HWI-EAS91_1_306UPAAXX:6:1:1651:646
+TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC
+>HWI-EAS91_1_306UPAAXX:6:1:1566:499
+TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG
+>HWI-EAS91_1_306UPAAXX:6:1:825:951
+ACAGGCCGTTTGAATGTTTACGGGGTGTACATAATA
+>HWI-EAS91_1_306UPAAXX:6:1:1745:1865
+TTAACTTCTGCGTCATGGAAGCGATAAAACTCTGCG
+>HWI-EAS91_1_306UPAAXX:6:1:973:1992
+TAGTAATTCCTGCTTTATCAAGATAATTTTTCGACT
+>HWI-EAS91_1_306UPAAXX:6:1:171:1653
+TAATAATGTTTTCCGTAAATTCAGCGCCTTCCATGT
+>HWI-EAS91_1_306UPAAXX:6:1:397:363
+TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT
+>HWI-EAS91_1_306UPAAXX:6:1:1336:1155
+ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG
+>HWI-EAS91_1_306UPAAXX:6:1:685:629
+AGTATGCAAATTAGCATAAGCAGCTTGCAGACCCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1409:510
+ACATAATAAGCAATGACGGCAGCAATAAACTCAACA
+>HWI-EAS91_1_306UPAAXX:6:1:1631:998
+AACCATCAGCATGAGCCTGTCGCATTGCATTCATCC
+>HWI-EAS91_1_306UPAAXX:6:1:260:1698
+TTATTATGTTCATCCCGTCAACATTCAAACTGCCTT
+>HWI-EAS91_1_306UPAAXX:6:1:578:971
+TTAACGCTACTAAATTCCGCGGATTGGTTTCGTTGT
+>HWI-EAS91_1_306UPAAXX:6:1:1613:642
+ATAGAAATTTCACGCGGCGGCAAGTTGCCATACAAA
+>HWI-EAS91_1_306UPAAXX:6:1:237:650
+GACGGTATAATAACCACCATCATGGCGACCATTCAA
+>HWI-EAS91_1_306UPAAXX:6:1:1100:1875
+TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG
+>HWI-EAS91_1_306UPAAXX:6:1:352:32
+GTACCATAAACGCAAGCCTCAACGCAGCGACGAGCC
+>HWI-EAS91_1_306UPAAXX:6:1:443:229
+GCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAAC
+>HWI-EAS91_1_306UPAAXX:6:1:1131:731
+AGCAGTCGGCGTGTGAATCATTAGCCTTGCGACCCT
+>HWI-EAS91_1_306UPAAXX:6:1:133:1089
+AAGGTTAGTGCTGAGGTTGACTTAGTTCATCATCAA
+>HWI-EAS91_1_306UPAAXX:6:1:65:1307
+TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT
+>HWI-EAS91_1_306UPAAXX:6:1:905:1493
+TCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTT
+>HWI-EAS91_1_306UPAAXX:6:1:733:540
+TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAT
+>HWI-EAS91_1_306UPAAXX:6:1:161:1707
+TAATGTCGTCACTGATGCTGCTTCTGTTGTTGTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:380:1861
+TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC
+>HWI-EAS91_1_306UPAAXX:6:1:1761:566
+TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:1486:651
+TGGCGGTATTTCTTCTTCTCTTTCTTGTTGCGCCCT
+>HWI-EAS91_1_306UPAAXX:6:1:508:1380
+TCCATCAACATCATAGCCAGATGCCCAGAGATTAGA
+>HWI-EAS91_1_306UPAAXX:6:1:1763:855
+TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1553:553
+TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA
+>HWI-EAS91_1_306UPAAXX:6:1:1424:507
+TCCACTGCAACAACTGAACGGACTGGAAACACTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:988:135
+TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC
+>HWI-EAS91_1_306UPAAXX:6:1:810:1918
+TTTTCATCCCGAAGTTGCGGCTCATTCTGATTCTGT
+>HWI-EAS91_1_306UPAAXX:6:1:588:559
+TCTGGTTGAACGGCGTCGCGTCGTAACCCAGCTTGG
+>HWI-EAS91_1_306UPAAXX:6:1:1264:1214
+ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC
+>HWI-EAS91_1_306UPAAXX:6:1:1000:1475
+TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG
+>HWI-EAS91_1_306UPAAXX:6:1:1389:160
+TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT
+>HWI-EAS91_1_306UPAAXX:6:1:422:1296
+TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGT
+>HWI-EAS91_1_306UPAAXX:6:1:1273:856
+TAGCCATAGCACCAGAAACAAAACTAGGGGCGGCCT
+>HWI-EAS91_1_306UPAAXX:6:1:450:969
+TGTTTTCCATAATAGACGCAACGCGAGCAGTAGACT
+>HWI-EAS91_1_306UPAAXX:6:1:1202:828
+ATCGTCAACGTTATATTTTGATAGTTTGACGTTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1721:1800
+GGGTTAGGGACATTAGAGCCTTGACTGACTGAGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:228:2019
+TTGAGTAAGCATTTGGCGCATAATCTCGGAAACCTG
+>HWI-EAS91_1_306UPAAXX:6:1:1579:1214
+ACGTTTGGTCAGTTCCATCAACATCATAGCCAGATG
+>HWI-EAS91_1_306UPAAXX:6:1:429:1055
+TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1359:1689
+AAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAA
+>HWI-EAS91_1_306UPAAXX:6:1:1474:1056
+TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC
+>HWI-EAS91_1_306UPAAXX:6:1:105:1818
+TTGGGGATTGAGAAAGAGTAGAAATGCCACAAGCCT
+>HWI-EAS91_1_306UPAAXX:6:1:208:1538
+TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+>HWI-EAS91_1_306UPAAXX:6:1:1361:1623
+AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA
+>HWI-EAS91_1_306UPAAXX:6:1:595:1670
+TGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACA
+>HWI-EAS91_1_306UPAAXX:6:1:6:1885
+TCTAATGTCGTCACTGATGCTGCTTCTGGTGTGTTT
+>HWI-EAS91_1_306UPAAXX:6:1:706:1085
+TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG
+>HWI-EAS91_1_306UPAAXX:6:1:1307:825
+AGCGGTAAAGTTAGACCAAACCATGAAACCAACATA
+>HWI-EAS91_1_306UPAAXX:6:1:762:802
+TGGCATTAACACCATCCTTCATGAACTTAATCCACT
+>HWI-EAS91_1_306UPAAXX:6:1:1657:506
+TTGCGACCCTCGGCAGCAAGAACCATACGACCAATT
+>HWI-EAS91_1_306UPAAXX:6:1:184:811
+TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC
+>HWI-EAS91_1_306UPAAXX:6:1:1469:1718
+TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTT
+>HWI-EAS91_1_306UPAAXX:6:1:815:1640
+TGGCGGCGATTGCGTACCCGACGACCCAAATTAGGG
+>HWI-EAS91_1_306UPAAXX:6:1:1580:1388
+AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG
+>HWI-EAS91_1_306UPAAXX:6:1:1617:1554
+TACGGGGAAGGACGTCAATAGTCACACAGTCCTTGA
+>HWI-EAS91_1_306UPAAXX:6:1:1544:431
+TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA
+>HWI-EAS91_1_306UPAAXX:6:1:1604:1541
+TCAGTGACGACATTAGAAATATCCTTTGCAGTAGCG
+>HWI-EAS91_1_306UPAAXX:6:1:1485:741
+ATCAAACGCTGAATAGTAAAGCCTCTACGCGATTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1226:393
+TGCCACAAGCCTCAATAGCAGGTTTAAGAGCCTCGA
+>HWI-EAS91_1_306UPAAXX:6:1:1506:973
+ATTAGGGTCAACGCTACCTGTAGGAAGTGTCCGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:890:1838
+TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC
+>HWI-EAS91_1_306UPAAXX:6:1:453:1527
+TAAGAGGGCGTTCAGCAGCCAGCTTGCGGCAAAACT
+>HWI-EAS91_1_306UPAAXX:6:1:1056:570
+ACATTGTAGCATTGTGCCAATTCATCCATTAACTTC
+>HWI-EAS91_1_306UPAAXX:6:1:1736:74
+TATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGT
+>HWI-EAS91_1_306UPAAXX:6:1:169:1896
+GTATGCAAATTAGCATAAGCAGCTTGCAGACCCATA
+>HWI-EAS91_1_306UPAAXX:6:1:259:949
+TGAGGATAAATTATGTCTAATATTCAAACTTGCTCC
+>HWI-EAS91_1_306UPAAXX:6:1:1205:893
+ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT
+>HWI-EAS91_1_306UPAAXX:6:1:732:1335
+TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT
+>HWI-EAS91_1_306UPAAXX:6:1:667:664
+TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG
+>HWI-EAS91_1_306UPAAXX:6:1:535:587
+TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT
+>HWI-EAS91_1_306UPAAXX:6:1:412:446
+GTGTGGTTGATATTTTTCATGGTATTGATAAAGCTT
+>HWI-EAS91_1_306UPAAXX:6:1:507:1599
+TTGCTGGCGGTTTTTCTTTTTTTTTTTTTTTTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:575:1818
+TAAAATGCACCGCATGGAAATGAAGACGGCCATTAG
+>HWI-EAS91_1_306UPAAXX:6:1:1568:1428
+ACCAGTTATATGGCTGGTTGTTTTTTTTTTTTTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:1417:982
+AACAAGAGAATCTCTACCATGAACAAAATGTGACTC
+>HWI-EAS91_1_306UPAAXX:6:1:280:1340
+GGCCAAACCAGTGGCGATGGCCGCGCTGGAGGTTTT
+>HWI-EAS91_1_306UPAAXX:6:1:966:144
+TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT
+>HWI-EAS91_1_306UPAAXX:6:1:1391:1987
+TAATAATGTTTTCCGTAAATTCAGCGCCTTCCATGT
+>HWI-EAS91_1_306UPAAXX:6:1:1280:278
+ATGGAAATGAAGACGGCCATTAGCTGTACCATACTC
+>HWI-EAS91_1_306UPAAXX:6:1:631:858
+TGATATTGGTCGTATGGTTCTTGCTTCCGTGGGTCT
+>HWI-EAS91_1_306UPAAXX:6:1:518:573
+TTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGT
+>HWI-EAS91_1_306UPAAXX:6:1:54:981
+TTGACATTTTAAAAGAGCGTGGATTACTATCTGATT
+>HWI-EAS91_1_306UPAAXX:6:1:218:1165
+TATTGACTCTACTGTAGACATTTTTACTTTTTATTT
+>HWI-EAS91_1_306UPAAXX:6:1:1727:1530
+TCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCA
+>HWI-EAS91_1_306UPAAXX:6:1:519:657
+TGAACAGCATCGGACTCAGATAGTAATCCACGCTCT
+>HWI-EAS91_1_306UPAAXX:6:1:939:967
+ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC
+>HWI-EAS91_1_306UPAAXX:6:1:299:1060
+TATAACTGGTAGCTTTAAGCGGCTCACCTTTAGCAT
+>HWI-EAS91_1_306UPAAXX:6:1:438:665
+TAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTAT
+>HWI-EAS91_1_306UPAAXX:6:1:1303:1971
+AGCATTGTGCCAATTCATCCATTAACTTCTCAGTAA
+>HWI-EAS91_1_306UPAAXX:6:1:214:1264
+TCAGCACCAACAGAAACAACCTGATTAGCGGCGTTG
+>HWI-EAS91_1_306UPAAXX:6:1:1454:1423
+AACGGAAAACATCCTTCATAGAAATTTCACGCGGCG
+>HWI-EAS91_1_306UPAAXX:6:1:1633:340
+TTCCATAATAGACGCAACGCGAGCAGTAGACTCCTT
+>HWI-EAS91_1_306UPAAXX:6:1:671:1196
+ATACGAAAAGACAGAATCTCTTCCAAGAGCTTGATG
diff -r 8d149264b777 -r efdb6fb5de34 test-data/lastz_wrapper_out1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lastz_wrapper_out1.sam Fri Nov 27 10:53:50 2009 -0500
@@ -0,0 +1,494 @@
+@HD VN:1.0 SO:unsorted
+@SQ SN:phiX LN:5386
+HWI-EAS91_1_306UPAAXX 16 phiX 4295 255 1H35M * 0 0 CCCCCAACTTGATATTAATAACACTATAGACCACC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3522 255 36M * 0 0 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 229 255 36M * 0 0 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2071 255 36M * 0 0 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1067 255 1H35M * 0 0 GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1788 255 36M * 0 0 GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1193 255 36M * 0 0 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4563 255 33M3H * 0 0 GGTTGGTTTATCGTTTTTGACACTCTCACGTTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 2668 255 36M * 0 0 GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4248 255 36M * 0 0 GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2863 255 36M * 0 0 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2557 255 36M * 0 0 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2511 255 34M2H * 0 0 GTCAACGTTATATTTTGATAGTTTGACGGTTAAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 5152 255 36M * 0 0 GGATGAAAATGCTCACAATGACAAATCTGTCCACGG *
+HWI-EAS91_1_306UPAAXX 16 phiX 1590 255 36M * 0 0 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4884 255 36M * 0 0 GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG *
+HWI-EAS91_1_306UPAAXX 0 phiX 5052 255 36M * 0 0 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4909 255 36M * 0 0 GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2863 255 36M * 0 0 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4173 255 30M6H * 0 0 GTTGAGTTCGATAATGGTGATATGTATGTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 1701 255 36M * 0 0 GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1683 255 36M * 0 0 CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3126 255 1H35M * 0 0 GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1665 255 36M * 0 0 CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3213 255 36M * 0 0 GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3420 255 36M * 0 0 GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG *
+HWI-EAS91_1_306UPAAXX 0 phiX 513 255 36M * 0 0 GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2882 255 3H33M * 0 0 AGGTTATTAAAGAGATTATTTGTCTCCAGCCAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4471 255 36M * 0 0 GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1229 255 36M * 0 0 GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 615 255 36M * 0 0 GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 257 255 36M * 0 0 GCACGTTCGTCAAGGACTGGTTTAGATATGAGTCAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2381 255 36M * 0 0 TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4098 255 36M * 0 0 ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC *
+HWI-EAS91_1_306UPAAXX 0 phiX 5099 255 36M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG *
+HWI-EAS91_1_306UPAAXX 0 phiX 4254 255 36M * 0 0 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3408 255 36M * 0 0 GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG *
+HWI-EAS91_1_306UPAAXX 16 phiX 4043 255 36M * 0 0 GGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4560 255 36M * 0 0 GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 1888 255 36M * 0 0 GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3434 255 1H35M * 0 0 GCAAAATGAGACTCAAAAAGAGATTGCTGGCATTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4539 255 36M * 0 0 GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1828 255 36M * 0 0 CTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3708 255 36M * 0 0 GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3326 255 36M * 0 0 GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4176 255 36M * 0 0 GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 22 255 36M * 0 0 GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2557 255 36M * 0 0 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3277 255 36M * 0 0 ATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3592 255 36M * 0 0 AGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 358 255 35M1H * 0 0 GATGCTGTTCAACCACTAATAGGTAAGAAATCATG *
+HWI-EAS91_1_306UPAAXX 0 phiX 1775 255 36M * 0 0 GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3504 255 36M * 0 0 GTATATGCACAAAATGAGATGCTTGCTTATCAACAG *
+HWI-EAS91_1_306UPAAXX 16 phiX 1554 255 36M * 0 0 CGACTTCTACCACATCTATTGACATTATGGGTCTGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1002 255 36M * 0 0 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3626 255 36M * 0 0 GCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3572 255 36M * 0 0 GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1265 255 36M * 0 0 GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1332 255 36M * 0 0 GCACGATTAACCCTGATACCAATAAAATCCCTAAGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4254 255 36M * 0 0 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 4170 255 36M * 0 0 GGCGTTGAGTTCGATAATGGTGATATGTATGTTGAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2812 255 6H30M * 0 0 GTTTATGTTGGTTTCATGGTTTGGTCTAAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3119 255 36M * 0 0 CCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1670 255 36M * 0 0 GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 640 255 36M * 0 0 ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2750 255 35M1H * 0 0 GTTATTATACCGTCAAGGACTGTGTGACTATTGAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4606 255 36M * 0 0 GATTAGAGGCGTTTTATGATAATCCCAATGCTTTGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3573 255 36M * 0 0 GAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 5105 255 36M * 0 0 GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG *
+HWI-EAS91_1_306UPAAXX 16 phiX 1 255 15H21M * 0 0 GAGTTTTATCGCTTCCATGAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1674 255 36M * 0 0 GTAAAACCTCTTATGACGCTGACAACCGTCCTTTAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4095 255 36M * 0 0 CCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4551 255 36M * 0 0 GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT *
+HWI-EAS91_1_306UPAAXX 16 phiX 3284 255 36M * 0 0 TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2938 255 20M16H * 0 0 GTGCTATTGCTGGCGGTATT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4005 255 36M * 0 0 GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2479 255 36M * 0 0 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA *
+HWI-EAS91_1_306UPAAXX 16 phiX 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3045 255 1H35M * 0 0 GCTACCGATAACAATACTGTAGGCATGGGTGATGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1115 255 36M * 0 0 GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 636 255 33M3H * 0 0 GCTTATTATGTTCATCCCGTCAACATTCAAACG *
+HWI-EAS91_1_306UPAAXX 0 phiX 1139 255 34M2H * 0 0 GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG *
+HWI-EAS91_1_306UPAAXX 16 phiX 852 255 36M * 0 0 CTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 5272 255 36M * 0 0 GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4330 255 36M * 0 0 GCCCCGAAGGGGACNANAAATGGTTTTTAGAGAACG *
+HWI-EAS91_1_306UPAAXX 0 phiX 4891 255 36M * 0 0 GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 4785 255 2H34M * 0 0 TTTATGCGGACACTTCCTACAGGTAGCGTTGACC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3619 255 36M * 0 0 GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4455 255 32M4H * 0 0 GGTATTAAGGATGAGTGTTCAAGATTGCTGGA *
+HWI-EAS91_1_306UPAAXX 16 phiX 632 255 36M * 0 0 CATTGCTTATTATGTTCATCCCGTCAACATTCAAAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2964 255 35M1H * 0 0 GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGG *
+HWI-EAS91_1_306UPAAXX 16 phiX 2763 255 36M * 0 0 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2766 255 36M * 0 0 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1719 255 36M * 0 0 GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG *
+HWI-EAS91_1_306UPAAXX 16 phiX 3100 255 36M * 0 0 AAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 598 255 29M7H * 0 0 GCTTTCCTGCTCCTGTTGAGTTTATTGCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 4126 255 36M * 0 0 ACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4026 255 36M * 0 0 GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2621 255 36M * 0 0 GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2749 255 36M * 0 0 GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 379 255 36M * 0 0 GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG *
+HWI-EAS91_1_306UPAAXX 0 phiX 2160 255 36M * 0 0 GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2873 255 36M * 0 0 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1508 255 1H35M * 0 0 TGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3863 255 36M * 0 0 TTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 5187 255 36M * 0 0 GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4196 255 36M * 0 0 GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG *
+HWI-EAS91_1_306UPAAXX 16 phiX 635 255 36M * 0 0 TGCTTATTATGTTCATCCCGTCAACATTCAAACGGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1294 255 1H35M * 0 0 TAACACTACTGGTTATATTGACCATGCCGCTTTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 5157 255 36M * 0 0 AAAATGCTCACAATGACAAATCTGTCCACGGAGTGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 772 255 36M * 0 0 GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG *
+HWI-EAS91_1_306UPAAXX 0 phiX 1224 255 36M * 0 0 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA *
+HWI-EAS91_1_306UPAAXX 16 phiX 1544 255 3H33M * 0 0 CGCCAAATGACGACTTCTACCACATCTATTGAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4840 255 36M * 0 0 GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 204 255 35M1H * 0 0 GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGA *
+HWI-EAS91_1_306UPAAXX 16 phiX 3263 255 7H29M * 0 0 TGATAAAGGAAAGGATACTCGTGATTATC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2481 255 36M * 0 0 ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 332 255 36M * 0 0 AAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3978 255 36M * 0 0 TTTATGGTTCGTTCTTATTACCCTTCTGAATGTCAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4865 255 36M * 0 0 GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 3271 255 36M * 0 0 GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4174 255 36M * 0 0 TTGAGTTCGATAATGGTGATATGTATGTTGACGGCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3810 255 30M6H * 0 0 GTGGTTGATATTTTTCATGGTATTGATAAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4635 255 28M8H * 0 0 GCTTTGCGTGACTATTTTCGTGATATTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 2738 255 36M * 0 0 GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 2192 255 22M14H * 0 0 GTTCAGTTGTTGCATTGGAATA *
+HWI-EAS91_1_306UPAAXX 16 phiX 2703 255 1H35M * 0 0 CCCGACTGCCTATGATGTTTATCCTTTGAATGGTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2943 255 36M * 0 0 ATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3861 255 36M * 0 0 AATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3093 255 36M * 0 0 GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG *
+HWI-EAS91_1_306UPAAXX 0 phiX 3151 255 36M * 0 0 GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG *
+HWI-EAS91_1_306UPAAXX 0 phiX 1193 255 36M * 0 0 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 157 255 36M * 0 0 CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4792 255 36M * 0 0 GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 3849 255 36M * 0 0 GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 2743 255 1H35M * 0 0 GATGGTGGTTATTATACCGTCAAGGACTGTGTGAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3015 255 36M * 0 0 GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1091 255 36M * 0 0 ATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 798 255 1H35M * 0 0 GACGCAGAAGAAAACGTGCGTCAAAAATTACGTGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4866 255 36M * 0 0 CAAAATACGTGGCCTTATGGTTACAGTATGCCCATC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4404 255 36M * 0 0 GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1655 255 36M * 0 0 GTTATTTCTTCATTTGGAGGTAAAACCTCTTATGAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 5162 255 36M * 0 0 GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1249 255 1H35M * 0 0 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3261 255 36M * 0 0 GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 3096 255 36M * 0 0 ATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2812 255 1H35M * 0 0 GTTTATGTTGGTTTCATGGTTTGGTCTAACTTTAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 81 255 30M6H * 0 0 GAATTACTACTGCTTGTTTACGAATTAAAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3459 255 36M * 0 0 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG *
+HWI-EAS91_1_306UPAAXX 0 phiX 789 255 35M1H * 0 0 GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3699 255 36M * 0 0 GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2641 255 31M5H * 0 0 GCCGACCCTAAATTTTTTGCCTGTTTGGTTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 305 255 36M * 0 0 GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 3066 255 35M1H * 0 0 GGCATGGGTGATGCTGGTATTAAATCTGCCATTCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4428 255 36M * 0 0 GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG *
+HWI-EAS91_1_306UPAAXX 16 phiX 1461 255 36M * 0 0 AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4000 255 36M * 0 0 CTTCTGAATGTCACGCTGATTATTTTGACTTTGAGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 220 255 36M * 0 0 GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3194 255 33M3H * 0 0 GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 1266 255 32M4H * 0 0 GTGTTAATGCCACTCCTCTCCCGACTGTTAAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4596 255 36M * 0 0 GCTGACGACCGATTAGAGGCGTTTTATGATAATCCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1172 255 1H35M * 0 0 GGCCTTGCTATTGACTCTACTGTAGACATTTTTAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 636 255 36M * 0 0 GCTTATTATGTTCATCCCGTCAACATTCAAACGGCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2873 255 36M * 0 0 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1014 255 36M * 0 0 AAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2689 255 36M * 0 0 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2148 255 36M * 0 0 GCGTACTTATTCGCCACCATGATTATTACCAGTGTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 5191 255 35M1H * 0 0 GCTTAATCCAACTTACCAAGCTGGGTTACGACGCG *
+HWI-EAS91_1_306UPAAXX 16 phiX 1590 255 36M * 0 0 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 571 255 35M1H * 0 0 GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT *
+HWI-EAS91_1_306UPAAXX 0 phiX 242 255 36M * 0 0 GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 338 255 36M * 0 0 GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1112 255 30M6H * 0 0 GCTGGCGACTCCTTCGAGATGGACGCCGTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1254 255 2H34M * 0 0 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3731 255 18M18H * 0 0 GAATCAGCGGTATGGCTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2970 255 36M * 0 0 GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 5151 255 36M * 0 0 GGGATGAAAATGCTCACAATGACAAATCTGTCCACG *
+HWI-EAS91_1_306UPAAXX 16 phiX 348 255 36M * 0 0 ATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAA *
+HWI-EAS91_1_306UPAAXX 16 phiX 4888 255 1H35M * 0 0 ACAGTATGCCCATCGCAGTTCGCTACACGCAGGAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3972 255 33M3H * 0 0 GGCTTTTTTATGGTTCGTTCTTATTACCCTTCT *
+HWI-EAS91_1_306UPAAXX 0 phiX 5033 255 36M * 0 0 GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1552 255 1H35M * 0 0 GACGACTTCTACCACATCTATTGACATTATGGGTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1764 255 36M * 0 0 AAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1529 255 36M * 0 0 GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4950 255 36M * 0 0 CCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4484 255 34M2H * 0 0 GGAGGCCTCCACTATGAAATCGCGTAGAGGCTTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 4767 255 1H35M * 0 0 CATTTCCATGCGGTGCATTTTATGCGGACACTTCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 177 255 36M * 0 0 CTTTGCGACCTTTCGCCATCAACTAACGATTCTGTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2577 255 36M * 0 0 GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 156 255 36M * 0 0 GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG *
+HWI-EAS91_1_306UPAAXX 0 phiX 227 255 36M * 0 0 TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT *
+HWI-EAS91_1_306UPAAXX 16 phiX 574 255 36M * 0 0 CGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3021 255 36M * 0 0 GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3731 255 36M * 0 0 GAATCAGCGGTATGGCTCTTCTCATATTGGCGCTAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2436 255 36M * 0 0 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2710 255 36M * 0 0 GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4228 255 28M8H * 0 0 TTCGTGATGAGTTTGTATCTGTTACTGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4606 255 34M2H * 0 0 GATTAGAGGCGTTTTATGATAATCCCAATGCTTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 2766 255 36M * 0 0 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 582 255 34M2H * 0 0 TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTG *
+HWI-EAS91_1_306UPAAXX 16 phiX 664 255 10H26M * 0 0 AAACGGCCTGTCTCATCATGGAAGGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1144 255 36M * 0 0 CGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1514 255 36M * 0 0 GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4036 255 26M10H * 0 0 GTATCGAGGCTCTTAAACCTGCTATT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1657 255 36M * 0 0 TATTTCTTCATTTGGAGGTAAAACCTCTTATGACGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2071 255 36M * 0 0 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 1626 255 36M * 0 0 GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3250 255 36M * 0 0 GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 1982 255 36M * 0 0 GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 2217 255 36M * 0 0 AGGTTAAATTTAATGTGACCGTTTATCGCAATCTGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3486 255 7H29M * 0 0 CAGAATACGAAAGACCAGGTATATGCACA *
+HWI-EAS91_1_306UPAAXX 16 phiX 1690 255 36M * 0 0 CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAA *
+HWI-EAS91_1_306UPAAXX 16 phiX 3252 255 7H29M * 0 0 AAGTCTGCCGATGATAAAGGAAAGGATAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4282 255 36M * 0 0 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4136 255 34M2H * 0 0 GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAG *
+HWI-EAS91_1_306UPAAXX 0 phiX 4414 255 36M * 0 0 TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA *
+HWI-EAS91_1_306UPAAXX 16 phiX 3988 255 36M * 0 0 GTTCTTATTACCCTTCTGAATGTCACGCTGATTATT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4203 255 36M * 0 0 GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG *
+HWI-EAS91_1_306UPAAXX 16 phiX 4098 255 36M * 0 0 ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4307 255 35M1H * 0 0 TATTAATAACACTATAGACCACCGCCCCGAAGGGG *
+HWI-EAS91_1_306UPAAXX 0 phiX 1521 255 35M1H * 0 0 TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACG *
+HWI-EAS91_1_306UPAAXX 16 phiX 945 255 36M * 0 0 TAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1575 255 36M * 0 0 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2689 255 36M * 0 0 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2099 255 36M * 0 0 GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT *
+HWI-EAS91_1_306UPAAXX 16 phiX 524 255 36M * 0 0 TACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1252 255 36M * 0 0 GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4916 255 33M3H * 0 0 GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 3828 255 29M7H * 0 0 GGTATTGATAAAGCTGTTGCCGATACTTG *
+HWI-EAS91_1_306UPAAXX 16 phiX 3756 255 36M * 0 0 ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 664 255 10H26M * 0 0 AAACGGCCTGTCTCATCATGGAAGGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1116 255 36M * 0 0 GCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3099 255 36M * 0 0 CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3082 255 36M * 0 0 GTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4221 255 27M9H * 0 0 TCTGACGTTCGTGATGAGTTTGTATCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 613 255 36M * 0 0 TTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4936 255 36M * 0 0 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 289 255 36M * 0 0 TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4690 255 36M * 0 0 GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2547 255 31M5H * 0 0 TGGTAATGGTGGTTTTCTTCATTTCATTCAG *
+HWI-EAS91_1_306UPAAXX 16 phiX 3520 255 36M * 0 0 AGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3858 255 36M * 0 0 AACAATTTCTGGAAAGACGGTAAAGCTGATGGTATT *
+HWI-EAS91_1_306UPAAXX 16 phiX 3344 255 36M * 0 0 TTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4672 255 27M9H * 0 0 TTCTTGCTGCCGAGGGTCGCAAGGCTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1346 255 31M5H * 0 0 GATACCAATAAAATCCCTAAGCATTTGTTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1800 255 36M * 0 0 AGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 5077 255 36M * 0 0 GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2763 255 1H35M * 0 0 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4282 255 36M * 0 0 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4656 255 27M9H * 0 0 GATATTGGTCGTATGGTTCTTGCTGCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4935 255 18M18H * 0 0 TCTGGTTGGTTGTGGCCT *
+HWI-EAS91_1_306UPAAXX 0 phiX 1203 255 33M3H * 0 0 TTACTTTTTATGTCCCTCATCGTCACGTTTATG *
+HWI-EAS91_1_306UPAAXX 16 phiX 5107 255 36M * 0 0 TACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 5168 255 1H35M * 0 0 AATGACAAATCTGTCCACGGAGTGCTTAATCCAAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2956 255 36M * 0 0 TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 624 255 30M6H * 0 0 GCTGCCGTCATTGCTTATTATGTTCATCCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1877 255 1H35M * 0 0 CCGCCTACTGCGACTAAAGAGATTCAGTACCTTAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1214 255 36M * 0 0 GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT *
+HWI-EAS91_1_306UPAAXX 0 phiX 558 255 27M9H * 0 0 GCTTGCGTTTATGGTACGCTGGACTTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 3629 255 36M * 0 0 TACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2254 255 35M1H * 0 0 GACCACTCGCGATTCAATCATGACTTCGTGATAAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2479 255 36M * 0 0 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3001 255 36M * 0 0 GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 4667 255 35M1H * 0 0 TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATG *
+HWI-EAS91_1_306UPAAXX 16 phiX 3464 255 36M * 0 0 CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4911 255 35M1H * 0 0 TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4592 255 29M7H * 0 0 GTTGGCTGACGACCGATTAGAGGCGTTTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 2222 255 36M * 0 0 AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC *
+HWI-EAS91_1_306UPAAXX 0 phiX 646 255 35M1H * 0 0 TTCATCCCGTCAACATTCAAACGGCCTGTCTCATC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1364 255 36M * 0 0 AAGCATTTGTTTCAGGGTTATTTGAATATCTATAAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1613 255 1H35M * 0 0 ACTGACCAAGAACGTGATTACTTCATGCAGCGTTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1045 255 35M1H * 0 0 TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2885 255 33M3H * 0 0 TTATTAAAGAGATTATTTTTCTCCAGCCACTTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1588 255 36M * 0 0 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 339 255 36M * 0 0 TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4937 255 36M * 0 0 TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4344 255 2H34M * 0 0 GAAAAATGGTTTTTAGAGAACGAGAAGACGGTTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 3674 255 36M * 0 0 CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4945 255 36M * 0 0 TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG *
+HWI-EAS91_1_306UPAAXX 0 phiX 1946 255 36M * 0 0 GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2662 255 32M4H * 0 0 TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3313 255 36M * 0 0 TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 2827 255 3H33M * 0 0 ATGGTTTGGTCAAACTTTACCGCTACTAAATGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 727 255 36M * 0 0 GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 555 255 36M * 0 0 GAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 485 255 36M * 0 0 TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 318 255 36M * 0 0 TGTTGACATTTTAAAAGAGCGTGGATTACTATCTGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 910 255 36M * 0 0 TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT *
+HWI-EAS91_1_306UPAAXX 16 phiX 4936 255 36M * 0 0 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 5005 255 36M * 0 0 TCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1379 255 33M3H * 0 0 GGTTATTTGAATATCTATAACAACTATTTTAAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3168 255 30M6H * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAG *
+HWI-EAS91_1_306UPAAXX 0 phiX 2738 255 33M3H * 0 0 GCCATGATGGTGGTTATTATACCGTCAAGGACT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4099 255 36M * 0 0 TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2574 255 36M * 0 0 TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2453 255 36M * 0 0 TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 5179 255 36M * 0 0 TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG *
+HWI-EAS91_1_306UPAAXX 0 phiX 3778 255 30M6H * 0 0 TTTCTAATGTCGTCACTGATGCTGCTTCTG *
+HWI-EAS91_1_306UPAAXX 16 phiX 1843 255 36M * 0 0 TGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1728 255 36M * 0 0 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4637 255 36M * 0 0 TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2225 255 36M * 0 0 TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT *
+HWI-EAS91_1_306UPAAXX 16 phiX 3368 255 36M * 0 0 CGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3311 255 36M * 0 0 GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 5039 255 36M * 0 0 TATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2059 255 36M * 0 0 TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT *
+HWI-EAS91_1_306UPAAXX 0 phiX 388 255 36M * 0 0 TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2754 255 36M * 0 0 TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 2128 255 36M * 0 0 TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 154 255 36M * 0 0 TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 3617 255 36M * 0 0 GCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCA *
+HWI-EAS91_1_306UPAAXX 16 phiX 2728 255 36M * 0 0 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2775 255 36M * 0 0 GACTATTGACGTCCTTCCCCGTACGCCGGGCAATAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4217 255 36M * 0 0 TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4619 255 35M1H * 0 0 TTATGATAATCCCAATGCTTTGCGTGACTATTTTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 411 255 35M1H * 0 0 TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2730 255 35M1H * 0 0 GAATGGTCGCCATGATGGTGGTTATTATACCGTCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 521 255 35M1H * 0 0 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 4260 255 36M * 0 0 TTAATGGATGAATTGGCACAATGCTACAATGTGCTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1662 255 36M * 0 0 CTTCATTTGGAGGTAAAACCTCTTATGACGCTGACA *
+HWI-EAS91_1_306UPAAXX 16 phiX 533 255 36M * 0 0 CTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 195 255 35M1H * 0 0 TCAACTAACGATTCTGTCAAAAACTGACGCGTTGG *
+HWI-EAS91_1_306UPAAXX 0 phiX 2239 255 36M * 0 0 TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 1313 255 33M3H * 0 0 GACCATGCCGCTTTTCTTGGCACGATTAACCCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1545 255 36M * 0 0 GCCAAATGACGACTTCTACCACATCTATTGACATTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 557 255 36M * 0 0 GGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1249 255 36M * 0 0 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4174 255 33M3H * 0 0 TTGAGTTCGATAATGGTGATATGTATGTTGACG *
+HWI-EAS91_1_306UPAAXX 0 phiX 614 255 35M1H * 0 0 TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 206 255 36M * 0 0 TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT *
+HWI-EAS91_1_306UPAAXX 16 phiX 4981 255 36M * 0 0 CTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1702 255 30M6H * 0 0 TCCTTTACTTGTCATGCGCTCTAATCTCTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 2321 255 35M1H * 0 0 TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4184 255 35M1H * 0 0 TAATGGTGATATGTATGTTTACGTCCATAAGGCTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 4088 255 35M1H * 0 0 TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGG *
+HWI-EAS91_1_306UPAAXX 0 phiX 900 255 36M * 0 0 TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1155 255 36M * 0 0 TTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 3587 255 36M * 0 0 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCA *
+HWI-EAS91_1_306UPAAXX 16 phiX 3787 255 36M * 0 0 TCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3834 255 35M1H * 0 0 GATAAAGCTGTTGCCGATACTTGGAACAATTTCTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 989 255 36M * 0 0 TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC *
+HWI-EAS91_1_306UPAAXX 0 phiX 5358 255 29M7H * 0 0 ATAAAAATGATTGGCGTATCCAACCTGCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3712 255 36M * 0 0 TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT *
+HWI-EAS91_1_306UPAAXX 0 phiX 1207 255 36M * 0 0 TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA *
+HWI-EAS91_1_306UPAAXX 16 phiX 4300 255 15H21M * 0 0 AACTTGATATTAATAACACTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2116 255 36M * 0 0 TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT *
+HWI-EAS91_1_306UPAAXX 16 phiX 660 255 36M * 0 0 ATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1807 255 31M5H * 0 0 TAAACATTCTGTGCCGCGTTTCTTTGTTCCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1536 255 36M * 0 0 AGCTTTCTCGCCAAATGACGACTTCTACCACATCTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 2112 255 1H35M * 0 0 TCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAA *
+HWI-EAS91_1_306UPAAXX 16 phiX 2816 255 36M * 0 0 ATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 5176 255 36M * 0 0 ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3472 255 36M * 0 0 CGGCGACTTCACGCCAGAATACGAAAGACCAGGTAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1948 255 36M * 0 0 CGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2212 255 35M1H * 0 0 TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3817 255 35M1H * 0 0 ATATTTTTCATGGTATTGATAAAGCTGTTGCCGAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 3563 255 36M * 0 0 GTCTATTATGGAAAACACCAATCTTTCCAAGCAACA *
+HWI-EAS91_1_306UPAAXX 16 phiX 4198 255 1H35M * 0 0 ATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGT *
+HWI-EAS91_1_306UPAAXX 16 phiX 2907 255 1H35M * 0 0 CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2843 255 35M1H * 0 0 TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 4374 255 31M5H * 0 0 GTTACGCAGTTTTGCCGCAAGCTGGCTGCTG *
+HWI-EAS91_1_306UPAAXX 16 phiX 424 255 2H24M10H * 0 0 AGACCGCCTTGGCCTCTATTAAGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1940 255 1H35M * 0 0 ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 5073 255 36M * 0 0 GAATGGAACAACTCACTAAAAACCAAGCTGTCGCTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4434 255 36M * 0 0 TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG *
+HWI-EAS91_1_306UPAAXX 16 phiX 1274 255 1H35M * 0 0 GCCACTCCTCTCCCGACTGTTAACACTACTGGTTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4440 255 36M * 0 0 TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3920 255 36M * 0 0 GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 4587 255 1H35M * 0 0 CTCACGTTGGCTGACGACCGATTAGAGGCGTTTTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3730 255 24M12H * 0 0 AGAATCAGCGGTATGGCTCTTCTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1707 255 36M * 0 0 TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1582 255 36M * 0 0 GGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGA *
+HWI-EAS91_1_306UPAAXX 16 phiX 1588 255 36M * 0 0 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1180 255 34M2H * 0 0 TATTGACTCTACTGTAGACATTTTTACTTTTTAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 2698 255 36M * 0 0 ACCCTCCCGACTGCCTATGATGTTTATCCTTTGAAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3167 255 36M * 0 0 TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG *
+HWI-EAS91_1_306UPAAXX 16 phiX 2498 255 11H25M * 0 0 CTAAAGCTACATCGTCAACGTTATA *
+HWI-EAS91_1_306UPAAXX 16 phiX 2289 255 36M * 0 0 AGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAA *
+HWI-EAS91_1_306UPAAXX 16 phiX 441 255 36M * 0 0 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1012 255 36M * 0 0 TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 161 255 36M * 0 0 GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1165 255 1H35M * 0 0 GCGTCGTGGCCTTGCTATTGACTCTACTGTAGACA *
+HWI-EAS91_1_306UPAAXX 16 phiX 5015 255 5H31M * 0 0 TAAATACGTTAACAAAAAGTCAGATATGGAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2286 255 36M * 0 0 AAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGT *
+HWI-EAS91_1_306UPAAXX 16 phiX 801 255 32M4H * 0 0 GCAGAAGAAAACGTGCGTCAAAAATTACGTGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 1587 255 36M * 0 0 TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG *
+HWI-EAS91_1_306UPAAXX 0 phiX 4578 255 36M * 0 0 TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG *
+HWI-EAS91_1_306UPAAXX 16 phiX 3570 255 36M * 0 0 ATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 496 255 36M * 0 0 TTCTGACGAGTAACAAAGTTTGGATTGCTACTGACC *
+HWI-EAS91_1_306UPAAXX 0 phiX 441 255 36M * 0 0 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 4754 255 30M6H * 0 0 TAATGGCCGTCTTCATTTCCATGCGGTGCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4235 255 35M1H * 0 0 TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATG *
+HWI-EAS91_1_306UPAAXX 16 phiX 2293 255 36M * 0 0 TGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1579 255 1H35M * 0 0 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3332 255 31M5H * 0 0 TGGTGCTGATGCTTCCTCTGCTGGTATGGTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4132 255 36M * 0 0 TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4775 255 36M * 0 0 TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG *
+HWI-EAS91_1_306UPAAXX 16 phiX 657 255 18H18M * 0 0 AACATTCAAACGGCCTGT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1 255 4H32M * 0 0 GAGTTTTATCGCTTCCATGACGCAGAAGTTAA *
+HWI-EAS91_1_306UPAAXX 16 phiX 54 255 36M * 0 0 AGTCGAAAAATTATCTTGATAAAGCAGGAATTACTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 680 255 1H35M * 0 0 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 231 255 36M * 0 0 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4192 255 36M * 0 0 ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG *
+HWI-EAS91_1_306UPAAXX 16 phiX 1580 255 36M * 0 0 ATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACT *
+HWI-EAS91_1_306UPAAXX 16 phiX 611 255 36M * 0 0 TGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT *
+HWI-EAS91_1_306UPAAXX 16 phiX 4532 255 1H35M * 0 0 GATGAATGCAATGCGACAGGCTCATGCTGATGGTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 638 255 30M6H * 0 0 TTATTATGTTCATCCCGTCAACATTCAAAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2847 255 4H28M4H * 0 0 CGCTACTAAATTCCGCGGATTGGTTTCG *
+HWI-EAS91_1_306UPAAXX 16 phiX 1957 255 36M * 0 0 TTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 2728 255 36M * 0 0 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 3979 255 36M * 0 0 TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG *
+HWI-EAS91_1_306UPAAXX 16 phiX 540 255 1H35M * 0 0 GCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 1852 255 36M * 0 0 GTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4684 255 36M * 0 0 AGGGTCGCAAGGCTAATGATTCACACGCCGACTGCT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3690 255 32M4H * 0 0 AAGGTTAGTGCTGAGGTTGACTTAGTTCATCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 584 255 36M * 0 0 TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 3852 255 1H35M * 0 0 ACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2857 255 35M1H * 0 0 TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3782 255 26M10H * 0 0 TAATGTCGTCACTGATGCTGCTTCTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 1728 255 36M * 0 0 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC *
+HWI-EAS91_1_306UPAAXX 0 phiX 4658 255 35M1H * 0 0 TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCA *
+HWI-EAS91_1_306UPAAXX 16 phiX 1721 255 36M * 0 0 TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1954 255 36M * 0 0 TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC *
+HWI-EAS91_1_306UPAAXX 0 phiX 962 255 36M * 0 0 TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA *
+HWI-EAS91_1_306UPAAXX 16 phiX 2175 255 36M * 0 0 ACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2442 255 36M * 0 0 TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 5126 255 1H35M * 0 0 CAGAATCAGAATGAGCCGCAACTTCGGGATGAAAA *
+HWI-EAS91_1_306UPAAXX 16 phiX 5206 255 36M * 0 0 CCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2879 255 36M * 0 0 ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 2004 255 36M * 0 0 TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 2154 255 36M * 0 0 TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 1093 255 35M1H * 0 0 TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCG *
+HWI-EAS91_1_306UPAAXX 16 phiX 3127 255 36M * 0 0 AGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 3544 255 36M * 0 0 AGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2508 255 31M5H * 0 0 ATCGTCAACGTTATATTTTGATAGTTTGACG *
+HWI-EAS91_1_306UPAAXX 16 phiX 3098 255 12H24M * 0 0 TCAAGGCTCTAATGTCCCTAACCC *
+HWI-EAS91_1_306UPAAXX 16 phiX 3600 255 36M * 0 0 CAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA *
+HWI-EAS91_1_306UPAAXX 16 phiX 1734 255 36M * 0 0 CATCTGGCTATGATGTTGATGGAACTGACCAAACGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2655 255 33M3H * 0 0 TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 2934 255 36M * 0 0 TTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 1522 255 36M * 0 0 TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4063 255 36M * 0 0 AGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3395 255 36M * 0 0 TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 409 255 36M * 0 0 AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 1867 255 36M * 0 0 TGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 3780 255 33M3H * 0 0 TCTAATGTCGTCACTGATGCTGCTTCTGGTGTG *
+HWI-EAS91_1_306UPAAXX 0 phiX 3982 255 36M * 0 0 TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG *
+HWI-EAS91_1_306UPAAXX 16 phiX 2815 255 36M * 0 0 TATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 1242 255 36M * 0 0 AGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCA *
+HWI-EAS91_1_306UPAAXX 16 phiX 4659 255 1H35M * 0 0 ATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2436 255 36M * 0 0 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC *
+HWI-EAS91_1_306UPAAXX 0 phiX 527 255 35M1H * 0 0 TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 4817 255 36M * 0 0 CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2100 255 36M * 0 0 AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG *
+HWI-EAS91_1_306UPAAXX 16 phiX 2762 255 36M * 0 0 TCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA *
+HWI-EAS91_1_306UPAAXX 0 phiX 4955 255 36M * 0 0 TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 3761 255 36M * 0 0 CGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA *
+HWI-EAS91_1_306UPAAXX 16 phiX 4499 255 36M * 0 0 GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 4039 255 36M * 0 0 TCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCA *
+HWI-EAS91_1_306UPAAXX 16 phiX 4788 255 36M * 0 0 ATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 1002 255 36M * 0 0 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4381 255 36M * 0 0 AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 4256 255 36M * 0 0 GAAGTTAATGGATGAATTGGCACAATGCTACAATGT *
+HWI-EAS91_1_306UPAAXX 16 phiX 10 255 1H35M * 0 0 CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA *
+HWI-EAS91_1_306UPAAXX 16 phiX 1579 255 36M * 0 0 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC *
+HWI-EAS91_1_306UPAAXX 0 phiX 989 255 30M6H * 0 0 TGAGGATAAATTATGTCTAATATTCAAACT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3862 255 36M * 0 0 ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3278 255 36M * 0 0 TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT *
+HWI-EAS91_1_306UPAAXX 0 phiX 349 255 36M * 0 0 TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG *
+HWI-EAS91_1_306UPAAXX 0 phiX 4608 255 36M * 0 0 TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT *
+HWI-EAS91_1_306UPAAXX 0 phiX 3808 255 35M1H * 0 0 GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 4753 255 31M5H * 0 0 CTAATGGCCGTCTTCATTTCCATGCGGTGCA *
+HWI-EAS91_1_306UPAAXX 16 phiX 286 255 36M * 0 0 GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT *
+HWI-EAS91_1_306UPAAXX 0 phiX 2850 255 36M * 0 0 TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT *
+HWI-EAS91_1_306UPAAXX 16 phiX 680 255 1H35M * 0 0 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 4740 255 36M * 0 0 GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT *
+HWI-EAS91_1_306UPAAXX 0 phiX 4655 255 25M11H * 0 0 TGATATTGGTCGTATGGTTCTTGCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 2467 255 1H35M * 0 0 CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA *
+HWI-EAS91_1_306UPAAXX 0 phiX 320 255 34M2H * 0 0 TTGACATTTTAAAAGAGCGTGGATTACTATCTGA *
+HWI-EAS91_1_306UPAAXX 0 phiX 1180 255 34M2H * 0 0 TATTGACTCTACTGTAGACATTTTTACTTTTTAT *
+HWI-EAS91_1_306UPAAXX 16 phiX 521 255 36M * 0 0 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA *
+HWI-EAS91_1_306UPAAXX 16 phiX 333 255 36M * 0 0 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA *
+HWI-EAS91_1_306UPAAXX 0 phiX 2756 255 36M * 0 0 ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC *
+HWI-EAS91_1_306UPAAXX 16 phiX 4957 255 36M * 0 0 ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA *
+HWI-EAS91_1_306UPAAXX 16 phiX 72 255 36M * 0 0 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA *
+HWI-EAS91_1_306UPAAXX 16 phiX 4249 255 36M * 0 0 TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT *
+HWI-EAS91_1_306UPAAXX 16 phiX 2592 255 36M * 0 0 CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA *
+HWI-EAS91_1_306UPAAXX 16 phiX 1974 255 36M * 0 0 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT *
+HWI-EAS91_1_306UPAAXX 16 phiX 3540 255 36M * 0 0 AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA *
+HWI-EAS91_1_306UPAAXX 16 phiX 4130 255 36M * 0 0 CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT *
diff -r 8d149264b777 -r efdb6fb5de34 test-data/lastz_wrapper_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lastz_wrapper_out3.tabular Fri Nov 27 10:53:50 2009 -0500
@@ -0,0 +1,26 @@
+phiX 1164 1165 + 5386 HWI-EAS91_1_306UPAAXX:6:1:112:1280 26 27 + 36 G T GTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTG GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG
+phiX 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC
+phiX 2205 2206 + 5386 HWI-EAS91_1_306UPAAXX:6:1:217:737 14 15 + 36 G T GTTCAGTTGTTGCAGTGGAATA GTTCAGTTGTTGCATTGGAATA
+phiX 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT
+phiX 578 579 + 5386 HWI-EAS91_1_306UPAAXX:6:1:317:1411 8 9 + 36 G T GTACGCTGGACTTTGTGGGATACCCTCGCTTTCCT GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT
+phiX 2992 2993 + 5386 HWI-EAS91_1_306UPAAXX:6:1:458:1629 23 24 + 36 G T GCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGT GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT
+phiX 4783 4784 + 5386 HWI-EAS91_1_306UPAAXX:6:1:646:59 18 19 - 36 C T CATTTCCATGCGGTGCACTTTATGCGGACACTTCC CATTTCCATGCGGTGCATTTTATGCGGACACTTCC
+phiX 1649 1650 + 5386 HWI-EAS91_1_306UPAAXX:6:1:295:694 24 25 + 36 A G GTGATTACTTCATGCAGCGTTACCATGATGTTATTT GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT
+phiX 1995 1996 + 5386 HWI-EAS91_1_306UPAAXX:6:1:590:331 14 15 + 36 G T GAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGAT GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT
+phiX 3261 3262 + 5386 HWI-EAS91_1_306UPAAXX:6:1:221:1238 17 18 - 36 C A AAGTCTGCCGCTGATAAAGGAAAGGATAC AAGTCTGCCGATGATAAAGGAAAGGATAC
+phiX 4109 4110 + 5386 HWI-EAS91_1_306UPAAXX:6:1:478:252 12 13 - 36 C A ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC
+phiX 3126 3127 + 5386 HWI-EAS91_1_306UPAAXX:6:1:589:96 28 29 - 36 A G CAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCC CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC
+phiX 2569 2570 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1472:716 23 24 + 36 G T TGGTAATGGTGGTTTTCTTCATTGCATTCAG TGGTAATGGTGGTTTTCTTCATTTCATTCAG
+phiX 2972 2973 + 5386 HWI-EAS91_1_306UPAAXX:6:1:836:1204 17 18 + 36 G T TTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAAT TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT
+phiX 2234 2235 + 5386 HWI-EAS91_1_306UPAAXX:6:1:172:1412 13 14 - 36 C A AAATTTAATGTGACCGTTTATCGCAATCTGCCGACC AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC
+phiX 2902 2903 + 5386 HWI-EAS91_1_306UPAAXX:6:1:540:1415 18 19 + 36 G T TTATTAAAGAGATTATTTGTCTCCAGCCACTTA TTATTAAAGAGATTATTTTTCTCCAGCCACTTA
+phiX 2837 2838 + 5386 HWI-EAS91_1_306UPAAXX:6:1:253:1162 14 15 - 36 T A ATGGTTTGGTCTAACTTTACCGCTACTAAATGC ATGGTTTGGTCAAACTTTACCGCTACTAAATGC
+phiX 4662 4663 + 5386 HWI-EAS91_1_306UPAAXX:6:1:828:754 26 27 + 36 G T TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGT TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT
+phiX 4202 4203 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 19 20 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG
+phiX 4206 4207 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 23 24 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG
+phiX 430 431 + 5386 HWI-EAS91_1_306UPAAXX:6:1:203:667 9 10 - 36 T C AGACCGCTTTGGCCTCTATTAAGC AGACCGCCTTGGCCTCTATTAAGC
+phiX 4783 4784 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1566:499 9 10 + 36 C T TGCGGTGCACTTTATGCGGACACTTCCTACAGGTAG TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG
+phiX 2857 2858 + 5386 HWI-EAS91_1_306UPAAXX:6:1:578:971 15 16 + 36 G T CGCTACTAAATGCCGCGGATTGGTTTCG CGCTACTAAATTCCGCGGATTGGTTTCG
+phiX 3112 3113 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1721:1800 27 28 - 36 T C TCAAGGCTCTAATGTTCCTAACCC TCAAGGCTCTAATGTCCCTAACCC
+phiX 4825 4826 + 5386 HWI-EAS91_1_306UPAAXX:6:1:815:1640 9 10 - 36 T G CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCA CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA
+phiX 4517 4518 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1485:741 19 20 - 36 G A GAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGAT GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT
diff -r 8d149264b777 -r efdb6fb5de34 test-data/phiX.fa
--- a/test-data/phiX.fa Wed Nov 25 14:06:28 2009 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
->phiX
-GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
-GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
-ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
-TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
-GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
-TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
-TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
-CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
-TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
-TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
-GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
-CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG
-TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
-AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
-CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
-TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
-TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
-CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
-GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
-GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
-ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
-TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
-TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
-ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC
-CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
-GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
-CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
-TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
-TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
-TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
-AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
-TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
-ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
-GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
-TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
-TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
-TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
-TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
-CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
-AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
-CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
-TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
-CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
-AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
-GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
-GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
-TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
-CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
-TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
-GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
-CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
-TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
-AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
-TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
-CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
-TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
-TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
-CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
-TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
-ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
-TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
-ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
-GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
-CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
-GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG
-GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
-ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
-CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
-CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
-GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
-CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
-CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
-TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
-TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
-TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
-AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
-TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
-
diff -r 8d149264b777 -r efdb6fb5de34 test-data/phiX.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX.fasta Fri Nov 27 10:53:50 2009 -0500
@@ -0,0 +1,79 @@
+>phiX
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+
diff -r 8d149264b777 -r efdb6fb5de34 tool-data/lastz_seqs.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/lastz_seqs.loc Fri Nov 27 10:53:50 2009 -0500
@@ -0,0 +1,2 @@
+#ref path
+hg19 /depot/data2/galaxy/hg19/seq/hg19.2bit
diff -r 8d149264b777 -r efdb6fb5de34 tool_conf.xml.sample
--- a/tool_conf.xml.sample Wed Nov 25 14:06:28 2009 -0500
+++ b/tool_conf.xml.sample Fri Nov 27 10:53:50 2009 -0500
@@ -187,7 +187,7 @@
<tool file="solid_tools/solid_qual_boxplot.xml" />
</section>
<section name="NGS: Mapping" id="solexa_tools">
- <!-- <tool file="sr_mapping/lastz_wrapper.xml" /> -->
+ <tool file="sr_mapping/lastz_wrapper.xml" />
<tool file="sr_mapping/bowtie_wrapper.xml" />
<tool file="sr_mapping/bwa_wrapper.xml" />
<tool file="metag_tools/megablast_wrapper.xml" />
diff -r 8d149264b777 -r efdb6fb5de34 tools/sr_mapping/bwa_wrapper.xml
--- a/tools/sr_mapping/bwa_wrapper.xml Wed Nov 25 14:06:28 2009 -0500
+++ b/tools/sr_mapping/bwa_wrapper.xml Fri Nov 27 10:53:50 2009 -0500
@@ -169,7 +169,7 @@
<test>
<param name="solidSolexa" value="solid" />
<param name="refGenomeSource" value="history" />
- <param name="ownFile" value="phiX.fa" />
+ <param name="ownFile" value="phiX.fasta" />
<param name="sPaired" value="single" />
<param name="input1" value="bwa_wrapper_in0.fastq" ftype="fastqsanger" />
<param name="source_select" value="pre_set" />
diff -r 8d149264b777 -r efdb6fb5de34 tools/sr_mapping/lastz_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_mapping/lastz_wrapper.py Fri Nov 27 10:53:50 2009 -0500
@@ -0,0 +1,133 @@
+#! /usr/bin/python
+
+"""
+ --lastzSeqsFileDir: Directory of local lastz_seqs.loc file
+"""
+import optparse, os, subprocess, shutil, sys, tempfile, threading
+from Queue import Queue
+
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( 'bx-python' )
+from bx.seq.twobit import *
+
+def stop_err( msg ):
+ sys.stderr.write( "%s\n" % msg )
+ sys.exit()
+
+class LastzJobRunner( object ):
+ """
+ Lastz job runner backed by a pool of "num_threads" worker threads. FIFO scheduling
+ """
+ def __init__( self, num_threads, commands ):
+ """Start the job runner with "num_threads" worker threads"""
+ # start workers
+ self.queue = Queue()
+ for command in commands:
+ self.queue.put( command )
+ self.threads = []
+ for i in range( num_threads ):
+ worker = threading.Thread( target=self.run_next )
+ worker.start()
+ self.threads.append( worker )
+ def run_next( self ):
+ """Run the next command, waiting until one is available if necessary"""
+ while not self.queue.empty():
+ command = self.queue.get()
+ self.run_job( command )
+ def run_job( self, command ):
+ try:
+ proc = subprocess.Popen( args=command, shell=True )
+ sts = os.waitpid( proc.pid, 0 )
+ except Exception, e:
+ stop_err( "Error executing command (%s) - %s" % ( str( command ), str( e ) ) )
+
+def __main__():
+ #Parse Command Line
+ parser = optparse.OptionParser()
+ parser.add_option( '', '--ref_name', dest='ref_name', help='' )
+ parser.add_option( '', '--ref_source', dest='ref_source', help='' )
+ parser.add_option( '', '--ref_sequences', dest='ref_sequences', help='Number of sequences in the reference dataset' )
+ parser.add_option( '', '--source_select', dest='source_select', help='' )
+ parser.add_option( '', '--out_format', dest='out_format', help='' )
+ parser.add_option( '', '--input1', dest='input1', help='' )
+ parser.add_option( '', '--input2', dest='input2', help='' )
+ parser.add_option( '', '--pre_set_options', dest='pre_set_options', help='' )
+ parser.add_option( '', '--strand', dest='strand', help='' )
+ parser.add_option( '', '--seed', dest='seed', help='' )
+ parser.add_option( '', '--transition', dest='transition', help='' )
+ parser.add_option( '', '--gfextend', dest='gfextend', help='' )
+ parser.add_option( '', '--nogfextend', dest='nogfextend', help='' )
+ parser.add_option( '', '--chain', dest='chain', help='' )
+ parser.add_option( '', '--nochain', dest='nochain', help='' )
+ parser.add_option( '', '--gapped', dest='gapped', help='' )
+ parser.add_option( '', '--nogapped', dest='nogapped', help='' )
+ parser.add_option( '', '--O', dest='O', help='' )
+ parser.add_option( '', '--E', dest='E', help='' )
+ parser.add_option( '', '--X', dest='X', help='' )
+ parser.add_option( '', '--Y', dest='Y', help='' )
+ parser.add_option( '', '--K', dest='K', help='' )
+ parser.add_option( '', '--L', dest='L', help='' )
+ parser.add_option( '', '--entropy', dest='entropy', help='' )
+ parser.add_option( '', '--identity_min', dest='identity_min', help='' )
+ parser.add_option( '', '--identity_max', dest='identity_max', help='' )
+ parser.add_option( '', '--coverage', dest='coverage', help='' )
+ parser.add_option( '', '--format', dest='format', help='' )
+ parser.add_option( '', '--output', dest='output', help='The output file' )
+ parser.add_option( '', '--num_threads', dest='num_threads', help='' )
+ parser.add_option( '', '--lastzSeqsFileDir', dest='lastzSeqsFileDir', help='Directory of local lastz_seqs.loc file' )
+ ( options, args ) = parser.parse_args()
+
+ commands = []
+ if options.ref_name != 'None':
+ ref_name = '%s::' % options.ref_name
+ else:
+ ref_name = ''
+ # Prepare for commonly-used preset options
+ if options.source_select == 'pre_set':
+ set_options = '--%s' % options.pre_set_options
+ # Prepare for user-specified options
+ else:
+ set_options = '%s %s --%s --%s --%s --%s O=%s E=%s X=%s Y=%s K=%s L=%s %s' % \
+ ( options.gfextend, options.chain, options.gapped, options.strand,
+ options.seed, options.transition, options.O, options.E, options.X,
+ options.Y, options.K, options.L, options.entropy )
+ # Specify input2 and add [fullnames] modifier if output format is diffs
+ if options.format == 'diffs':
+ input2 = '%s[fullnames]' % options.input2
+ else:
+ input2 = options.input2
+ if options.format == 'tabular':
+ # Change output format to general if it's tabular and add field names for tabular output
+ format = 'general'
+ tabular_fields = ':score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle'
+ else:
+ format = options.format
+ tabular_fields = ''
+ if options.ref_source == 'history':
+ # Reference is a fasta dataset from the history, so split job across number of
+ # sequences in the dataset
+ try:
+ error_msg = "The reference dataset is missing metadata, click the pencil icon in the history item and 'auto-detect' the metadata attributes."
+ ref_sequences = int( options.ref_sequences )
+ if ref_sequences < 1:
+ stop_err( error_msg )
+ except:
+ stop_err( error_msg )
+ for seq in range( ref_sequences ):
+ command = 'lastz %s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s >> %s' % \
+ ( ref_name, options.input1, input2, set_options, options.identity_min,
+ options.identity_max, options.coverage, format, tabular_fields, options.output )
+ commands.append( command )
+ else:
+ # Reference is a locally cached 2bit file, split job across number of chroms in 2bit file
+ tbf = TwoBitFile( open( options.input1, 'r' ) )
+ for chrom in tbf.keys():
+ command = 'lastz %s%s/%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s >> %s' % \
+ ( ref_name, options.input1, chrom, input2, set_options, options.identity_min,
+ options.identity_max, options.coverage, format, tabular_fields, options.output )
+ commands.append( command )
+ tbf.close()
+ job_runner = LastzJobRunner( int( options.num_threads ), commands )
+
+if __name__=="__main__": __main__()
diff -r 8d149264b777 -r efdb6fb5de34 tools/sr_mapping/lastz_wrapper.xml
--- a/tools/sr_mapping/lastz_wrapper.xml Wed Nov 25 14:06:28 2009 -0500
+++ b/tools/sr_mapping/lastz_wrapper.xml Fri Nov 27 10:53:50 2009 -0500
@@ -1,124 +1,183 @@
-<tool id="lastz_wrapper_1" name="Lastz" version="1.0.0">
- <description> map short reads against reference sequence</description>
- <command>
- #if ($params.source_select=="pre_set" and $seq_name.how_to_name=="No" and $out_format.value=="diffs") #lastz $input1 ${input2}[fullnames] --${params.pre_set_options} --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1
- #elif ($params.source_select=="pre_set" and $seq_name.how_to_name=="Yes" and $out_format.value=="diffs") #lastz $seq_name.ref_name::$input1 ${input2}[fullnames] --${params.pre_set_options} --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1
- #elif ($params.source_select=="full" and $seq_name.how_to_name=="No" and $out_format.value=="diffs") #lastz $input1 ${input2}[fullnames] $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1
- #elif ($params.source_select=="full" and $seq_name.how_to_name=="Yes" and $out_format.value=="diffs") #lastz $seq_name.ref_name::$input1 ${input2}[fullnames] $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1
- #elif ($params.source_select=="pre_set" and $seq_name.how_to_name=="No" and $out_format.value=="maf") #lastz $input1 read::${input2} --${params.pre_set_options} --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1
- #elif ($params.source_select=="pre_set" and $seq_name.how_to_name=="Yes" and $out_format.value=="maf") #lastz $seq_name.ref_name::$input1 read::${input2} --${params.pre_set_options} --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1
- #elif ($params.source_select=="full" and $seq_name.how_to_name=="No" and $out_format.value=="maf") #lastz $input1 read::${input2} $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1
- #elif ($params.source_select=="full" and $seq_name.how_to_name=="Yes" and $out_format.value=="maf") #lastz $seq_name.ref_name::$input1 read::${input2} $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1
- #end if#
- </command>
- <inputs>
- <param name="input2" format="fasta" type="data" label="Align sequencing reads" />
- <param name="input1" format="fasta" type="data" label="against reference" help="must be a single sequence"/>
- <param name="out_format" type="select" label="Select output format">
- <option value="diffs">Polymorphisms</option>
- <option value="maf-">Alignments in MAF format</option>
- </param>
-
- <conditional name="params">
- <param name="source_select" type="select" label="Lastz settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">
- <option value="pre_set">Commonly used</option>
- <option value="full">Full Parameter List</option>
- </param>
- <when value="pre_set">
- <param name="pre_set_options" type="select" label="Select mapping mode">
- <option value="yasra95short">Illumina-Solexa/AB-SOLiD 95% identity</option>
- <option value="yasra85short">Illumina-Solexa/AB-SOLiD 85% identity</option>
- <option value="yasra98">Roche-454 98% identity</option>
- <option value="yasra95">Roche-454 95% identity</option>
- <option value="yasra90">Roche-454 90% identity</option>
- <option value="yasra85">Roche-454 85% identity</option>
- <option value="yasra75">Roche-454 75% identity</option>
- </param>
- </when>
- <when value="full">
- <param name="strand" type="select" label="Which strand to search?">
- <option value="--strand=both">Both</option>
- <option value="--strand=plus">Search forward strand only (the one in the reference)</option>
- <option value="--strand=minus">Search the reverse complement strand only (opposite of the reference)</option>
- </param>
- <param name="seed" type="select" label="Select seeding settings" help="allows you set word size and number of mismatches">
- <option value="--seed=12of19">Seed hits require a 19 bp word with matches in 12 specific positions</option>
- <option value="--seed=14of22">Seed hits require a 22 bp word with matches in 14 specific positions</option>
- </param>
- <param name="transition" type="select" label="Select transition settings" help="affects the number of allowed transition substitutions">
- <option value="--transition">Allow one transition in each seed hit</option>
- <option value="--transition2">Allow two transitions in a seed hit </option>
- <option value="--notransition">Don't allow any transitions in seed hits</option>
- </param>
- <param name="gfextend" type="boolean" truevalue="--gfextend" falsevalue="--nogfextend " label="Perform gap-free extension of seed hits to HSPs (high scoring segment pairs)?" />
- <param name="chain" type="boolean" truevalue="--chain" falsevalue="--nochain" label="Perform chaining of HSPs?" />
- <param name="gapped" type="boolean" truevalue="--gapped" falsevalue="--nogapped" label="Perform gapped alignment (instead of gap-free)?" />
- <param name="O" type="integer" size="5" value="400" label="Gap opening penalty"/>
- <param name="E" type="integer" size="5" value="30" label="Gap extension penalty"/>
- <param name="X" type="integer" size="5" value="910" label="X-drop threshold "/>
- <param name="Y" type="integer" size="5" value="9370" label="Y-drop threshold"/>
- <param name="K" type="integer" size="5" value="3000" label="Set the threshold for HSPs (ungapped extensions scoring lower are discarded)"/>
- <param name="L" type="integer" size="5" value="3000" label="Set the threshold for gapped alignments (gapped extensions scoring lower are discarded)"/>
- <param name="entropy" type="boolean" truevalue="--entropy" falsevalue="--noentropy " label="Involve entropy when filtering HSPs?" />
- </when>
- </conditional>
- <conditional name="seq_name">
- <param name="how_to_name" type="select" label="Do you want to modify reference name?">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- <when value="Yes">
- <param name="ref_name" type="text" size="25" value="Type sequence name here" label="Enter name for the Reference sequence"/>
- </when>
- <when value="No" />
- </conditional>
- <param name="min_ident" type="integer" size="3" value="0" label="Do not report matches below this identity (%)"/>
- <param name="max_ident" type="integer" size="3" value="100" label="Do not report matches above this identity (%)"/>
- <param name="min_cvrg" type="integer" size="3" value="0" label="Do not report matches that cover less than this fraction (%) of each read"/>
- </inputs>
+<tool id="lastz_wrapper_2" name="Lastz" version="1.0.0">
+ <description> map short reads against reference sequence</description>
+ <command interpreter="python">lastz_wrapper.py
+#if $seq_name.how_to_name=="Yes":
+--ref_name=$seq_name.ref_name
+#else:
+--ref_name="None"
+#end if
+--ref_source=$source.ref_source --source_select=$params.source_select --out_format=$out_format.value --input1=$source.input1 --input2=$input2
+#if $source.ref_source=="history":
+--ref_sequences=$input1.metadata.sequences
+#else:
+--ref_sequences="None"
+#end if
+#if $params.source_select=="pre_set":
+--pre_set_options=${params.pre_set_options} --strand="None" --seed="None" --transition="None" --O="None" --E="None" --X="None" --Y="None" --K="None" --L="None" --entropy="None"
+#else:
+--pre_set_options="None" --strand=$params.strand --seed=$params.seed --transition=$params.transition --O=$params.O --E=$params.E --X=$params.X --Y=$params.Y --K=$params.K --L=$params.L --entropy=$params.entropy
+#end if
+--identity_min=$min_ident --identity_max=$max_ident --coverage=$min_cvrg --format=$out_format --output=$output1 --num_threads=$num_threads --lastzSeqsFileDir=${GALAXY_DATA_INDEX_DIR}
+ </command>
+ <inputs>
+ <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />
+ <conditional name="source">
+ <param name="ref_source" type="select" label="Against reference sequences">
+ <option value="cached">that are locally cached</option>
+ <option value="history">in your history</option>
+ </param>
+ <when value="cached">
+ <param name="input1" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+ <options from_file="lastz_seqs.loc">
+ <column name="value" index="1" />
+ <column name="name" index="0" />
+ </options>
+ </param>
+ </when>
+ <when value="history">
+ <param name="input1" type="data" format="fasta" label="Select a reference dataset" help="must be a single sequence" />
+ </when>
+ </conditional>
+ <param name="out_format" type="select" label="Output format">
+ <option value="sam">SAM</option>
+ <option value="diffs">Polymorphisms</option>
+ <option value="tabular">Tabular</option>
+ </param>
+ <conditional name="params">
+ <param name="source_select" type="select" label="Lastz settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">
+ <option value="pre_set">Commonly used</option>
+ <option value="full">Full Parameter List</option>
1
0

02 Dec '09
details: http://www.bx.psu.edu/hg/galaxy/rev/71b779fde315
changeset: 3126:71b779fde315
user: guru
date: Mon Nov 30 11:56:58 2009 -0500
description:
Added 'N' to the list of mask characters, as per Melissa's request.
diffstat:
tools/regVariation/maf_cpg_filter.py | 2 +-
tools/regVariation/maf_cpg_filter.xml | 1 +
tools/regVariation/quality_filter.py | 2 +-
tools/regVariation/quality_filter.xml | 1 +
4 files changed, 4 insertions(+), 2 deletions(-)
diffs (46 lines):
diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/maf_cpg_filter.py
--- a/tools/regVariation/maf_cpg_filter.py Mon Nov 30 09:35:21 2009 -0500
+++ b/tools/regVariation/maf_cpg_filter.py Mon Nov 30 11:56:58 2009 -0500
@@ -39,7 +39,7 @@
reader = bx.align.maf.Reader( open(inp_file, 'r') )
writer = bx.align.maf.Writer( open(out_file,'w') )
- mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?'}
+ mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?', 5:'N'}
mask = mask_chr_dict[mask]
if sitetype == "CpG":
diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/maf_cpg_filter.xml
--- a/tools/regVariation/maf_cpg_filter.xml Mon Nov 30 09:35:21 2009 -0500
+++ b/tools/regVariation/maf_cpg_filter.xml Mon Nov 30 11:56:58 2009 -0500
@@ -21,6 +21,7 @@
<option value="2">^</option>
<option value="3">*</option>
<option value="4">?</option>
+ <option value="5">N</option>
</param>
<conditional name="masksite">
<param name="type" size="5" type="select" label="Sites to be masked">
diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/quality_filter.py
--- a/tools/regVariation/quality_filter.py Mon Nov 30 09:35:21 2009 -0500
+++ b/tools/regVariation/quality_filter.py Mon Nov 30 11:56:58 2009 -0500
@@ -100,7 +100,7 @@
stop_err( "No mask species selected, try again by selecting at least one species to mask." )
mask_chr_count = 0
- mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?'}
+ mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?', 5:'N'}
mask_reg_dict = {0:'Current pos', 1:'Current+Downstream', 2:'Current+Upstream', 3:'Current+Both sides'}
#ensure dbkey is present in the twobit loc file
diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/quality_filter.xml
--- a/tools/regVariation/quality_filter.xml Mon Nov 30 09:35:21 2009 -0500
+++ b/tools/regVariation/quality_filter.xml Mon Nov 30 11:56:58 2009 -0500
@@ -37,6 +37,7 @@
<option value="2">^</option>
<option value="3">*</option>
<option value="4">?</option>
+ <option value="5">N</option>
</param>
<conditional name="mask_region">
<param name="region" type="select" label="Mask region">
1
0

02 Dec '09
details: http://www.bx.psu.edu/hg/galaxy/rev/a8234f4d7012
changeset: 3125:a8234f4d7012
user: rc
date: Mon Nov 30 09:35:21 2009 -0500
description:
Fix for request_events table migration script for MySQL & sqlite
diffstat:
lib/galaxy/model/migrate/versions/0027_request_events.py | 5 +++--
1 files changed, 3 insertions(+), 2 deletions(-)
diffs (16 lines):
diff -r 341d7c1c5c9a -r a8234f4d7012 lib/galaxy/model/migrate/versions/0027_request_events.py
--- a/lib/galaxy/model/migrate/versions/0027_request_events.py Mon Nov 30 09:05:28 2009 -0500
+++ b/lib/galaxy/model/migrate/versions/0027_request_events.py Mon Nov 30 09:35:21 2009 -0500
@@ -73,9 +73,10 @@
"%s AS create_time," + \
"%s AS update_time," + \
"request.id AS request_id," + \
- "request.state AS state " + \
+ "request.state AS state," + \
+ "'%s' AS comment " + \
"FROM request;"
- cmd = cmd % ( nextval('request_event'), localtimestamp(), localtimestamp() )
+ cmd = cmd % ( nextval('request_event'), localtimestamp(), localtimestamp(), 'Imported from request table')
db_session.execute( cmd )
# Delete the state column
1
0