August 2009 - galaxy-dev - lists.galaxyproject.org

Bar charts
by Pieter Neerincx 05 Aug '09

05 Aug '09

Hi, The bar chart generator does not work for me. It looks like gnuplot is complaining (see below or attached screenshot), but I'm not sure if this is the problem. I'm on CentOS 5.3 and have gnuplot version 4.0.0-14.el5. In addition I installed gnuplot-py 1.8. How do I fix this? Cheers, Pi gnuplot> set style histogram clustered gap 5 title offset character 0, 0, 0 ^ line 0: expecting 'data', 'function', 'line', 'fill' or 'arrow' line 0: undefined variable: in line 0: undefined variable: invert gnuplot> set style data histograms ^ line 0: expecting 'lines', 'points', 'linespoints', 'dots', 'impulses', 'yerrorbars', 'xerrorbars', 'xyerrorbars', 'steps', 'fsteps', 'histeps', 'filledcurves', 'boxes', 'boxerrorbars', 'boxxyerrorbars', 'vectors', 'financebars', 'candlesticks', 'errorlines', 'xerrorlines', 'yerrorlines', 'xyerrorlines', 'pm3d' gnuplot: unable to open display 'localhost:13.0' gnuplot: X11 aborted. ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ------------------------------------------------------------

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Re: [galaxy-dev] [galaxy-user] custom tool output path
by James Taylor 04 Aug '09

04 Aug '09

Paul, This would break a lot of things in Galaxy. Everything expects that a tool output is a "Dataset", and that it has a corresponding file with its contents under "file_path". Changing this would be complex and have far reaching consequences, though not impossible (on a per tool basis, the directory where the output is deposited would be changes, and the dataset would be setup pointing to the right place, however this affects how datasets get shared to the cluster among other things). Maybe it would help to better understand what you want to accomplish by doing this. (Moved to galaxy-dev since this is about framework internals not using the galaxy interface). -- jt On Aug 4, 2009, at 11:35 AM, Paul Rigor (prigor@uci) wrote: > But in defining a tool, can the default path be overridden by > assigning a different path to a variable, eg, $outputpath? > > Thanks, > paul > > On Tue, Aug 4, 2009 at 5:07 AM, Nate Coraor <nate(a)bx.psu.edu> wrote: > Paul Rigor (prigor@uci) wrote: > > For custom tools, I was wondering how the output path can be set in > the xml file describing the tool? Are there 'default' variables I > should be aware of in order to use as the output path the > "user_library_import_dir = database/users" in my universe_wsgi.ini? > > Hi Paul, > > Galaxy manages output paths internally. The directory containing > datasets can be changed with 'file_path' in universe_wsgi.ini. By > default, it's database/files/ > > --nate > > > > -- > Paul Rigor > http://www.paulrigor.net/ > http://www.ics.uci.edu/~prigor > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)bx.psu.edu > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user

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[hg] galaxy 2528: Maintain centering
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4ca7f95f854a changeset: 2528:4ca7f95f854a user: Kanwei Li <kanwei(a)gmail.com> date: Mon Aug 03 17:23:52 2009 -0400 description: Maintain centering 1 file(s) affected in this change: templates/base_panels.mako diffs (12 lines): diff -r 19b47949aa8a -r 4ca7f95f854a templates/base_panels.mako --- a/templates/base_panels.mako Mon Aug 03 17:19:04 2009 -0400 +++ b/templates/base_panels.mako Mon Aug 03 17:23:52 2009 -0400 @@ -125,7 +125,7 @@ </a> </div> - <div style="position: absolute; left: 200px; width: 500px;"> + <div style="position: absolute; left: 200px; width: 60%; text-align: center"> <table class="tab-group" border="0" cellspacing="0" style="margin: auto;"> <tr>

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[hg] galaxy 2527: Merging from central
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/19b47949aa8a changeset: 2527:19b47949aa8a user: Kanwei Li <kanwei(a)gmail.com> date: Mon Aug 03 17:19:04 2009 -0400 description: Merging from central 0 file(s) affected in this change: diffs (truncated from 4323 to 3000 lines): diff -r 692c384c1ca0 -r 19b47949aa8a lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Mon Aug 03 16:07:36 2009 -0400 +++ b/lib/galaxy/datatypes/metadata.py Mon Aug 03 17:19:04 2009 -0400 @@ -497,7 +497,7 @@ return None def get_dataset_metadata_key( self, dataset ): return "%s_%d" % ( dataset.__class__.__name__, dataset.id ) #set meta can be called on library items and history items, need to make different keys for them, since ids can overlap - def setup_external_metadata( self, datasets, exec_dir = None, tmp_dir = None, dataset_files_path = None, output_fnames = None, kwds = {} ): + def setup_external_metadata( self, datasets, exec_dir = None, tmp_dir = None, dataset_files_path = None, output_fnames = None, config_root = None, datatypes_config = None, kwds = {} ): #fill in metadata_files_dict and return the command with args required to set metadata def __metadata_files_list_to_cmd_line( metadata_files ): def __get_filename_override(): @@ -515,6 +515,10 @@ tmp_dir = MetadataTempFile.tmp_dir if dataset_files_path is None: dataset_files_path = galaxy.model.Dataset.file_path + if config_root is None: + config_root = os.path.abspath( os.getcwd() ) + if datatypes_config is None: + datatypes_config = 'datatypes_conf.xml' metadata_files_list = [] for dataset in datasets: key = self.get_dataset_metadata_key( dataset ) @@ -547,7 +551,7 @@ metadata_files.flush() metadata_files_list.append( metadata_files ) #return command required to build - return "%s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, tmp_dir, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) ) + return "%s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, tmp_dir, config_root, datatypes_config, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) ) def external_metadata_set_successfully( self, dataset ): metadata_files = self.get_output_filenames_by_dataset( dataset ) diff -r 692c384c1ca0 -r 19b47949aa8a lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Mon Aug 03 16:07:36 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Mon Aug 03 17:19:04 2009 -0400 @@ -71,7 +71,7 @@ # add composite files name = composite_file.get( 'name', None ) if name is None: - log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) + self.log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) optional = composite_file.get( 'optional', False ) mimetype = composite_file.get( 'mimetype', None ) self.datatypes_by_extension[extension].add_composite_file( name, optional=optional, mimetype=mimetype ) diff -r 692c384c1ca0 -r 19b47949aa8a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Mon Aug 03 16:07:36 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Mon Aug 03 17:19:04 2009 -0400 @@ -595,7 +595,7 @@ self.real_path = real_path self.false_path = false_path def __str__( self ): - if false_path is None: + if self.false_path is None: return self.real_path else: return self.false_path @@ -616,14 +616,18 @@ for outfile in [ str( o ) for o in output_paths ]: sizes.append( ( outfile, os.stat( outfile ).st_size ) ) return sizes - def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, **kwds ): + def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, **kwds ): if tmp_dir is None: #this dir should should relative to the exec_dir tmp_dir = self.app.config.new_file_path if dataset_files_path is None: dataset_files_path = self.app.model.Dataset.file_path + if config_root is None: + config_root = self.app.config.root + if datatypes_config is None: + datatypes_config = self.app.config.datatypes_config job = model.Job.get( self.job_id ) - return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], exec_dir = exec_dir, tmp_dir = tmp_dir, dataset_files_path = dataset_files_path, **kwds ) + return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], exec_dir = exec_dir, tmp_dir = tmp_dir, dataset_files_path = dataset_files_path, config_root = config_root, datatypes_config = datatypes_config, **kwds ) class DefaultJobDispatcher( object ): def __init__( self, app ): diff -r 692c384c1ca0 -r 19b47949aa8a lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Aug 03 16:07:36 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Mon Aug 03 17:19:04 2009 -0400 @@ -13,7 +13,31 @@ # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" + class HistoryListGrid( grids.Grid ): + # Custom column types + class DatasetsByStateColumn( grids.GridColumn ): + def get_value( self, trans, grid, history ): + rval = [] + for state in ( 'ok', 'running', 'queued', 'error' ): + total = sum( 1 for d in history.active_datasets if d.state == state ) + if total: + rval.append( '<div class="count-box state-color-%s">%s</div>' % ( state, total ) ) + else: + rval.append( '' ) + return rval + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, history ): + if history.deleted: + return "deleted" + elif history.users_shared_with: + return "shared" + return "" + def get_link( self, trans, grid, item ): + if item.users_shared_with: + return dict( operation="sharing", id=item.id ) + return None + # Grid definition title = "Stored histories" model_class = model.History default_sort_key = "-create_time" @@ -21,12 +45,8 @@ grids.GridColumn( "Name", key="name", link=( lambda item: iff( item.deleted, None, dict( operation="switch", id=item.id ) ) ), attach_popup=True ), - grids.GridColumn( "Datasets (by state)", method='_build_datasets_by_state', ncells=4 ), - grids.GridColumn( "Status", method='_build_status', - link=( lambda item: iff( item.users_shared_with, - dict( operation="sharing", id=item.id ), - None ) ), - attach_popup=False ), + DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), + StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Age", key="create_time", format=time_ago ), grids.GridColumn( "Last update", key="update_time", format=time_ago ), # Valid for filtering but invisible @@ -49,21 +69,6 @@ return trans.get_history() def apply_default_filter( self, trans, query ): return query.filter_by( user=trans.user, purged=False ) - def _build_datasets_by_state( self, trans, history ): - rval = [] - for state in ( 'ok', 'running', 'queued', 'error' ): - total = sum( 1 for d in history.active_datasets if d.state == state ) - if total: - rval.append( '<div class="count-box state-color-%s">%s</div>' % ( state, total ) ) - else: - rval.append( '' ) - return rval - def _build_status( self, trans, history ): - if history.deleted: - return "deleted" - elif history.users_shared_with: - return "shared" - return "" class HistoryController( BaseController ): diff -r 692c384c1ca0 -r 19b47949aa8a lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Aug 03 16:07:36 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Aug 03 17:19:04 2009 -0400 @@ -40,16 +40,9 @@ if column.key: if "f-" + column.key in kwargs: column_filter = kwargs.get( "f-" + column.key ) - if column_filter == "True": - filter_args[column.key] = True - elif column_filter == "False": - filter_args[column.key] = False - elif column_filter == "All": - del filter_args[column.key] + query = column.filter( query, column_filter, filter_args ) # Carry filter along to newly generated urls extra_url_args[ "f-" + column.key ] = column_filter - if filter_args: - query = query.filter_by( **filter_args ) # Process sort arguments sort_key = sort_order = None if 'sort' in kwargs: @@ -143,6 +136,26 @@ if self.format: value = self.format( value ) return value + def get_link( self, trans, grid, item ): + if self.link and self.link( item ): + return self.link( item ) + return None + def filter( self, query, column_filter, filter_args ): + """ + Must modify filter_args for carrying forward, and return query + (possibly filtered). + """ + if column_filter == "True": + filter_args[self.key] = True + query = query.filter_by( **{ self.key: True } ) + elif column_filter == "False": + filter_args[self.key] = False + query = query.filter_by( **{ self.key: False } ) + elif column_filter == "All": + del filter_args[self.key] + return query + + class GridOperation( object ): def __init__( self, label, key=None, condition=None, allow_multiple=True ): diff -r 692c384c1ca0 -r 19b47949aa8a scripts/set_metadata.py --- a/scripts/set_metadata.py Mon Aug 03 16:07:36 2009 -0400 +++ b/scripts/set_metadata.py Mon Aug 03 17:19:04 2009 -0400 @@ -5,6 +5,9 @@ top level directly. """ + +import logging +logging.basicConfig() import os, sys, cPickle assert sys.version_info[:2] >= ( 2, 4 ) @@ -27,6 +30,12 @@ tmp_dir = sys.argv.pop( 1 ) galaxy.model.Dataset.file_path = file_path galaxy.datatypes.metadata.MetadataTempFile.tmp_dir = tmp_dir + + # Set up datatypes registry + config_root = sys.argv.pop( 1 ) + datatypes_config = sys.argv.pop( 1 ) + galaxy.model.set_datatypes_registry( galaxy.datatypes.registry.Registry( config_root, datatypes_config ) ) + for filenames in sys.argv[1:]: filename_in, filename_kwds, filename_out, filename_results_code, dataset_filename_override = filenames.split( ',' ) try: diff -r 692c384c1ca0 -r 19b47949aa8a templates/history/grid.mako --- a/templates/history/grid.mako Mon Aug 03 16:07:36 2009 -0400 +++ b/templates/history/grid.mako Mon Aug 03 17:19:04 2009 -0400 @@ -137,8 +137,9 @@ %if column.visible: <% # Link - if column.link and column.link( item ): - href = url( **column.link( item ) ) + link = column.get_link( trans, grid, item ) + if link: + href = url( **link ) else: href = None # Value (coerced to list so we can loop) diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_phiX_sanger.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_phiX_sanger.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759 +GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC ++ +II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_phiX_sanger_f.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_phiX_sanger_f.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759/2 +ACGCTCCTTTAAAATATC ++/2 +IIIII$%*$G$A31I&&B diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_phiX_sanger_r.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_phiX_sanger_r.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759/1 +GGACTCAGATAGTAATCC ++/1 +II#IIIIIII$5+.(9II diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_sanger.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_sanger.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,76 @@ +@HWI-EAS91_1_30788AAXX:1:1:1761:343 +AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG ++ +IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIHI""I""IIII"I"""""""IIIIIIHIIII""1III +@HWI-EAS91_1_30788AAXX:1:1:1578:331 +GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIIII""II7I +@HWI-EAS91_1_30788AAXX:1:1:1647:512 +GTTCCATNNATCTGTGTGTCTATTTTTGTGCAAGTAANNCNNTGTTNANNNNNNNTGAAGAAGACANNAAGA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIGII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1570:620 +GAGGTGTNNAAAATGAGAAAGGTCAAGGAGCATGTGCNNGNNTCAGNGNNNNNNNCACTGTACTGCNNGCTA ++ +IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIIIII""I""IIII"I"""""""IIII@4EIII:""I?E6 +@HWI-EAS91_1_30788AAXX:1:1:1599:330 +GTTGGAGNNTGTCAAATGCCTTCTCTGCATCTATTGCNNANNGCTTNCNNNNNNNATCCTACCAAANNTTCA ++ +IIIIIII""IIIIIIIIIIIIIIIIIII<III@IIII""I""IIII"I"""""""@IIHI16IF51""I:A< +@HWI-EAS91_1_30788AAXX:1:1:1652:270 +GCCAAGCNNAGCAAATGTTTGAAGTCTCTAGGAGTGANNANNTTCANTNNNNNNNTCTTCTCTCTTNNGTAT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6IIII""I""IIII"I"""""""IIIIIIIIIII""<D9I +@HWI-EAS91_1_30788AAXX:1:1:1746:351 +GCCTTCGNNAGGTCTCAGCGCTTTCTCTGTGTTCTTTNNANNATACNANNNNNNNAAACTAAAAAANNCAAA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""BIIIH:7IIII""I0>I +@HWI-EAS91_1_30788AAXX:1:1:1582:633 +GGATGTGNNGAAAGGAGAACCCTCATACACTGCTGGGNNTNNTCTGNTNNNNNNNATACCCTCAAGNNCCAT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIFIIIIIC3I""IIII +@HWI-EAS91_1_30788AAXX:1:1:1598:534 +GAATCATNNAATCCGCTTGGTTTGACACTTTGGATTTNNANNTCCANANNNNNNNGACTAAGAAACNNAGAT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""II.IIIICIII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1572:324 +GGTGGTGNNGTCAGATCAGACAGGCTCCCAAGAAGCTNNTNNGCTTNGNNNNNNNTCAGTAAAGCGNNACAA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05III""I""IIII"I"""""""II3II-/EIGI""A84; +@HWI-EAS91_1_30788AAXX:1:1:1749:466 +GTTGTGTNNTTTCTTTCAATATTGTGATCTGGTTTAANNTNNATCCNCNNNNNNNGAGGCTTTTGTNNGGAC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""ICIIIIIGII@""EI1: +@HWI-EAS91_1_30788AAXX:1:1:1629:446 +GCAAAGGNNATGGGCAAAACAGTTCTTTGGTTAATGTNNTNNTAAANANNNNNNNTAAATCTTTCTNNAATG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIII?H<EII""I:I? +@HWI-EAS91_1_30788AAXX:1:1:1763:587 +GATACAGNNCTGTTTTCCTTATTAATTTCCAGTAGCTNNANNTTGTNTNNNNNNNAATCTTGAGTTNNGCCA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIIII"")II? +@HWI-EAS91_1_30788AAXX:1:1:1616:363 +GATGAAANNCGGAAGCGATTGAAAAAATAGAAGGGGANNANNGAAANCNNNNNNNTGAACGATTTTNNATTT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIIIII""I""IIII"I"""""""FI@7II1IIII""-III +@HWI-EAS91_1_30788AAXX:1:1:1768:715 +GTATCATNNCAGAAACACCATAAGTAGCTGCTTTTTANNANNTTAANANNNNNNNAACCCTTTATTNNTGAC ++ +IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIIII""I9F< +@HWI-EAS91_1_30788AAXX:1:1:1572:270 +GATTAGGNNTGCAAAGAAACTGCGTTTCACAGGCCTCNNGNNGGCTNCNNNNNNNAGGGCGAGTTGNNCCCC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII":"""""""IIII5IIIBII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1785:1272 +GTTNNNNNNATGCACATTNNATNAAATNNTTGCAGTGNNANNTGGGNCNNNNNNNCAAGTGAACTTNNACGT ++ +III""""""IIIIIIIII""FI"IIII""II+ICIII""I""IIII"I"""""""IIIIIIIIGII""I;I@ +@HWI-EAS91_1_30788AAXX:1:1:1673:514 +GTTTTGANNATGGTTTCTCTTCTGTTGTAACTCCATANNANNAAAANTNNNNNNNCGAACTGGTTCNNGAAC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1II""I""IIII"I"""""""II%I'$+ACI/""3(.I +@HWI-EAS91_1_30788AAXX:1:1:1634:330 +GCTCTGCNNAGTGCTCTTACAGCCTAGTGGGAACATANNANNTGGANGNNNNNNNCTGTGGGGCACNNCTCG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8IIII""I""IIII"I"""""""IIIEIIIII8I""@7>I \ No newline at end of file diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_sanger_f.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_sanger_f.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,76 @@ +@HWI-EAS91_1_30788AAXX:1:1:1761:343/2 +CNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG ++/2 +I""I""IIII"I"""""""IIIIIIHIIII""1III +@HWI-EAS91_1_30788AAXX:1:1:1578:331/2 +CNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG ++/2 +I""I""IIII"I"""""""IIIIIIIIIII""II7I +@HWI-EAS91_1_30788AAXX:1:1:1647:512/2 +ANNCNNTGTTNANNNNNNNTGAAGAAGACANNAAGA ++/2 +I""I""IIII"I"""""""IIIIIIIIGII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1570:620/2 +CNNGNNTCAGNGNNNNNNNCACTGTACTGCNNGCTA ++/2 +I""I""IIII"I"""""""IIII@4EIII:""I?E6 +@HWI-EAS91_1_30788AAXX:1:1:1599:330/2 +CNNANNGCTTNCNNNNNNNATCCTACCAAANNTTCA ++/2 +I""I""IIII"I"""""""@IIHI16IF51""I:A< +@HWI-EAS91_1_30788AAXX:1:1:1652:270/2 +ANNANNTTCANTNNNNNNNTCTTCTCTCTTNNGTAT ++/2 +I""I""IIII"I"""""""IIIIIIIIIII""<D9I +@HWI-EAS91_1_30788AAXX:1:1:1746:351/2 +TNNANNATACNANNNNNNNAAACTAAAAAANNCAAA ++/2 +I""I""IIII"I"""""""BIIIH:7IIII""I0>I +@HWI-EAS91_1_30788AAXX:1:1:1582:633/2 +GNNTNNTCTGNTNNNNNNNATACCCTCAAGNNCCAT ++/2 +I""I""IIII"I"""""""IIFIIIIIC3I""IIII +@HWI-EAS91_1_30788AAXX:1:1:1598:534/2 +TNNANNTCCANANNNNNNNGACTAAGAAACNNAGAT ++/2 +I""I""IIII"I"""""""II.IIIICIII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1572:324/2 +TNNTNNGCTTNGNNNNNNNTCAGTAAAGCGNNACAA ++/2 +I""I""IIII"I"""""""II3II-/EIGI""A84; +@HWI-EAS91_1_30788AAXX:1:1:1749:466/2 +ANNTNNATCCNCNNNNNNNGAGGCTTTTGTNNGGAC ++/2 +I""I""IIII"I"""""""ICIIIIIGII@""EI1: +@HWI-EAS91_1_30788AAXX:1:1:1629:446/2 +TNNTNNTAAANANNNNNNNTAAATCTTTCTNNAATG ++/2 +I""I""IIII"I"""""""IIIII?H<EII""I:I? +@HWI-EAS91_1_30788AAXX:1:1:1763:587/2 +TNNANNTTGTNTNNNNNNNAATCTTGAGTTNNGCCA ++/2 +I""I""IIII"I"""""""IIIIIIIIIII"")II? +@HWI-EAS91_1_30788AAXX:1:1:1616:363/2 +ANNANNGAAANCNNNNNNNTGAACGATTTTNNATTT ++/2 +I""I""IIII"I"""""""FI@7II1IIII""-III +@HWI-EAS91_1_30788AAXX:1:1:1768:715/2 +ANNANNTTAANANNNNNNNAACCCTTTATTNNTGAC ++/2 +I""I""IIII"I"""""""IIIIIIIIIII""I9F< +@HWI-EAS91_1_30788AAXX:1:1:1572:270/2 +CNNGNNGGCTNCNNNNNNNAGGGCGAGTTGNNCCCC ++/2 +I""I""IIII":"""""""IIII5IIIBII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1785:1272/2 +GNNANNTGGGNCNNNNNNNCAAGTGAACTTNNACGT ++/2 +I""I""IIII"I"""""""IIIIIIIIGII""I;I@ +@HWI-EAS91_1_30788AAXX:1:1:1673:514/2 +ANNANNAAAANTNNNNNNNCGAACTGGTTCNNGAAC ++/2 +I""I""IIII"I"""""""II%I'$+ACI/""3(.I +@HWI-EAS91_1_30788AAXX:1:1:1634:330/2 +ANNANNTGGANGNNNNNNNCTGTGGGGCACNNCTCG ++/2 +I""I""IIII"I"""""""IIIEIIIII8I""@7>I diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_sanger_r.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_sanger_r.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,76 @@ +@HWI-EAS91_1_30788AAXX:1:1:1761:343/1 +AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAA ++/1 +IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIH +@HWI-EAS91_1_30788AAXX:1:1:1578:331/1 +GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1647:512/1 +GTTCCATNNATCTGTGTGTCTATTTTTGTGCAAGTA ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1570:620/1 +GAGGTGTNNAAAATGAGAAAGGTCAAGGAGCATGTG ++/1 +IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1599:330/1 +GTTGGAGNNTGTCAAATGCCTTCTCTGCATCTATTG ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIII<III@III +@HWI-EAS91_1_30788AAXX:1:1:1652:270/1 +GCCAAGCNNAGCAAATGTTTGAAGTCTCTAGGAGTG ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6III +@HWI-EAS91_1_30788AAXX:1:1:1746:351/1 +GCCTTCGNNAGGTCTCAGCGCTTTCTCTGTGTTCTT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1582:633/1 +GGATGTGNNGAAAGGAGAACCCTCATACACTGCTGG ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1598:534/1 +GAATCATNNAATCCGCTTGGTTTGACACTTTGGATT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1572:324/1 +GGTGGTGNNGTCAGATCAGACAGGCTCCCAAGAAGC ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05II +@HWI-EAS91_1_30788AAXX:1:1:1749:466/1 +GTTGTGTNNTTTCTTTCAATATTGTGATCTGGTTTA ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1629:446/1 +GCAAAGGNNATGGGCAAAACAGTTCTTTGGTTAATG ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1763:587/1 +GATACAGNNCTGTTTTCCTTATTAATTTCCAGTAGC ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1616:363/1 +GATGAAANNCGGAAGCGATTGAAAAAATAGAAGGGG ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIIII +@HWI-EAS91_1_30788AAXX:1:1:1768:715/1 +GTATCATNNCAGAAACACCATAAGTAGCTGCTTTTT ++/1 +IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1572:270/1 +GATTAGGNNTGCAAAGAAACTGCGTTTCACAGGCCT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 +GTTNNNNNNATGCACATTNNATNAAATNNTTGCAGT ++/1 +III""""""IIIIIIIII""FI"IIII""II+ICII +@HWI-EAS91_1_30788AAXX:1:1:1673:514/1 +GTTTTGANNATGGTTTCTCTTCTGTTGTAACTCCAT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1I +@HWI-EAS91_1_30788AAXX:1:1:1634:330/1 +GCTCTGCNNAGTGCTCTTACAGCCTAGTGGGAACAT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8III diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_solid.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_solid.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,576 @@ +@1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG ++ +><C&&9952+C>5<.?<79,=42<292:<(9/-7 +@1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ++ +;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +@1831_573_1067/1 +AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++ +++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +@1831_573_1219/1 +CGCCCTATAATAATACAGCGCGTTAGACCGCTCA ++ +@@=4/+)5)408?'665>*/5?<61';<3,:,5- +@1831_573_1242/1 +GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC ++ +>>::>17=A5?@@=;7A=;2.60>82<8=74+;; +@1831_573_1333/1 +AGAATCGTTACCACACACTGCGTCTGGGTATCCG ++ +='@#%3=.>)/34*117,,/6-4+.9742456<) +@1831_573_1362/1 +CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC ++ +B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +@1831_573_1448/1 +TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG ++ +7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ +@1831_573_1490/1 +CTCGTCATGTTACGCAAAGGCACGTCACAGCACC ++ +@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. +@1831_573_1523/1 +ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ++ +,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +@1831_573_1578/1 +CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ++ +?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +@1831_573_1647/1 +AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT ++ +?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +@1831_573_1684/1 +TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT ++ +>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +@1831_573_1769/1 +TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC ++ +54749&&767%/7;3$-7;3#,3//#,45/#&06 +@1831_573_1853/1 +CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC ++ +4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +@1831_573_1943/1 +ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC ++ +>/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +@1831_573_1977/1 +GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC ++ +@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +@1831_574_109/1 +TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT ++ +7651#4817>@65<2:84716=788<1995.7?6 +@1831_574_148/1 +CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC ++ +;->3;;3>//>0;;7=,=4-4/+>029<9<624; +@1831_574_185/1 +CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC ++ +<4;%%@7>#*>97%6;+8$#<07%1372$%<54# +@1831_574_243/1 +AGGCACCGTAACTCAGGACATTCTCGATTAGTTA ++ +@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 +@1831_574_257/1 +ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC ++ +>>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +@1831_574_293/1 +TGCTGCAAATAAACATACAGCCTTCTAATGACTA ++ +')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +@1831_574_389/1 +CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA ++ +)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +@1831_574_575/1 +TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG ++ +?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< +@1831_574_592/1 +TCATTTACCACGTCAGGGTCGGAGTCATTCATTA ++ +3-5)19,,<@>4067<2.-864346;9<1/;212 +@1831_574_617/1 +AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC ++ +>@?;>?=@==@>@=5?@+@:@40@><:0)')64- +@1831_574_725/1 +GACAAGATGGCTATTATTTACAATCCGATCTGCA ++ +'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +@1831_574_734/1 +CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG ++ +-&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 +@1831_574_824/1 +AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT ++ +@@@;;),+@<-<7;<&89??&29?<$2:A<);8? +@1831_574_959/1 +CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC ++ +A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +@1831_574_1062/1 +ACCGGTAATATAAGGCAACATGATTACGGCCACG ++ +@821<//:136/8<1/5.427.;>288/0<1$)/ +@1831_574_1092/1 +GACTGGCGAAATCATCGCGGAAAAACCCCTATCA ++ +8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +@1831_574_1103/1 +ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ++ +??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +@1831_574_1116/1 +CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC ++ +(a)++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +@1831_574_1194/1 +TTATCACATTTGGGGATCGGAAGGGACTACTTCG ++ +5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 +@1831_574_1204/1 +CTTACTGGTCTGCTGGACATATAGTGGCGATGAA ++ +A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* +@1831_574_1306/1 +ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA ++ +2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +@1831_574_1387/1 +GTACTTCTCAATGCTGCACTACTATGTACGCCCC ++ +?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +@1831_574_1431/1 +GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC ++ +7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +@1831_574_1560/1 +GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ++ +))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +@1831_574_1591/1 +TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG ++ +=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 +@1831_574_1624/1 +ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG ++ +<6.&(,7-+))7..'/;43.)927.(<85&13-) +@1831_574_1826/1 +TACGTCGCGACCGAGCGTTATATAGTCTGACCCC ++ +@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +@1831_574_1903/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ +@1831_574_1961/1 +GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA ++ +>-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 +@1831_575_54/1 +TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA ++ +=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 +@1831_575_80/1 +TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ++ +?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +@1831_575_192/1 +AACTACGCCCCTTAATTACACAGCGCGTTAGACC ++ +:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +@1831_575_197/1 +TTCGCCTACACTTAGATACCTCTTAAACTCAATG ++ +-:?463@A:88?6?437<=.2&1.;@67.4@%2, +@1831_575_223/1 +ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ++ +?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +@1831_575_420/1 +CCCACATGGAAAACACTCACCGCCGAACAGAGCG ++ +2?.>?(-''2+..@),$%1@;')1)?+)7.').. +@1831_575_434/1 +ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC ++ +@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +@1831_575_444/1 +TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA ++ +2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> +@1831_575_459/1 +CTTATCAGCACACGGTTTACCAGTCCGACTCCAA ++ +@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +@1831_575_506/1 +CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ++ +?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +@1831_575_569/1 +AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT ++ +'9-,@29+479%&>9#&08=>7#9>,69/+'*3) +@1831_575_622/1 +CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC ++ +A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ +@1831_575_644/1 +CTTGAATGGCGATCTCGTCGAGGAAATACCACTA ++ +<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +@1831_575_663/1 +GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA ++ +@@@@A</;A>@6>0792<5966:?;25+:><1,+ +@1831_575_681/1 +TCTCCTGATTAGACATATCACTGTTGAACACAGC ++ +72?.)25;96-14'*.03'#4#++$)/8+%/((& +@1831_575_711/1 +TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC ++ +%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +@1831_575_730/1 +CACACAGGAACCATAGCGTATGTTATTCACCCCC ++ +%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +@1831_575_904/1 +ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC ++ +<><.689@@7@<54:4=@>69=:+6-=42;8<:# +@1831_575_938/1 +TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA ++ +:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 +@1831_575_970/1 +TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC ++ +@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 +@1831_575_991/1 +TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA ++ +>>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +@1831_575_1138/1 +TTGAAAGACCTGAACGCGATTTCATGTTTACTGC ++ +=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 +@1831_575_1157/1 +TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC ++ +B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 +@1831_575_1180/1 +GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA ++ +<B>5?':/78?;1;55:997@@>94=7<186->7 +@1831_575_1283/1 +GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT ++ +C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +@1831_575_1302/1 +CGACTATTCGTTTCGTCTAGAACGTGACACTAGC ++ +12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* +@1831_575_1310/1 +CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT ++ +<<>663?99@(@7=11@:@@/7??<@<;>'3-7; +@1831_575_1321/1 +CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG ++ +;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 +@1831_575_1373/1 +CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA ++ +@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< +@1831_575_1419/1 +TGGGGAATATAACAGCGTAGCGTTGAACACTAGA ++ +//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +@1831_575_1436/1 +TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC ++ +2@=;39*3<*4<:>52>>9'7:<='0=>1'136< +@1831_575_1442/1 +TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG ++ +>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> +@1831_575_1454/1 +CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT ++ +4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +@1831_575_1500/1 +CACAAAAGGTCCCTACCTGTCTACCCTACATAGC ++ +?@@?A@?8<6<:985=99999==B3<5<<,7?>9 +@1831_575_1535/1 +CTCGACGATATGACCGCCAGCCACTTAACTCCGC ++ +B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< +@1831_575_1724/1 +TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA ++ +<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +@1831_575_1829/1 +CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC ++ +2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +@1831_575_1898/1 +CTTACCATATCATCTCAACCCATAACAGCACTTA ++ +B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +@1831_575_1964/1 +GACAGACCATGAGGCTGAAGACTACTAAGTGCGT ++ +>39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +@1831_576_32/1 +TACGCAACGATTTATGGCCTTATAATTGAGGCCA ++ +<>?>?=7<2)522;><<@40@>704<>5=23@+& +@1831_576_74/1 +ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA ++ +=@@?@>(??<B5?@@@9<@><+><;@';>6961? +@1831_576_86/1 +ATGAAAACGCATTAGGACAACCATAATGGCCTCA ++ +811)2:*.++5</:3+43924*))/:,6&29)2/ +@1831_576_89/1 +GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA ++ +)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +@1831_576_266/1 +ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT ++ +@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 +@1831_576_327/1 +GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA ++ +@?@6@@;<@?><@>==3@:==<3@@>53<9><6= +@1831_576_331/1 +GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA ++ +-2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +@1831_576_387/1 +ACACGCCATGATCCGATAAGAAGGGAACGTAAGG ++ +8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +@1831_576_406/1 +AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC ++ +4<>%%14:*4656)&<251&2+3#&19,6&4>5( +@1831_576_449/1 +CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA ++ ++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +@1831_576_519/1 +TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC ++ +=46<97@>2/6?;2<4A881>9121+<1/4.9+7 +@1831_576_603/1 +CAATATGTCTTAGTCGTGACTCGGCAACTTATCC ++ +@46=@C.??<A79@@;-<@@>29B?>55<B7598 +@1831_576_655/1 +GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG ++ +@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +@1831_576_677/1 +TTTACTCAGTTGATACATCACTGTAGCACATAGG ++ +290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +@1831_576_718/1 +CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT ++ +4###$0###%(#########,####%####$### +@1831_576_722/1 +CGTATGATGGCGAGTCTTTATAATCCAATCTGAA ++ +*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +@1831_576_754/1 +AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA ++ +4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +@1831_576_815/1 +TAGGCCTGATATGACACGATCACAGTGCAACATC ++ +3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +@1831_576_882/1 +TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG ++ +26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +@1831_576_898/1 +AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT ++ +@@C2?C>?<>@886B?;?.??87=B<8<15??=. +@1831_576_923/1 +CTGGACATGAGAGACTGCACGCGGTACACGTCGG ++ +6.51=;.699<96>;;49<;;11;<@59:9=647 +@1831_576_930/1 +CTGGCATGTACGTCCATGTCAGACGAGCAGAACT ++ +#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +@1831_576_1019/1 +GATGCGCGCTGTCATGGCATCGAACCATCGGTCG ++ +<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +@1831_576_1068/1 +AAGAGTGACTCACTTACCGGGATGCGATGGAGCC ++ +>><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +@1831_576_1131/1 +AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA ++ +04@#@/@,4>9?2+?1571@',>=;(759;*92< +@1831_576_1168/1 +CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA ++ +@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +@1831_576_1207/1 +CAACCTGACTAAACGGGGATACGCTGGCGCTACA ++ +$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +@1831_576_1289/1 +TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT ++ +9<>1B@@;7@@663==28,5':8<<,.=2>>.50 +@1831_576_1329/1 +CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA ++ +>&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +@1831_576_1367/1 +GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT ++ +?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 +@1831_576_1416/1 +TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC ++ +';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ +@1831_576_1461/1 +GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA ++ +1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +@1831_576_1605/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +<@C@@>1;@:;<<@@9@???9<3?5-21=4877, +@1831_576_1664/1 +CGCGCACAACTCGCCATGATACGACAAGACCCGA ++ +@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +@1831_576_1671/1 +GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT ++ +@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +@1831_576_1729/1 +CGTTTCGTCTACAACGTGACACTAGCACAGTATA ++ +?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> +@1831_576_1880/1 +TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT ++ +515/792,:,7/%/05,%$):+#8%2(1754))3 +@1831_576_1982/1 +AATGTCGTCAGACGACTTTGGCGCGAAAACCATA ++ +@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +@1831_576_1987/1 +AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ++ +##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +@1831_576_2014/1 +CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT ++ +@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +@1831_576_2028/1 +ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA ++ +<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +@1831_577_40/1 +CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT ++ +2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 +@1831_577_119/1 +TCCCACAAGCCATTGACATGCTCGCTCTAAACAG ++ +>?C11)-1/)#;#/,850*+.+$$5550+%-.40 +@1831_577_133/1 +TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG ++ +4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +@1831_577_255/1 +ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG ++ +<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +@1831_577_281/1 +TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA ++ +-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +@1831_577_288/1 +CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA ++ +;/79??&=B::298*6.7/+4&21,7,6?.7#'6 +@1831_577_322/1 +GAATGCTGGAGTACATTATGACAAACTATCGGAG ++ +=;>4506;255464-<#7+194&2<?65968)7/ +@1831_577_362/1 +CGATTAGTTACCACTCGTATTCGCACGCCCAGGA ++ +2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +@1831_577_382/1 +GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA ++ +2957/:1))=76(*24;,3+:<.&.&-=1=2/5* +@1831_577_464/1 +TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG ++ +=<7/<826)>#.'&4204+5#/041.7*91&756 +@1831_577_488/1 +TGAATAGTTATGGCCAGAATGTCTGCACCGATAC ++ +48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +@1831_577_511/1 +GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT ++ +7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +@1831_577_545/1 +ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT ++ +><<9?<>?A<481@<@8==@76/61<95.5988- +@1831_577_559/1 +GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG ++ +<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' +@1831_577_562/1 +GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ++ +((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +@1831_577_637/1 +GCCTTCGCGGGAGCATATCAGTCGATACATCCCA ++ +-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +@1831_577_641/1 +TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT ++ +47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +@1831_577_692/1 +CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA ++ +B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_solid_f.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_solid_f.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/2 +GTTCGTGGCCGGTGGGTGTTTGGG ++ +###$$#$#$&#####$'$#$###$ +@1378_17_1788/2 +TGGGTGGATGTGTTGTCGTTCATG ++ +#$#$###$#$#######$#$#### +@1378_25_2035/2 +GTGCGTCGGGGAGGGTGCTGTCGG ++ +######%#$%#$$###($###&&% +@1378_28_770/2 +GGTTGGGAGTTGGCGCGCGTGGTT ++ +###$##%%$####%#%$#%%#($$ +@1378_33_1945/2 +GGGGGGGGGGGGGGGGGGGGGGGG ++ +.6;?;55697>8779457986264 +@1378_34_789/2 +GGGCTTGCGTTAGTGAGAGGTTGT ++ +###%$%$%%###$####$###$#& +@1378_35_263/2 +GGCGGGGGGGGGGGGGGGGGGGGG ++ +$%%&,)3/)%$-6'$&5&#$''5. +@1378_43_186/2 +GCTAGGGTTTGGGTTTGCGGTGGG ++ +$%#$########%##%#$###'#' +@1378_51_1671/2 +GGTGTTGTTCGGATGTAGCGTGGG ++ +##%$$####$########$##0## +@1378_56_324/2 +GCTGGGTGATCTAAGGAATGTAAT ++ +#$#####$$$#$$$$##%###*(# +@1378_56_773/2 +TCTGGTCGGTTTCGGGGAGTGGAA ++ +##%%#&$###$#$##%$####%%$ +@1378_62_2027/2 +GTTGGCCTGGCCTGCCGTGCTGCG ++ +*##),/%##$)#%##1$#'%.#&# +@1378_62_2029/2 +GGCGGTGTGTGGTGCGGCTGTGCG ++ +/$$$=(####%####)$$%$-&%# +@1378_67_1795/2 +CGTGCCAACGACCGTCCTACGGAG ++ +@@.?7@@@.@:@A<<>>=>70<@7 +@1378_68_466/2 +GTGTCATCTGAGGTAAAGCATTGT ++ +/##$09#$#.=$#$76+$%1'### +@1378_68_1692/2 +TGTTCGATTTAGGTCTTGCCTCGC ++ +###%%$%%##%$#$##$###$$#$ +@1378_80_664/2 +TGTCTGCGTTGTATCTCTGGTGTA ++ +%##%,%$$#&$$###$#$%##'%# +@1378_85_1786/2 +CCCTAGGAGCGTATACCGGACGAG ++ +,'&/%/@,&1,&'/)&,6&&1)(( +@1378_86_1011/2 +AGGCGATGGGATATTATTTTACTT ++ +:$###)%##$9$###1$$#$2### +@1378_86_1789/2 +GGCCAGGTACTAATAAATTCAACA ++ +1.51/&%#'$,*?%#6&0$$5,20 +@1378_91_1596/2 +GCTTTTTCATTCGGTGCCTTTGGA ++ +'>%/3%=()8'#.%?50$&5>%)% +@1378_94_1595/2 +GCGGGTTAACCCAGTACCTCTGGC ++ +,8@6'>8<76>@@(->9)7'*941 +@1378_95_1039/2 +GTTCTGTGCCAGGTGAGGTACGGA ++ +&##,./#$&)6##+,'#$$0(##$ +@1378_95_1767/2 +CTAATTGACCGGGCAAGCTATTAA ++ +',,2'(10/>:=/7).3&%6&)&6 +@1378_96_1037/2 +CTGCTGGGCCATTTGACTTACTCA ++ +'$#+#(##-%5##+*&###-.$$$ +@1378_96_1764/2 +TCTTTGTAACCCACTTAGTATTTC ++ +4='28>.@4881B807:822>%)1 +@1378_98_1574/2 +AGGCGAGTGTGGGGGTTGTTTGAG ++ ++%%$#)##%##$####%###$%$# +@1378_107_1647/2 +GGTCTGGTTCTATGTTGGTCGACT ++ +###'$$#$$$(#%###(#$##$%# +@1378_111_829/2 +GGTCTTCTATGGTGCTAAATTAGT ++ +$##'&###$##)#%($#$%#$'%# +@1378_111_1900/2 +GCACGCCTTTGGGCTAAGCCGTAA ++ +)$)'#%$########$'#&%$#(# +@1378_112_1483/2 +TGGAGTGGTGTGTTTGCTGAGCCA ++ +#$#)#############$#%#%'% +@1378_125_1287/2 +TGACGTGGGTTGTCCCGTGAGATT ++ +##$%%#$###$##$$#&%##$(%% +@1378_126_468/2 +AAAAAACGGGCCGGGCGGACTAGG ++ +@@B@@@>@2>1+?:92)>@8&&<+ +@1378_127_664/2 +TCGCTTTGCCTATGTTTGTTCGGA ++ +#%$%#&##$%#%%###$$###)-' +@1378_129_463/2 +AAAAAAAAAAAAAAAAAAAAAAAA ++ +,)&20%8'(&35-***1-2&+510 +@1378_129_875/2 +GACCTTTACGTATTGGGGGTTGGC ++ +###)###+###$##$#&%##$,#$ +@1378_140_1251/2 +TTTCCTTCGTGTGCGTGCGGAGTG ++ +#%#%$##$$$######.$$$%#%( +@1378_141_809/2 +TCTCGTGGTTTCTTTTTTATGTGT ++ +##%)##$$#####%$#$#%%#'## +@1378_144_983/2 +GTTCGTTCGTGGTGTACGAGGGTG ++ +#(#%#####($#%##$$#%##%#) +@1378_153_270/2 +GGCCGTGTGCGGGTGTAGATTGGA ++ +%$##($######&##$&$$$$%## +@1378_155_1689/2 +CGCGTTCGGACAAAGCTAGCACCT ++ +@4@@=6=@@<4:@@681@@@.24. +@1378_157_1580/2 +GGGATTGAAGGGATGTATGCTAGG ++ +#%$&%#$$'%$%#$##*#%$$$$# +@1378_161_317/2 +AATCCATACCCACAAAAGCAGGCC ++ +.&%','(@''?7//+&)+2.+)0) +@1378_177_735/2 +CGAGCCCTAAACCATGAGATCGGA ++ +@@B>@AC9@A<B8@=9>7@5)>,0 +@1378_181_1684/2 +TTTCTGTTGTGGTTTTGTTGGGGT ++ +$##'$%'##%##$%$#$$####$* +@1378_187_1407/2 +TTGGGTGAAATCTTGTCGAGTGGA ++ +####&##$$###$#####%##%%) +@1378_203_721/2 +CCTTTACGATCATAAACCATGACC ++ +9<&./1&@;12')?<1',?/)&/. +@1378_206_2039/2 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +?=>>?=:;<>>4::<=56199(05 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_solid_r.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_solid_r.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/1 +AGACCGGGCGGGGTGGCGTTCGGT ++ +%##+'#######%###$#$##$(# +@1378_17_1788/1 +TGCCGTGTCTTGCTAACGCCGATT ++ +#'#$$#$###%%##$$$$###### +@1378_25_2035/1 +CTGCGTGTTGGTGTCTACTGGGGT ++ +#%#'##$#$##&%#%$$$%#%#'# +@1378_28_770/1 +CTGCTATGCCGGCCGCCTGCCCCT ++ +%##(#$$#%$#$%###$%%$##$# +@1378_33_1945/1 +GGGGGGGGGGGGGGGGGGGGGGGG ++ ++9;64287788752796/576352 +@1378_34_789/1 +ATGGTGGCTGACGCGTTTGACTGT ++ +#$##%#$##$&$#%##$##$###$ +@1378_35_263/1 +GGGCGGGGGGCGGCGGGGGGGGGG ++ +),,#%'$)'-(%&%'%',%%&&(& +@1378_43_186/1 +ATACTAGTTGGGACGCGTTGTGCT ++ +#$(4%$########$#$###$$$# +@1378_51_1671/1 +TGGGTAGGTGCGGCTCTTGCGGTC ++ +##$#$%###%%#%#$##$$##### +@1378_56_324/1 +AGGCTTGGATTGTTGCGCTGACCT ++ +/+#**###%%##%#####$$$#$# +@1378_56_773/1 +TGTCGTGAGGTCACTTATCCCCAT ++ +&%#%##%%#####&#$%##$%##$ +@1378_62_2027/1 +CTTCCACGATCTGCTCGCTGTGGT ++ +(#&&$##$$#$%#%$$$#$###'# +@1378_62_2029/1 +TCTGGGCTGTCTTCGGGTCGGTGT ++ +$%$$####$##$$#)##%%#$### +@1378_67_1795/1 +TAGTGGGCTAGTCCGGGATCTACC ++ +B@C2@@?;-@@1>'A@@91@.@1' +@1378_68_466/1 +GTGATCGTCGGTGCCAGTCCCTGT ++ +#(%)+##$#$#%#+$%##$##### +@1378_68_1692/1 +GGTCTTCTGGGCACGGGCCAAGTT ++ +###)%'&%##$###%#######$# +@1378_80_664/1 +CTGCTTTGATCCCCGGTGGAGCAC ++ +7#%###$$6#######$##$$$## +@1378_85_1786/1 +ATACTATGTCGATCTGTAAAAAAA ++ +)&.)#3%(a)$&%-,2#&+.-%0&./ +@1378_86_1011/1 +CTACGTTATTGCTCTGTTTGTCCT ++ +######$%##$$$%###%#$#### +@1378_86_1789/1 +CGAATATCCCCTGGTTTAGAAGTA ++ +61?1;@/>@<=/(.7'(<5@=%$= +@1378_91_1596/1 +TTAGCGGTTGACTATCTGCTGACA ++ +*&+'#9'(%*'#//,&<),/)'*# +@1378_94_1595/1 +CGTGCGACAGCCCATGTTTTCAGA ++ +-=..5,3826&*+.+#+#%%6;%# +@1378_95_1039/1 +CGGCGTCCATCTTCGCCTTGAGAT ++ +$##.#$##$$#%$#$%%$###$)$ +@1378_95_1767/1 +ACACGCACCATCTGGCGGCTAACC ++ +86<65<4<C27/$5+#;-$+#2%$ +@1378_96_1037/1 +ATCCCCCAAGATGCCTGTTGATTG ++ +$#$'##$$$#%$$#%###+##$#$ +@1378_96_1764/1 +TACACCGGAACCTTGCACTAAAGC ++ +6-9'<#+81?+*<8-=69&6;*3) +@1378_98_1574/1 +GTTCTGCCGGTGTCTGTGGCGGGC ++ +$$#+&$$####%$$$###$%#%%# +@1378_107_1647/1 +AGGCCTACTACGCGTCATTGATAG ++ +&#$$#$(.#%#$$####&$%##($ +@1378_111_829/1 +TGCGGCACTTGCTTCTTCGTATTT ++ +%#%##%#$%#$#%###$$##&#$$ +@1378_111_1900/1 +TCCCCTCGCTCGGCTCTGTGCTGT ++ +$&%*$#(#)##$#'##%(##$#$% +@1378_112_1483/1 +TGTCCAGCTATGCGGCTTCCTCCT ++ +%#$+#%#&#$#####%####%$## +@1378_125_1287/1 +TGTCTCTGGGGGGCCTGGTTAGGT ++ +$##13$'%#$###$$###$$$#&# +@1378_126_468/1 +TCTCCTGATTAGACATATCTCCGT ++ +7>@318?=,=8@49579?..7,7) +@1378_127_664/1 +AGAGGTTGGTGTCTTGTCGCAGCT ++ +##'#$######$$%######$$$# +@1378_129_463/1 +CCTGTGGGCCAAGCCCAATGAAAG ++ +8),,<6(--)<()5&.&/8+;.2+ +@1378_129_875/1 +TTTCTATGGCTTACGCTGTCTGCC ++ +#$($##%####%$#$#####$### +@1378_140_1251/1 +ATCCTAGCGCGGTGTCTTGGGGAC ++ +#$%1#$$$##$##$#$#$##$%$$ +@1378_141_809/1 +TGTCCTCCAGTGTCTGTTGGGTGT ++ +%&,-##$$#(%###$#$$'###'# +@1378_144_983/1 +AGCGCCCGGTTGGTGCGGCTCGTC ++ +-$(&%*$#*#))#$$$#%%$#$## +@1378_153_270/1 +AGTCCTTGTCCCCTGGGTTTTCCC ++ ++''$#&%$%#$##&$$($#&#$$# +@1378_155_1689/1 +TTGGGAGGGAGAGAGACTAGACCG ++ +?4@@4<<??<?-@4@=4<5<?:/> +@1378_157_1580/1 +TGGGCCTCGGTGCCCTTGGTCTGT ++ +#%)$##'#$$$&#####%#$#$## +@1378_161_317/1 +TTGGCCGGCAACCCCGGTACCTAA ++ +7<,<'@)@>.)2@/')'&(?/-<( +@1378_177_735/1 +AGTACGCCATGTATTTGCGACCAG ++ +=?@?C<88@=>:7>@55/.,416, +@1378_181_1684/1 +CGACTCCCGCATTCACGGTCAAGT ++ +&*#,##$#&$*$$#$#$$$#%$## +@1378_187_1407/1 +TGGCGTCCACTCGTGGGTCTATCG ++ +$#$'%#$%$%&$%#####$#$#%# +@1378_203_721/1 +CCTAAATAACCCAGGGTAAAAGAT ++ +9<1+2+1@=259@+;2.71&@+2& +@1378_206_2039/1 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +9@?8>;>>><<994;=895895-8 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out0.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out0.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,2 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M = 322 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out0b.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out0b.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,2 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +081017-and-081020:1:1:1715:1759 4 * 0 0 * * 0 0 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out1.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,145 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +1831_573_1004 0 PHIX174 278 25 33M = 278 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +1831_573_1219 16 PHIX174 2202 37 33M = 2202 0 TGCAGTGGAATAGTCAGGTTAAATTTAATGTGA KJOOHX]KAP[]]MBQ\TUFO]QMFGG=CLZ]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1242 0 PHIX174 648 37 33M = 648 0 CATCCCGTCAACATTCAAACGGCCTGTCTCATC ]]]]XQ]]]]]]]][]]]VIMOW]SW]]]T*1] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1333 4 * 0 0 * * 0 0 AGAATCGTTACCACACACTGCGTCTGGGTATCCG ='@#%3=.>)/34*117,,/6-4+.9742456<) +1831_573_1362 4 * 0 0 * * 0 0 CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +1831_573_1448 16 PHIX174 2563 25 33M = 2563 0 CTTCATTGCATTCAGATGGATACATCTGTCAAC :BMPX5.QUW6+R]RIOU]]]]]]]]WCTQS]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1490 0 PHIX174 1767 25 33M = 1767 0 CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC ]]]TU]]]=;]]]R9=BQQDF>QZQ1,LBIGEN XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1523 4 * 0 0 * * 0 0 ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +1831_573_1578 4 * 0 0 * * 0 0 CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +1831_573_1647 16 PHIX174 1118 37 33M = 1118 0 GACTCCTTCGAGATGGACGCCGTTGGCGCTCTC XSU]YZSLKMZ]Y[]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1684 16 PHIX174 3696 37 33M = 3696 0 AGTGCTGAGGTTGACTTAGTTCATCAGCAAACG ]]]]V]]]]]]]]]]]]]]]]]]]]]U\]][TX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1769 4 * 0 0 * * 0 0 TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC 54749&&767%/7;3$-7;3#,3//#,45/#&06 +1831_573_1853 4 * 0 0 * * 0 0 CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC 4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +1831_573_1943 4 * 0 0 * * 0 0 ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC >/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +1831_573_1977 4 * 0 0 * * 0 0 GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC @?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +1831_574_109 0 PHIX174 3729 37 33M = 3729 0 CAGAATCAGCGGTATGGCTCTTCTCATATTGGC VTO/2URQ]]]TZWU[UTQP\]XY]VS[WLN]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_148 16 PHIX174 2369 37 33M = 2369 0 TAGGTTTTCTGCTTAGGAGTTTAATCATGTTTC XOQ[]]]TKWRCLJJZRR][]TWVGVZW]WZTQ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_185 4 * 0 0 * * 0 0 CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC <4;%%@7>#*>97%6;+8$#<07%1372$%<54# +1831_574_243 0 PHIX174 2129 37 33M = 2129 0 TCTGGTGATTTGCAAGAACGCGTACTTATTCGC ]]]W]]]]RQ]YRBI]]Y0<]]]CI]]]FM]]Y XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_257 4 * 0 0 * * 0 0 ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC >>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +1831_574_293 4 * 0 0 * * 0 0 TGCTGCAAATAAACATACAGCCTTCTAATGACTA ')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +1831_574_389 4 * 0 0 * * 0 0 CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA )$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +1831_574_575 16 PHIX174 4006 37 33M = 4006 0 AATGTCACGCTGATTATTTTGACTTTGAGCGTA TMHGZ]UE<L]]]EM]K"&I]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_592 16 PHIX174 2950 37 33M = 2950 0 GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCA LLVSIV]]ZSPPSWNDIW\VOM[]]QANSCGKI XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_617 4 * 0 0 * * 0 0 AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC >@?;>?=@==@>@=5?@+@:@40@><:0)')64- +1831_574_725 4 * 0 0 * * 0 0 GACAAGATGGCTATTATTTACAATCCGATCTGCA '>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +1831_574_734 16 PHIX174 5263 25 33M = 5263 0 GAGAGATGAGATTGAGGCTGGGAAAAGTTACTG P]VXTGPLRN@KE=ALXC7ARL7;>;OKA/!!< XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_574_824 16 PHIX174 3997 37 33M = 3997 0 ACCCTTCTGAATGTCACGCTGATTATTTTGACT ]\MN]]U?I]]TAN]]ZGK][\RR]T@>M]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_959 4 * 0 0 * * 0 0 CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +1831_574_1062 4 * 0 0 * * 0 0 ACCGGTAATATAAGGCAACATGATTACGGCCACG @821<//:136/8<1/5.427.;>288/0<1$)/ +1831_574_1092 4 * 0 0 * * 0 0 GACTGGCGAAATCATCGCGGAAAAACCCCTATCA 8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +1831_574_1103 4 * 0 0 * * 0 0 ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +1831_574_1116 4 * 0 0 * * 0 0 CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC @++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +1831_574_1194 0 PHIX174 1136 37 33M = 1136 0 GCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGT \]PT]]]]]]]ZZ]]]\Y]]]]\]]]V\]UMDK XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1204 16 PHIX174 1445 25 33M = 1445 0 CCTAATGAGCTTAATCAAGATGATGCTCGTTAT JGMO%.S]S>EW]V,=Y[]]PCU]]]X]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1306 4 * 0 0 * * 0 0 ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA 2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +1831_574_1387 4 * 0 0 * * 0 0 GTACTTCTCAATGCTGCACTACTATGTACGCCCC ?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +1831_574_1431 4 * 0 0 * * 0 0 GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC 7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +1831_574_1560 4 * 0 0 * * 0 0 GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +1831_574_1591 16 PHIX174 5118 37 33M = 5118 0 AAGCTGTTCAGAATCAGAATGAGCCGCAACTTC MLII]]\K!7]ST][]]]OO]]]]]X]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1624 16 PHIX174 4058 37 33M = 4058 0 TATTGAGGCTTGTGGCATTTCTACTCTTTCTCA ?IM@DV]M?NRTK@JPXS?>ENI;=AML=7=M[ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1826 4 * 0 0 * * 0 0 TACGTCGCGACCGAGCGTTATATAGTCTGACCCC @<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +1831_574_1903 0 PHIX174 5209 37 33M = 5209 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGA WT]]]][]]]][]]]]]]]]]]][X]QYYTYZ- XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1961 0 PHIX174 3555 25 33M = 3555 0 CGCGTTGCGTCTATTATGGAAAACACCAATCTT TFPMV]OCBP]H<OS]<1CN]]M=K]52KO]WT XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_54 16 PHIX174 3587 37 33M = 3587 0 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCG ]]4/WZUDARYXKAL]]MR]]]]\]]VW]W]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_80 4 * 0 0 * * 0 0 TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +1831_575_192 4 * 0 0 * * 0 0 AACTACGCCCCTTAATTACACAGCGCGTTAGACC :8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +1831_575_197 16 PHIX174 4861 37 33M = 4861 0 GCTTGCAAAATACGTGGCCTTATGGTTACAGTA G.<]KNV]]RH@AIT]\SP\]]]Y[]]\RS\]P XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_223 4 * 0 0 * * 0 0 ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +1831_575_420 4 * 0 0 * * 0 0 CCCACATGGAAAACACTCACCGCCGAACAGAGCG 2?.>?(-''2+..@),$%1@;')1)?+)7.').. +1831_575_434 4 * 0 0 * * 0 0 ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC @@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +1831_575_444 16 PHIX174 5098 37 33M = 5098 0 AGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAA ]Y0/[]]MM]]]VT]]]]]]]]QP]]]TS]]][ XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_459 4 * 0 0 * * 0 0 CTTATCAGCACACGGTTTACCAGTCCGACTCCAA @@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +1831_575_506 4 * 0 0 * * 0 0 CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +1831_575_569 0 PHIX174 5043 25 33M = 5043 0 GACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAA IOBU[TMHTYG4M]7$?Q]]]57]SKXQC;:FE XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_622 0 PHIX174 2485 37 33M = 2485 0 GTTTTACAGACACCTAAAGCTACATCGTCAACG ]]]]]]]]]]]]]]]X[YVYINYLTLJWHO[$! XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_644 4 * 0 0 * * 0 0 CTTGAATGGCGATCTCGTCGAGGAAATACCACTA <8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +1831_575_663 16 PHIX174 1554 25 33M = 1554 0 CGACTTCTACCACATCTATTGACATTATGGGTC !&V]]NIPV]]YUXWZWTYPW]]]]]ST]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_681 4 * 0 0 * * 0 0 TCTCCTGATTAGACATATCACTGTTGAACACAGC 72?.)25;96-14'*.03'#4#++$)/8+%/((& +1831_575_711 4 * 0 0 * * 0 0 TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC %+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +1831_575_730 4 * 0 0 * * 0 0 CACACAGGAACCATAGCGTATGTTATTCACCCCC %8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +1831_575_904 4 * 0 0 * * 0 0 ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC <><.689@@7@<54:4=@>69=:+6-=42;8<:# +1831_575_938 16 PHIX174 1133 37 33M = 1133 0 GACGCCGTTGGCGCTCTCCGTCTTTCTCCATTG XJFX]]WUY[]RKYXU]]]]]]]]\]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_970 16 PHIX174 232 37 33M = 232 0 GAGGAGAAGTGGCTTAATATGCTTGGCACGTTC Z]]]XU]]]]]]]]]]]]]]]\]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_991 4 * 0 0 * * 0 0 TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA >>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +1831_575_1138 0 PHIX174 1913 37 33M = 1913 0 GCTAAAGGTGCTTTGACTTATACCGATATTGCT VT7-SURJS]X]TT]Z]UY]]]]]]X[UN[NMT XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1157 16 PHIX174 3736 25 33M = 3736 0 AGCGGTATGGCTCTTCTCATATTGGCGCTACTG TX//[\]PQ]]]Z]]]]GN]]O!']]]]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1180 0 PHIX174 4169 37 33M = 4169 0 GGGCGTTGAGTTCGATAATGGTGATATGTATGT ]]\]OJROX]]UUYSX\[Y]]]]VZ]\VRWLT] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1283 4 * 0 0 * * 0 0 GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +1831_575_1302 16 PHIX174 5202 37 33M = 5202 0 CTTACCAAGCTGGGTTACGACGCGACGCCGTTC ?AGG9<JL@57BI,!6828KG54AH<6B>;VYL XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1310 16 PHIX174 1612 37 33M = 1612 0 TACTGACCAAGAACGTGATTACTTCATGCAGCG [M!!N]]]]]]]OX]]]ZKW]]QQ][][RU]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1321 0 PHIX174 2664 37 33M = 2664 0 TTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGAC ]]]]]]]]]]]]]]]]]]]\ND]]]7/]]]WPZ XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1373 16 PHIX174 4221 37 33M = 4221 0 TCTGACGTTCGTGATGAGTTTGTATCTGTTACT WGIZ]OHLR]]QU]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1419 4 * 0 0 * * 0 0 TGGGGAATATAACAGCGTAGCGTTGAACACTAGA //3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +1831_575_1436 0 PHIX174 3460 37 33M = 3460 0 CTGGCATTCAGTCGGCGACTTCACGCCAGAATA []]WULFXOGY]]\PY]]IGZ]]M@V]XAAMR[ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1442 0 PHIX174 3317 37 33M = 3317 0 TGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTC \V]]]]RE\]LEQ]]]X]]]]TZ]]QUPW]LIX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1454 4 * 0 0 * * 0 0 CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT 4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +1831_575_1500 16 PHIX174 4269 37 33M = 4269 0 GAATTGGCACAATGCTACAATGTGCTCCCCCAA ]]]LQ]ZZX]]]][[[[][VZ\][[]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1535 16 PHIX174 1225 37 33M = 1225 0 TCACGTTTATGGTGAACAGTGGATTAAGTTCAT Z\]]][Y][]]]]]]]W]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1724 4 * 0 0 * * 0 0 TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA <B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +1831_575_1829 4 * 0 0 * * 0 0 CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC 2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +1831_575_1898 4 * 0 0 * * 0 0 CTTACCATATCATCTCAACCCATAACAGCACTTA B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +1831_575_1964 4 * 0 0 * * 0 0 GACAGACCATGAGGCTGAAGACTACTAAGTGCGT >39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +1831_576_32 16 PHIX174 988 25 33M = 988 0 TTGAGGATAAATTATGTCTAATATTCAAACTGG !6\NX[\]YMP]]YM]]]]]VMPGDW\]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_576_74 4 * 0 0 * * 0 0 ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA =@@?@>(??<B5?@@@9<@><+><;@';>6961? +1831_576_86 16 PHIX174 2981 37 33M = 2981 0 CATGTCTAAATTGTTTGGAGGCGGTCAAAAAGC JDKTAEKORA;<GOTUPHGVRTZI?BAMUDCKR XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_89 4 * 0 0 * * 0 0 GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA )69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +1831_576_266 16 PHIX174 280 37 33M = 280 0 AGATATGAGTCACATTTTGTTCATGGTAGAGAT E4FXQMCG]]R<FZG5#.Z]SN]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_327 16 PHIX174 4517 37 33M = 4517 0 TACTATTCAGCGTTTGATGAATGCAATGCGACA \[]]]XQ\]]\X]]]]\Y]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_331 4 * 0 0 * * 0 0 GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +1831_576_387 4 * 0 0 * * 0 0 ACACGCCATGATCCGATAAGAAGGGAACGTAAGG 8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +1831_576_406 4 * 0 0 * * 0 0 AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC 4<>%%14:*4656)&<251&2+3#&19,6&4>5( +1831_576_449 4 * 0 0 * * 0 0 CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA +'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +1831_576_519 16 PHIX174 1625 37 33M = 1625 0 CGTGATTACTTCATGCAGCGTTACCGTGATGTT KMPKLIVPELLS]XRY]]YWV]]NJY]]Y][SZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_603 16 PHIX174 1576 37 33M = 1576 0 CATTATGGGTCTGCAAGCTGCTTATGCTAATTT ZWU]]ZS\]]]TY]]]RQ]]]Y]]]]VZ]]\S] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_655 16 PHIX174 3292 37 33M = 3292 0 TTGCTGCTGCATTTCCTGAGCTTAATGCTTGGG :@O]QV]]]TK]]]73]]]TM]]]QI[]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_677 4 * 0 0 * * 0 0 TTTACTCAGTTGATACATCACTGTAGCACATAGG 290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +1831_576_718 4 * 0 0 * * 0 0 CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT 4###$0###%(#########,####%####$### +1831_576_722 4 * 0 0 * * 0 0 CGTATGATGGCGAGTCTTTATAATCCAATCTGAA *,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +1831_576_754 4 * 0 0 * * 0 0 AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA 4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +1831_576_815 0 PHIX174 5186 37 33M = 5186 0 GGAGTGCTTAATCCAACTTACCAAGCTGGGTTA Z]]]]]]]]]]]]]]]]]]]UP[ZKIP]][ZUN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_882 0 PHIX174 5053 37 33M = 5053 0 CTAAAGGTCTAGGAGCTAAAGAATGGAACAACT Q]]]]]W[]]]X]]]]][EAV]]ZUS\]]]VX] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_898 0 PHIX174 518 37 33M = 518 0 GATTGCTACTGACCGCTCTCGTGCTCGTCGCTG ]]]Z]]]]]]]YW]]]]VV]]X]]]]]VO]]]T XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_923 0 PHIX174 1050 37 33M = 1050 0 ATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTC MLOW]RMX[]]X]]]XV]]]UKU]]]W\\]\ST XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_930 4 * 0 0 * * 0 0 CTGGCATGTACGTCCATGTCAGACGAGCAGAACT #*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +1831_576_1019 4 * 0 0 * * 0 0 GATGCGCGCTGTCATGGCATCGAACCATCGGTCG <$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +1831_576_1068 4 * 0 0 * * 0 0 AAGAGTGACTCACTTACCGGGATGCGATGGAGCC >><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +1831_576_1131 16 PHIX174 4061 37 33M = 4061 0 TGAGGCTTGTGGCATTTCTACTCTTTCTCAATC WTLN]WUHL]]S<PZQUOYSFZ]][IUXX>>]M XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1168 4 * 0 0 * * 0 0 CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA @CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +1831_576_1207 4 * 0 0 * * 0 0 CAACCTGACTAAACGGGGATACGCTGGCGCTACA $>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +1831_576_1289 16 PHIX174 1899 37 33M = 1899 0 TTCAGTACCTTAACGCTAAAGGTGCTTTGACTT NLU]YXTCQ]][JEJMSX]YRU]]][]]]\X]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1329 4 * 0 0 * * 0 0 CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA >&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +1831_576_1367 0 PHIX174 1839 37 33M = 1839 0 AGCATGGCACTATGTTTACTCTTGCGCTTGTTC ]]]]]]]]]]]]]]]]]]\]]]]]]]\YW]]XX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1416 0 PHIX174 4522 37 33M = 4522 0 TTCAGCGTTTGATGAATGCAATGCGACAGGCTC K]VEHHS]P>TQJML]]\UFU][L6K]\TMPZ] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1461 4 * 0 0 * * 0 0 GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA 1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +1831_576_1605 0 PHIX174 5209 37 33M = 5209 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGA ]]]]]XU]]]]]]]]]]]]]]X[]KHLWZUXW, XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1664 4 * 0 0 * * 0 0 CGCGCACAACTCGCCATGATACGACAAGACCCGA @?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +1831_576_1671 4 * 0 0 * * 0 0 GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT @?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +1831_576_1729 16 PHIX174 5194 37 33M = 5194 0 TAATCCAACTTACCAAGCTGGGTTACGACGCGA ]VDP]]][]]]]]]]]]]]]]]UW]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1880 4 * 0 0 * * 0 0 TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT 515/792,:,7/%/05,%$):+#8%2(1754))3 +1831_576_1982 16 PHIX174 5024 37 33M = 5024 0 TAACAAAAAGTCAGATATGGACCTTGCTGCTAA TP\NU]]]W[]]]][]]]]]]]]]]]]]VU]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1987 4 * 0 0 * * 0 0 AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +1831_576_2014 4 * 0 0 * * 0 0 CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT @@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +1831_576_2028 4 * 0 0 * * 0 0 ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA <>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +1831_577_40 0 PHIX174 2772 25 33M = 2772 0 TGTGACTATTGACGTCCTTCCCCGTACGCCGGG JLE8>>9:MOR=!&74KQDKU]M?IG@P]]]PK XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_119 4 * 0 0 * * 0 0 TCCCACAAGCCATTGACATGCTCGCTCTAAACAG >?C11)-1/)#;#/,850*+.+$$5550+%-.40 +1831_577_133 16 PHIX174 1714 37 33M = 1714 0 CATGCGCTCTAATCTCTGGGCATCTGGCTATGA &/BFXKGOZZEPOS]]]]]]PY]RN]YW]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_255 4 * 0 0 * * 0 0 ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG <=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +1831_577_281 16 PHIX174 4577 37 33M = 4577 0 TTTTGACACTCTCACGTTGGCTGACGACCGATT ]]OI]]]]]\ZY]]WTJS]]\[]]]]]]]\]]P XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_288 0 PHIX174 3201 25 33M = 3201 0 GGCACTTCTGCCGTTTCTGATAAGTTGCTTGAT SOY]]NL]]]UTZKIMNOCH/-LFLLK]VN5%F XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_322 16 PHIX174 458 37 33M = 458 0 TTCTGCCGTTTTGGATTTAACCGAAGATGATTT OIJWXWT]]WACVSEK5:RJSSRSPVZONR[]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_362 0 PHIX174 2153 37 33M = 2153 0 CTTATTCGCCACCATGATTATGACCAGTGTTTC ]]]]]]]]]WV]RHVONRSI6=O[NK[ZL?%(J XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_382 16 PHIX174 4686 37 33M = 4686 0 GGTCGCAAGGCTAATGATTCACACGCCGACTGC HMJXWWS<===S]NGHPXOE;GV]O;CTROUWT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_464 0 PHIX174 2126 25 33M = 2126 0 CCTTCTGGTGATTTGCAAGAACGCGTACTTATT ]\OT]SQHP<,>6COKMHI3-HMNHNJLS@FUT XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_488 16 PHIX174 4948 37 33M = 4948 0 GGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG ]OTZ]]]]]][V]Z]YW]]]]]][UTT]Q?COU XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_511 4 * 0 0 * * 0 0 GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT 7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +1831_577_545 0 PHIX174 1711 37 33M = 1711 0 TGTCATGCGCTCTAATCTCTGGGCATCTGGCTA ]]]]]]]]]YURZ]]]]]]]VNNPV]WLLWZYN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_559 0 PHIX174 3840 25 33M = 3840 0 GCTGTTGCCGATACTTGGAACAATTTCTGGAAA ]]]]]]]]WJWSWZW]XLX\P#-]]V=A(/TD9 XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_562 4 * 0 0 * * 0 0 GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +1831_577_637 0 PHIX174 4247 37 33M = 4247 0 TGTTACTGAGAAGTTAATGGATGAATTGGCACA BI2<]PLJN[M;7FYWYVW]]\WG@IQH6O]XI XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_641 4 * 0 0 * * 0 0 TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT 47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +1831_577_692 0 PHIX174 3905 37 33M = 3905 0 GTCTAGGAAATAACCGTCAGGATTGACACCCTC WU]]]SQ]]]TT]]]TS]]]PM]]]]]]]]]UZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out2.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,97 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +1378_11_329 69 * 0 0 * * 0 0 GTTCGTGGCCGGTGGGTGTTTGGG ###$$#$#$&#####$'$#$###$ +1378_11_329 133 * 0 0 * * 0 0 AGACCGGGCGGGGTGGCGTTCGGT %##+'#######%###$#$##$(# +1378_17_1788 69 * 0 0 * * 0 0 TGGGTGGATGTGTTGTCGTTCATG #$#$###$#$#######$#$#### +1378_17_1788 133 * 0 0 * * 0 0 TGCCGTGTCTTGCTAACGCCGATT #'#$$#$###%%##$$$$###### +1378_25_2035 69 * 0 0 * * 0 0 GTGCGTCGGGGAGGGTGCTGTCGG ######%#$%#$$###($###&&% +1378_25_2035 133 * 0 0 * * 0 0 CTGCGTGTTGGTGTCTACTGGGGT #%#'##$#$##&%#%$$$%#%#'# +1378_28_770 69 * 0 0 * * 0 0 GGTTGGGAGTTGGCGCGCGTGGTT ###$##%%$####%#%$#%%#($$ +1378_28_770 133 * 0 0 * * 0 0 CTGCTATGCCGGCCGCCTGCCCCT %##(#$$#%$#$%###$%%$##$# +1378_33_1945 69 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGG .6;?;55697>8779457986264 +1378_33_1945 133 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGG +9;64287788752796/576352 +1378_34_789 69 * 0 0 * * 0 0 GGGCTTGCGTTAGTGAGAGGTTGT ###%$%$%%###$####$###$#& +1378_34_789 133 * 0 0 * * 0 0 ATGGTGGCTGACGCGTTTGACTGT #$##%#$##$&$#%##$##$###$ +1378_35_263 69 * 0 0 * * 0 0 GGCGGGGGGGGGGGGGGGGGGGGG $%%&,)3/)%$-6'$&5&#$''5. +1378_35_263 133 * 0 0 * * 0 0 GGGCGGGGGGCGGCGGGGGGGGGG ),,#%'$)'-(%&%'%',%%&&(& +1378_43_186 69 * 0 0 * * 0 0 GCTAGGGTTTGGGTTTGCGGTGGG $%#$########%##%#$###'#' +1378_43_186 133 * 0 0 * * 0 0 ATACTAGTTGGGACGCGTTGTGCT #$(4%$########$#$###$$$# +1378_51_1671 69 * 0 0 * * 0 0 GGTGTTGTTCGGATGTAGCGTGGG ##%$$####$########$##0## +1378_51_1671 133 * 0 0 * * 0 0 TGGGTAGGTGCGGCTCTTGCGGTC ##$#$%###%%#%#$##$$##### +1378_56_324 69 * 0 0 * * 0 0 GCTGGGTGATCTAAGGAATGTAAT #$#####$$$#$$$$##%###*(# +1378_56_324 133 * 0 0 * * 0 0 AGGCTTGGATTGTTGCGCTGACCT /+#**###%%##%#####$$$#$# +1378_56_773 69 * 0 0 * * 0 0 TCTGGTCGGTTTCGGGGAGTGGAA ##%%#&$###$#$##%$####%%$ +1378_56_773 133 * 0 0 * * 0 0 TGTCGTGAGGTCACTTATCCCCAT &%#%##%%#####&#$%##$%##$ +1378_62_2027 69 * 0 0 * * 0 0 GTTGGCCTGGCCTGCCGTGCTGCG *##),/%##$)#%##1$#'%.#&# +1378_62_2027 133 * 0 0 * * 0 0 CTTCCACGATCTGCTCGCTGTGGT (#&&$##$$#$%#%$$$#$###'# +1378_62_2029 69 * 0 0 * * 0 0 GGCGGTGTGTGGTGCGGCTGTGCG /$$$=(####%####)$$%$-&%# +1378_62_2029 133 * 0 0 * * 0 0 TCTGGGCTGTCTTCGGGTCGGTGT $%$$####$##$$#)##%%#$### +1378_67_1795 69 * 0 0 * * 0 0 CGTGCCAACGACCGTCCTACGGAG @@.?7@@@.@:@A<<>>=>70<@7 +1378_67_1795 133 * 0 0 * * 0 0 TAGTGGGCTAGTCCGGGATCTACC B@C2@@?;-@@1>'A@@91@.@1' +1378_68_466 69 * 0 0 * * 0 0 GTGTCATCTGAGGTAAAGCATTGT /##$09#$#.=$#$76+$%1'### +1378_68_466 133 * 0 0 * * 0 0 GTGATCGTCGGTGCCAGTCCCTGT #(%)+##$#$#%#+$%##$##### +1378_68_1692 69 * 0 0 * * 0 0 TGTTCGATTTAGGTCTTGCCTCGC ###%%$%%##%$#$##$###$$#$ +1378_68_1692 133 * 0 0 * * 0 0 GGTCTTCTGGGCACGGGCCAAGTT ###)%'&%##$###%#######$# +1378_80_664 69 * 0 0 * * 0 0 TGTCTGCGTTGTATCTCTGGTGTA %##%,%$$#&$$###$#$%##'%# +1378_80_664 133 * 0 0 * * 0 0 CTGCTTTGATCCCCGGTGGAGCAC 7#%###$$6#######$##$$$## +1378_85_1786 69 * 0 0 * * 0 0 CCCTAGGAGCGTATACCGGACGAG ,'&/%/@,&1,&'/)&,6&&1)(( +1378_85_1786 133 * 0 0 * * 0 0 ATACTATGTCGATCTGTAAAAAAA )&.)#3%(a)$&%-,2#&+.-%0&./ +1378_86_1011 69 * 0 0 * * 0 0 AGGCGATGGGATATTATTTTACTT :$###)%##$9$###1$$#$2### +1378_86_1011 133 * 0 0 * * 0 0 CTACGTTATTGCTCTGTTTGTCCT ######$%##$$$%###%#$#### +1378_86_1789 69 * 0 0 * * 0 0 GGCCAGGTACTAATAAATTCAACA 1.51/&%#'$,*?%#6&0$$5,20 +1378_86_1789 133 * 0 0 * * 0 0 CGAATATCCCCTGGTTTAGAAGTA 61?1;@/>@<=/(.7'(<5@=%$= +1378_91_1596 69 * 0 0 * * 0 0 GCTTTTTCATTCGGTGCCTTTGGA '>%/3%=()8'#.%?50$&5>%)% +1378_91_1596 133 * 0 0 * * 0 0 TTAGCGGTTGACTATCTGCTGACA *&+'#9'(%*'#//,&<),/)'*# +1378_94_1595 69 * 0 0 * * 0 0 GCGGGTTAACCCAGTACCTCTGGC ,8@6'>8<76>@@(->9)7'*941 +1378_94_1595 133 * 0 0 * * 0 0 CGTGCGACAGCCCATGTTTTCAGA -=..5,3826&*+.+#+#%%6;%# +1378_95_1039 69 * 0 0 * * 0 0 GTTCTGTGCCAGGTGAGGTACGGA &##,./#$&)6##+,'#$$0(##$ +1378_95_1039 133 * 0 0 * * 0 0 CGGCGTCCATCTTCGCCTTGAGAT $##.#$##$$#%$#$%%$###$)$ +1378_95_1767 69 * 0 0 * * 0 0 CTAATTGACCGGGCAAGCTATTAA ',,2'(10/>:=/7).3&%6&)&6 +1378_95_1767 133 * 0 0 * * 0 0 ACACGCACCATCTGGCGGCTAACC 86<65<4<C27/$5+#;-$+#2%$ +1378_96_1037 69 * 0 0 * * 0 0 CTGCTGGGCCATTTGACTTACTCA '$#+#(##-%5##+*&###-.$$$ +1378_96_1037 133 * 0 0 * * 0 0 ATCCCCCAAGATGCCTGTTGATTG $#$'##$$$#%$$#%###+##$#$ +1378_96_1764 69 * 0 0 * * 0 0 TCTTTGTAACCCACTTAGTATTTC 4='28>.@4881B807:822>%)1 +1378_96_1764 133 * 0 0 * * 0 0 TACACCGGAACCTTGCACTAAAGC 6-9'<#+81?+*<8-=69&6;*3) +1378_98_1574 69 * 0 0 * * 0 0 AGGCGAGTGTGGGGGTTGTTTGAG +%%$#)##%##$####%###$%$# +1378_98_1574 133 * 0 0 * * 0 0 GTTCTGCCGGTGTCTGTGGCGGGC $$#+&$$####%$$$###$%#%%# +1378_107_1647 69 * 0 0 * * 0 0 GGTCTGGTTCTATGTTGGTCGACT ###'$$#$$$(#%###(#$##$%# +1378_107_1647 133 * 0 0 * * 0 0 AGGCCTACTACGCGTCATTGATAG &#$$#$(.#%#$$####&$%##($ +1378_111_829 69 * 0 0 * * 0 0 GGTCTTCTATGGTGCTAAATTAGT $##'&###$##)#%($#$%#$'%# +1378_111_829 133 * 0 0 * * 0 0 TGCGGCACTTGCTTCTTCGTATTT %#%##%#$%#$#%###$$##&#$$ +1378_111_1900 69 * 0 0 * * 0 0 GCACGCCTTTGGGCTAAGCCGTAA )$)'#%$########$'#&%$#(# +1378_111_1900 133 * 0 0 * * 0 0 TCCCCTCGCTCGGCTCTGTGCTGT $&%*$#(#)##$#'##%(##$#$% +1378_112_1483 69 * 0 0 * * 0 0 TGGAGTGGTGTGTTTGCTGAGCCA #$#)#############$#%#%'% +1378_112_1483 133 * 0 0 * * 0 0 TGTCCAGCTATGCGGCTTCCTCCT %#$+#%#&#$#####%####%$## +1378_125_1287 69 * 0 0 * * 0 0 TGACGTGGGTTGTCCCGTGAGATT ##$%%#$###$##$$#&%##$(%% +1378_125_1287 133 * 0 0 * * 0 0 TGTCTCTGGGGGGCCTGGTTAGGT $##13$'%#$###$$###$$$#&# +1378_126_468 69 * 0 0 * * 0 0 AAAAAACGGGCCGGGCGGACTAGG @@B@@@>@2>1+?:92)>@8&&<+ +1378_126_468 133 * 0 0 * * 0 0 TCTCCTGATTAGACATATCTCCGT 7>@318?=,=8@49579?..7,7) +1378_127_664 69 * 0 0 * * 0 0 TCGCTTTGCCTATGTTTGTTCGGA #%$%#&##$%#%%###$$###)-' +1378_127_664 133 * 0 0 * * 0 0 AGAGGTTGGTGTCTTGTCGCAGCT ##'#$######$$%######$$$# +1378_129_463 69 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAA ,)&20%8'(&35-***1-2&+510 +1378_129_463 133 * 0 0 * * 0 0 CCTGTGGGCCAAGCCCAATGAAAG 8),,<6(--)<()5&.&/8+;.2+ +1378_129_875 69 * 0 0 * * 0 0 GACCTTTACGTATTGGGGGTTGGC ###)###+###$##$#&%##$,#$ +1378_129_875 133 * 0 0 * * 0 0 TTTCTATGGCTTACGCTGTCTGCC #$($##%####%$#$#####$### +1378_140_1251 69 * 0 0 * * 0 0 TTTCCTTCGTGTGCGTGCGGAGTG #%#%$##$$$######.$$$%#%( +1378_140_1251 133 * 0 0 * * 0 0 ATCCTAGCGCGGTGTCTTGGGGAC #$%1#$$$##$##$#$#$##$%$$ +1378_141_809 69 * 0 0 * * 0 0 TCTCGTGGTTTCTTTTTTATGTGT ##%)##$$#####%$#$#%%#'## +1378_141_809 133 * 0 0 * * 0 0 TGTCCTCCAGTGTCTGTTGGGTGT %&,-##$$#(%###$#$$'###'# +1378_144_983 69 * 0 0 * * 0 0 GTTCGTTCGTGGTGTACGAGGGTG #(#%#####($#%##$$#%##%#) +1378_144_983 133 * 0 0 * * 0 0 AGCGCCCGGTTGGTGCGGCTCGTC -$(&%*$#*#))#$$$#%%$#$## +1378_153_270 69 * 0 0 * * 0 0 GGCCGTGTGCGGGTGTAGATTGGA %$##($######&##$&$$$$%## +1378_153_270 133 * 0 0 * * 0 0 AGTCCTTGTCCCCTGGGTTTTCCC +''$#&%$%#$##&$$($#&#$$# +1378_155_1689 69 * 0 0 * * 0 0 CGCGTTCGGACAAAGCTAGCACCT @4@@=6=@@<4:@@681@@@.24. +1378_155_1689 133 * 0 0 * * 0 0 TTGGGAGGGAGAGAGACTAGACCG ?4@@4<<??<?-@4@=4<5<?:/> +1378_157_1580 69 * 0 0 * * 0 0 GGGATTGAAGGGATGTATGCTAGG #%$&%#$$'%$%#$##*#%$$$$# +1378_157_1580 133 * 0 0 * * 0 0 TGGGCCTCGGTGCCCTTGGTCTGT #%)$##'#$$$&#####%#$#$## +1378_161_317 69 * 0 0 * * 0 0 AATCCATACCCACAAAAGCAGGCC .&%','(@''?7//+&)+2.+)0) +1378_161_317 133 * 0 0 * * 0 0 TTGGCCGGCAACCCCGGTACCTAA 7<,<'@)@>.)2@/')'&(?/-<( +1378_177_735 69 * 0 0 * * 0 0 CGAGCCCTAAACCATGAGATCGGA @@B>@AC9@A<B8@=9>7@5)>,0 +1378_177_735 133 * 0 0 * * 0 0 AGTACGCCATGTATTTGCGACCAG =?@?C<88@=>:7>@55/.,416, +1378_181_1684 69 * 0 0 * * 0 0 TTTCTGTTGTGGTTTTGTTGGGGT $##'$%'##%##$%$#$$####$* +1378_181_1684 133 * 0 0 * * 0 0 CGACTCCCGCATTCACGGTCAAGT &*#,##$#&$*$$#$#$$$#%$## +1378_187_1407 69 * 0 0 * * 0 0 TTGGGTGAAATCTTGTCGAGTGGA ####&##$$###$#####%##%%) +1378_187_1407 133 * 0 0 * * 0 0 TGGCGTCCACTCGTGGGTCTATCG $#$'%#$%$%&$%#####$#$#%# +1378_203_721 69 * 0 0 * * 0 0 CCTTTACGATCATAAACCATGACC 9<&./1&@;12')?<1',?/)&/. +1378_203_721 133 * 0 0 * * 0 0 CCTAAATAACCCAGGGTAAAAGAT 9<1+2+1@=259@+;2.71&@+2& +1378_206_2039 69 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC ?=>>?=:;<>>4::<=56199(05 +1378_206_2039 133 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC 9@?8>;>>><<994;=895895-8 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out3.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,2 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M = 322 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out4.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,3 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +081017-and-081020:1:1:1715:1759 113 PHIX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 +081017-and-081020:1:1:1715:1759 177 PHIX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/fastq_conv_out1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_conv_out1.fastqsanger Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759 +GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC ++ +++!+++++++!!!!!"+++++++!!!!)!%!!+!!%! diff -r 692c384c1ca0 -r 19b47949aa8a test-data/fastq_conv_out2.fastqsolexa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_conv_out2.fastqsolexa Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,8 @@ +@1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG ++ +][bEEXXTQJb]T[M^[VXK\SQ[QXQY[GXNLV +@1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ++ +Z__PV^_\]V^^_`W^\\_S`^`SHEJMFEJFPK diff -r 692c384c1ca0 -r 19b47949aa8a test-data/fastq_conv_out4.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_conv_out4.fasta Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,4 @@ +>1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG +>1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_out1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out1.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,576 @@ +@1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG ++ +><C&&9952+C>5<.?<79,=42<292:<(9/-7 +@1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ++ +;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +@1831_573_1067/1 +AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++ +++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +@1831_573_1219/1 +CGCCCTATAATAATACAGCGCGTTAGACCGCTCA ++ +@@=4/+)5)408?'665>*/5?<61';<3,:,5- +@1831_573_1242/1 +GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC ++ +>>::>17=A5?@@=;7A=;2.60>82<8=74+;; +@1831_573_1333/1 +AGAATCGTTACCACACACTGCGTCTGGGTATCCG ++ +='@#%3=.>)/34*117,,/6-4+.9742456<) +@1831_573_1362/1 +CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC ++ +B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +@1831_573_1448/1 +TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG ++ +7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ +@1831_573_1490/1 +CTCGTCATGTTACGCAAAGGCACGTCACAGCACC ++ +@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. +@1831_573_1523/1 +ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ++ +,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +@1831_573_1578/1 +CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ++ +?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +@1831_573_1647/1 +AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT ++ +?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +@1831_573_1684/1 +TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT ++ +>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +@1831_573_1769/1 +TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC ++ +54749&&767%/7;3$-7;3#,3//#,45/#&06 +@1831_573_1853/1 +CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC ++ +4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +@1831_573_1943/1 +ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC ++ +>/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +@1831_573_1977/1 +GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC ++ +@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +@1831_574_109/1 +TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT ++ +7651#4817>@65<2:84716=788<1995.7?6 +@1831_574_148/1 +CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC ++ +;->3;;3>//>0;;7=,=4-4/+>029<9<624; +@1831_574_185/1 +CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC ++ +<4;%%@7>#*>97%6;+8$#<07%1372$%<54# +@1831_574_243/1 +AGGCACCGTAACTCAGGACATTCTCGATTAGTTA ++ +@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 +@1831_574_257/1 +ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC ++ +>>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +@1831_574_293/1 +TGCTGCAAATAAACATACAGCCTTCTAATGACTA ++ +')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +@1831_574_389/1 +CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA ++ +)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +@1831_574_575/1 +TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG ++ +?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< +@1831_574_592/1 +TCATTTACCACGTCAGGGTCGGAGTCATTCATTA ++ +3-5)19,,<@>4067<2.-864346;9<1/;212 +@1831_574_617/1 +AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC ++ +>@?;>?=@==@>@=5?@+@:@40@><:0)')64- +@1831_574_725/1 +GACAAGATGGCTATTATTTACAATCCGATCTGCA ++ +'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +@1831_574_734/1 +CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG ++ +-&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 +@1831_574_824/1 +AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT ++ +@@@;;),+@<-<7;<&89??&29?<$2:A<);8? +@1831_574_959/1 +CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC ++ +A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +@1831_574_1062/1 +ACCGGTAATATAAGGCAACATGATTACGGCCACG ++ +@821<//:136/8<1/5.427.;>288/0<1$)/ +@1831_574_1092/1 +GACTGGCGAAATCATCGCGGAAAAACCCCTATCA ++ +8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +@1831_574_1103/1 +ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ++ +??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +@1831_574_1116/1 +CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC ++ +(a)++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +@1831_574_1194/1 +TTATCACATTTGGGGATCGGAAGGGACTACTTCG ++ +5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 +@1831_574_1204/1 +CTTACTGGTCTGCTGGACATATAGTGGCGATGAA ++ +A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* +@1831_574_1306/1 +ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA ++ +2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +@1831_574_1387/1 +GTACTTCTCAATGCTGCACTACTATGTACGCCCC ++ +?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +@1831_574_1431/1 +GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC ++ +7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +@1831_574_1560/1 +GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ++ +))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +@1831_574_1591/1 +TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG ++ +=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 +@1831_574_1624/1 +ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG ++ +<6.&(,7-+))7..'/;43.)927.(<85&13-) +@1831_574_1826/1 +TACGTCGCGACCGAGCGTTATATAGTCTGACCCC ++ +@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +@1831_574_1903/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ +@1831_574_1961/1 +GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA ++ +>-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 +@1831_575_54/1 +TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA ++ +=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 +@1831_575_80/1 +TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ++ +?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +@1831_575_192/1 +AACTACGCCCCTTAATTACACAGCGCGTTAGACC ++ +:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +@1831_575_197/1 +TTCGCCTACACTTAGATACCTCTTAAACTCAATG ++ +-:?463@A:88?6?437<=.2&1.;@67.4@%2, +@1831_575_223/1 +ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ++ +?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +@1831_575_420/1 +CCCACATGGAAAACACTCACCGCCGAACAGAGCG ++ +2?.>?(-''2+..@),$%1@;')1)?+)7.').. +@1831_575_434/1 +ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC ++ +@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +@1831_575_444/1 +TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA ++ +2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> +@1831_575_459/1 +CTTATCAGCACACGGTTTACCAGTCCGACTCCAA ++ +@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +@1831_575_506/1 +CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ++ +?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +@1831_575_569/1 +AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT ++ +'9-,@29+479%&>9#&08=>7#9>,69/+'*3) +@1831_575_622/1 +CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC ++ +A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ +@1831_575_644/1 +CTTGAATGGCGATCTCGTCGAGGAAATACCACTA ++ +<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +@1831_575_663/1 +GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA ++ +@@@@A</;A>@6>0792<5966:?;25+:><1,+ +@1831_575_681/1 +TCTCCTGATTAGACATATCACTGTTGAACACAGC ++ +72?.)25;96-14'*.03'#4#++$)/8+%/((& +@1831_575_711/1 +TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC ++ +%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +@1831_575_730/1 +CACACAGGAACCATAGCGTATGTTATTCACCCCC ++ +%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +@1831_575_904/1 +ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC ++ +<><.689@@7@<54:4=@>69=:+6-=42;8<:# +@1831_575_938/1 +TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA ++ +:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 +@1831_575_970/1 +TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC ++ +@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 +@1831_575_991/1 +TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA ++ +>>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +@1831_575_1138/1 +TTGAAAGACCTGAACGCGATTTCATGTTTACTGC ++ +=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 +@1831_575_1157/1 +TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC ++ +B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 +@1831_575_1180/1 +GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA ++ +<B>5?':/78?;1;55:997@@>94=7<186->7 +@1831_575_1283/1 +GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT ++ +C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +@1831_575_1302/1 +CGACTATTCGTTTCGTCTAGAACGTGACACTAGC ++ +12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* +@1831_575_1310/1 +CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT ++ +<<>663?99@(@7=11@:@@/7??<@<;>'3-7; +@1831_575_1321/1 +CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG ++ +;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 +@1831_575_1373/1 +CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA ++ +@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< +@1831_575_1419/1 +TGGGGAATATAACAGCGTAGCGTTGAACACTAGA ++ +//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +@1831_575_1436/1 +TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC ++ +2@=;39*3<*4<:>52>>9'7:<='0=>1'136< +@1831_575_1442/1 +TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG ++ +>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> +@1831_575_1454/1 +CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT ++ +4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +@1831_575_1500/1 +CACAAAAGGTCCCTACCTGTCTACCCTACATAGC ++ +?@@?A@?8<6<:985=99999==B3<5<<,7?>9 +@1831_575_1535/1 +CTCGACGATATGACCGCCAGCCACTTAACTCCGC ++ +B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< +@1831_575_1724/1 +TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA ++ +<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +@1831_575_1829/1 +CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC ++ +2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +@1831_575_1898/1 +CTTACCATATCATCTCAACCCATAACAGCACTTA ++ +B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +@1831_575_1964/1 +GACAGACCATGAGGCTGAAGACTACTAAGTGCGT ++ +>39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +@1831_576_32/1 +TACGCAACGATTTATGGCCTTATAATTGAGGCCA ++ +<>?>?=7<2)522;><<@40@>704<>5=23@+& +@1831_576_74/1 +ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA ++ +=@@?@>(??<B5?@@@9<@><+><;@';>6961? +@1831_576_86/1 +ATGAAAACGCATTAGGACAACCATAATGGCCTCA ++ +811)2:*.++5</:3+43924*))/:,6&29)2/ +@1831_576_89/1 +GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA ++ +)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +@1831_576_266/1 +ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT ++ +@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 +@1831_576_327/1 +GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA ++ +@?@6@@;<@?><@>==3@:==<3@@>53<9><6= +@1831_576_331/1 +GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA ++ +-2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +@1831_576_387/1 +ACACGCCATGATCCGATAAGAAGGGAACGTAAGG ++ +8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +@1831_576_406/1 +AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC ++ +4<>%%14:*4656)&<251&2+3#&19,6&4>5( +@1831_576_449/1 +CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA ++ ++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +@1831_576_519/1 +TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC ++ +=46<97@>2/6?;2<4A881>9121+<1/4.9+7 +@1831_576_603/1 +CAATATGTCTTAGTCGTGACTCGGCAACTTATCC ++ +@46=@C.??<A79@@;-<@@>29B?>55<B7598 +@1831_576_655/1 +GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG ++ +@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +@1831_576_677/1 +TTTACTCAGTTGATACATCACTGTAGCACATAGG ++ +290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +@1831_576_718/1 +CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT ++ +4###$0###%(#########,####%####$### +@1831_576_722/1 +CGTATGATGGCGAGTCTTTATAATCCAATCTGAA ++ +*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +@1831_576_754/1 +AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA ++ +4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +@1831_576_815/1 +TAGGCCTGATATGACACGATCACAGTGCAACATC ++ +3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +@1831_576_882/1 +TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG ++ +26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +@1831_576_898/1 +AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT ++ +@@C2?C>?<>@886B?;?.??87=B<8<15??=. +@1831_576_923/1 +CTGGACATGAGAGACTGCACGCGGTACACGTCGG ++ +6.51=;.699<96>;;49<;;11;<@59:9=647 +@1831_576_930/1 +CTGGCATGTACGTCCATGTCAGACGAGCAGAACT ++ +#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +@1831_576_1019/1 +GATGCGCGCTGTCATGGCATCGAACCATCGGTCG ++ +<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +@1831_576_1068/1 +AAGAGTGACTCACTTACCGGGATGCGATGGAGCC ++ +>><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +@1831_576_1131/1 +AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA ++ +04@#@/@,4>9?2+?1571@',>=;(759;*92< +@1831_576_1168/1 +CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA ++ +@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +@1831_576_1207/1 +CAACCTGACTAAACGGGGATACGCTGGCGCTACA ++ +$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +@1831_576_1289/1 +TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT ++ +9<>1B@@;7@@663==28,5':8<<,.=2>>.50 +@1831_576_1329/1 +CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA ++ +>&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +@1831_576_1367/1 +GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT ++ +?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 +@1831_576_1416/1 +TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC ++ +';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ +@1831_576_1461/1 +GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA ++ +1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +@1831_576_1605/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +<@C@@>1;@:;<<@@9@???9<3?5-21=4877, +@1831_576_1664/1 +CGCGCACAACTCGCCATGATACGACAAGACCCGA ++ +@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +@1831_576_1671/1 +GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT ++ +@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +@1831_576_1729/1 +CGTTTCGTCTACAACGTGACACTAGCACAGTATA ++ +?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> +@1831_576_1880/1 +TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT ++ +515/792,:,7/%/05,%$):+#8%2(1754))3 +@1831_576_1982/1 +AATGTCGTCAGACGACTTTGGCGCGAAAACCATA ++ +@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +@1831_576_1987/1 +AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ++ +##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +@1831_576_2014/1 +CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT ++ +@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +@1831_576_2028/1 +ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA ++ +<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +@1831_577_40/1 +CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT ++ +2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 +@1831_577_119/1 +TCCCACAAGCCATTGACATGCTCGCTCTAAACAG ++ +>?C11)-1/)#;#/,850*+.+$$5550+%-.40 +@1831_577_133/1 +TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG ++ +4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +@1831_577_255/1 +ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG ++ +<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +@1831_577_281/1 +TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA ++ +-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +@1831_577_288/1 +CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA ++ +;/79??&=B::298*6.7/+4&21,7,6?.7#'6 +@1831_577_322/1 +GAATGCTGGAGTACATTATGACAAACTATCGGAG ++ +=;>4506;255464-<#7+194&2<?65968)7/ +@1831_577_362/1 +CGATTAGTTACCACTCGTATTCGCACGCCCAGGA ++ +2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +@1831_577_382/1 +GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA ++ +2957/:1))=76(*24;,3+:<.&.&-=1=2/5* +@1831_577_464/1 +TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG ++ +=<7/<826)>#.'&4204+5#/041.7*91&756 +@1831_577_488/1 +TGAATAGTTATGGCCAGAATGTCTGCACCGATAC ++ +48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +@1831_577_511/1 +GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT ++ +7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +@1831_577_545/1 +ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT ++ +><<9?<>?A<481@<@8==@76/61<95.5988- +@1831_577_559/1 +GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG ++ +<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' +@1831_577_562/1 +GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ++ +((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +@1831_577_637/1 +GCCTTCGCGGGAGCATATCAGTCGATACATCCCA ++ +-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +@1831_577_641/1 +TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT ++ +47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +@1831_577_692/1 +CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA ++ +B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out2.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/2 +GTTCGTGGCCGGTGGGTGTTTGGG ++ +###$$#$#$&#####$'$#$###$ +@1378_17_1788/2 +TGGGTGGATGTGTTGTCGTTCATG ++ +#$#$###$#$#######$#$#### +@1378_25_2035/2 +GTGCGTCGGGGAGGGTGCTGTCGG ++ +######%#$%#$$###($###&&% +@1378_28_770/2 +GGTTGGGAGTTGGCGCGCGTGGTT ++ +###$##%%$####%#%$#%%#($$ +@1378_33_1945/2 +GGGGGGGGGGGGGGGGGGGGGGGG ++ +.6;?;55697>8779457986264 +@1378_34_789/2 +GGGCTTGCGTTAGTGAGAGGTTGT ++ +###%$%$%%###$####$###$#& +@1378_35_263/2 +GGCGGGGGGGGGGGGGGGGGGGGG ++ +$%%&,)3/)%$-6'$&5&#$''5. +@1378_43_186/2 +GCTAGGGTTTGGGTTTGCGGTGGG ++ +$%#$########%##%#$###'#' +@1378_51_1671/2 +GGTGTTGTTCGGATGTAGCGTGGG ++ +##%$$####$########$##0## +@1378_56_324/2 +GCTGGGTGATCTAAGGAATGTAAT ++ +#$#####$$$#$$$$##%###*(# +@1378_56_773/2 +TCTGGTCGGTTTCGGGGAGTGGAA ++ +##%%#&$###$#$##%$####%%$ +@1378_62_2027/2 +GTTGGCCTGGCCTGCCGTGCTGCG ++ +*##),/%##$)#%##1$#'%.#&# +@1378_62_2029/2 +GGCGGTGTGTGGTGCGGCTGTGCG ++ +/$$$=(####%####)$$%$-&%# +@1378_67_1795/2 +CGTGCCAACGACCGTCCTACGGAG ++ +@@.?7@@@.@:@A<<>>=>70<@7 +@1378_68_466/2 +GTGTCATCTGAGGTAAAGCATTGT ++ +/##$09#$#.=$#$76+$%1'### +@1378_68_1692/2 +TGTTCGATTTAGGTCTTGCCTCGC ++ +###%%$%%##%$#$##$###$$#$ +@1378_80_664/2 +TGTCTGCGTTGTATCTCTGGTGTA ++ +%##%,%$$#&$$###$#$%##'%# +@1378_85_1786/2 +CCCTAGGAGCGTATACCGGACGAG ++ +,'&/%/@,&1,&'/)&,6&&1)(( +@1378_86_1011/2 +AGGCGATGGGATATTATTTTACTT ++ +:$###)%##$9$###1$$#$2### +@1378_86_1789/2 +GGCCAGGTACTAATAAATTCAACA ++ +1.51/&%#'$,*?%#6&0$$5,20 +@1378_91_1596/2 +GCTTTTTCATTCGGTGCCTTTGGA ++ +'>%/3%=()8'#.%?50$&5>%)% +@1378_94_1595/2 +GCGGGTTAACCCAGTACCTCTGGC ++ +,8@6'>8<76>@@(->9)7'*941 +@1378_95_1039/2 +GTTCTGTGCCAGGTGAGGTACGGA ++ +&##,./#$&)6##+,'#$$0(##$ +@1378_95_1767/2 +CTAATTGACCGGGCAAGCTATTAA ++ +',,2'(10/>:=/7).3&%6&)&6 +@1378_96_1037/2 +CTGCTGGGCCATTTGACTTACTCA ++ +'$#+#(##-%5##+*&###-.$$$ +@1378_96_1764/2 +TCTTTGTAACCCACTTAGTATTTC ++ +4='28>.@4881B807:822>%)1 +@1378_98_1574/2 +AGGCGAGTGTGGGGGTTGTTTGAG ++ ++%%$#)##%##$####%###$%$# +@1378_107_1647/2 +GGTCTGGTTCTATGTTGGTCGACT ++ +###'$$#$$$(#%###(#$##$%# +@1378_111_829/2 +GGTCTTCTATGGTGCTAAATTAGT ++ +$##'&###$##)#%($#$%#$'%# +@1378_111_1900/2 +GCACGCCTTTGGGCTAAGCCGTAA ++ +)$)'#%$########$'#&%$#(# +@1378_112_1483/2 +TGGAGTGGTGTGTTTGCTGAGCCA ++ +#$#)#############$#%#%'% +@1378_125_1287/2 +TGACGTGGGTTGTCCCGTGAGATT ++ +##$%%#$###$##$$#&%##$(%% +@1378_126_468/2 +AAAAAACGGGCCGGGCGGACTAGG ++ +@@B@@@>@2>1+?:92)>@8&&<+ +@1378_127_664/2 +TCGCTTTGCCTATGTTTGTTCGGA ++ +#%$%#&##$%#%%###$$###)-' +@1378_129_463/2 +AAAAAAAAAAAAAAAAAAAAAAAA ++ +,)&20%8'(&35-***1-2&+510 +@1378_129_875/2 +GACCTTTACGTATTGGGGGTTGGC ++ +###)###+###$##$#&%##$,#$ +@1378_140_1251/2 +TTTCCTTCGTGTGCGTGCGGAGTG ++ +#%#%$##$$$######.$$$%#%( +@1378_141_809/2 +TCTCGTGGTTTCTTTTTTATGTGT ++ +##%)##$$#####%$#$#%%#'## +@1378_144_983/2 +GTTCGTTCGTGGTGTACGAGGGTG ++ +#(#%#####($#%##$$#%##%#) +@1378_153_270/2 +GGCCGTGTGCGGGTGTAGATTGGA ++ +%$##($######&##$&$$$$%## +@1378_155_1689/2 +CGCGTTCGGACAAAGCTAGCACCT ++ +@4@@=6=@@<4:@@681@@@.24. +@1378_157_1580/2 +GGGATTGAAGGGATGTATGCTAGG ++ +#%$&%#$$'%$%#$##*#%$$$$# +@1378_161_317/2 +AATCCATACCCACAAAAGCAGGCC ++ +.&%','(@''?7//+&)+2.+)0) +@1378_177_735/2 +CGAGCCCTAAACCATGAGATCGGA ++ +@@B>@AC9@A<B8@=9>7@5)>,0 +@1378_181_1684/2 +TTTCTGTTGTGGTTTTGTTGGGGT ++ +$##'$%'##%##$%$#$$####$* +@1378_187_1407/2 +TTGGGTGAAATCTTGTCGAGTGGA ++ +####&##$$###$#####%##%%) +@1378_203_721/2 +CCTTTACGATCATAAACCATGACC ++ +9<&./1&@;12')?<1',?/)&/. +@1378_206_2039/2 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +?=>>?=:;<>>4::<=56199(05 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_out3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out3.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/1 +AGACCGGGCGGGGTGGCGTTCGGT ++ +%##+'#######%###$#$##$(# +@1378_17_1788/1 +TGCCGTGTCTTGCTAACGCCGATT ++ +#'#$$#$###%%##$$$$###### +@1378_25_2035/1 +CTGCGTGTTGGTGTCTACTGGGGT ++ +#%#'##$#$##&%#%$$$%#%#'# +@1378_28_770/1 +CTGCTATGCCGGCCGCCTGCCCCT ++ +%##(#$$#%$#$%###$%%$##$# +@1378_33_1945/1 +GGGGGGGGGGGGGGGGGGGGGGGG ++ ++9;64287788752796/576352 +@1378_34_789/1 +ATGGTGGCTGACGCGTTTGACTGT ++ +#$##%#$##$&$#%##$##$###$ +@1378_35_263/1 +GGGCGGGGGGCGGCGGGGGGGGGG ++ +),,#%'$)'-(%&%'%',%%&&(& +@1378_43_186/1 +ATACTAGTTGGGACGCGTTGTGCT ++ +#$(4%$########$#$###$$$# +@1378_51_1671/1 +TGGGTAGGTGCGGCTCTTGCGGTC ++ +##$#$%###%%#%#$##$$##### +@1378_56_324/1 +AGGCTTGGATTGTTGCGCTGACCT ++ +/+#**###%%##%#####$$$#$# +@1378_56_773/1 +TGTCGTGAGGTCACTTATCCCCAT ++ +&%#%##%%#####&#$%##$%##$ +@1378_62_2027/1 +CTTCCACGATCTGCTCGCTGTGGT ++ +(#&&$##$$#$%#%$$$#$###'# +@1378_62_2029/1 +TCTGGGCTGTCTTCGGGTCGGTGT ++ +$%$$####$##$$#)##%%#$### +@1378_67_1795/1 +TAGTGGGCTAGTCCGGGATCTACC ++ +B@C2@@?;-@@1>'A@@91@.@1' +@1378_68_466/1 +GTGATCGTCGGTGCCAGTCCCTGT ++ +#(%)+##$#$#%#+$%##$##### +@1378_68_1692/1 +GGTCTTCTGGGCACGGGCCAAGTT ++ +###)%'&%##$###%#######$# +@1378_80_664/1 +CTGCTTTGATCCCCGGTGGAGCAC ++ +7#%###$$6#######$##$$$## +@1378_85_1786/1 +ATACTATGTCGATCTGTAAAAAAA ++ +)&.)#3%(a)$&%-,2#&+.-%0&./ +@1378_86_1011/1 +CTACGTTATTGCTCTGTTTGTCCT ++ +######$%##$$$%###%#$#### +@1378_86_1789/1 +CGAATATCCCCTGGTTTAGAAGTA ++ +61?1;@/>@<=/(.7'(<5@=%$= +@1378_91_1596/1 +TTAGCGGTTGACTATCTGCTGACA ++ +*&+'#9'(%*'#//,&<),/)'*# +@1378_94_1595/1 +CGTGCGACAGCCCATGTTTTCAGA ++ +-=..5,3826&*+.+#+#%%6;%# +@1378_95_1039/1 +CGGCGTCCATCTTCGCCTTGAGAT ++ +$##.#$##$$#%$#$%%$###$)$ +@1378_95_1767/1 +ACACGCACCATCTGGCGGCTAACC ++ +86<65<4<C27/$5+#;-$+#2%$ +@1378_96_1037/1 +ATCCCCCAAGATGCCTGTTGATTG ++ +$#$'##$$$#%$$#%###+##$#$ +@1378_96_1764/1 +TACACCGGAACCTTGCACTAAAGC ++ +6-9'<#+81?+*<8-=69&6;*3) +@1378_98_1574/1 +GTTCTGCCGGTGTCTGTGGCGGGC ++ +$$#+&$$####%$$$###$%#%%# +@1378_107_1647/1 +AGGCCTACTACGCGTCATTGATAG ++ +&#$$#$(.#%#$$####&$%##($ +@1378_111_829/1 +TGCGGCACTTGCTTCTTCGTATTT ++ +%#%##%#$%#$#%###$$##&#$$ +@1378_111_1900/1 +TCCCCTCGCTCGGCTCTGTGCTGT ++ +$&%*$#(#)##$#'##%(##$#$% +@1378_112_1483/1 +TGTCCAGCTATGCGGCTTCCTCCT ++ +%#$+#%#&#$#####%####%$## +@1378_125_1287/1 +TGTCTCTGGGGGGCCTGGTTAGGT ++ +$##13$'%#$###$$###$$$#&# +@1378_126_468/1 +TCTCCTGATTAGACATATCTCCGT ++ +7>@318?=,=8@49579?..7,7) +@1378_127_664/1 +AGAGGTTGGTGTCTTGTCGCAGCT ++ +##'#$######$$%######$$$# +@1378_129_463/1 +CCTGTGGGCCAAGCCCAATGAAAG ++ +8),,<6(--)<()5&.&/8+;.2+ +@1378_129_875/1 +TTTCTATGGCTTACGCTGTCTGCC ++ +#$($##%####%$#$#####$### +@1378_140_1251/1 +ATCCTAGCGCGGTGTCTTGGGGAC ++ +#$%1#$$$##$##$#$#$##$%$$ +@1378_141_809/1 +TGTCCTCCAGTGTCTGTTGGGTGT ++ +%&,-##$$#(%###$#$$'###'# +@1378_144_983/1 +AGCGCCCGGTTGGTGCGGCTCGTC ++ +-$(&%*$#*#))#$$$#%%$#$## +@1378_153_270/1 +AGTCCTTGTCCCCTGGGTTTTCCC ++ ++''$#&%$%#$##&$$($#&#$$# +@1378_155_1689/1 +TTGGGAGGGAGAGAGACTAGACCG ++ +?4@@4<<??<?-@4@=4<5<?:/> +@1378_157_1580/1 +TGGGCCTCGGTGCCCTTGGTCTGT ++ +#%)$##'#$$$&#####%#$#$## +@1378_161_317/1 +TTGGCCGGCAACCCCGGTACCTAA ++ +7<,<'@)@>.)2@/')'&(?/-<( +@1378_177_735/1 +AGTACGCCATGTATTTGCGACCAG ++ +=?@?C<88@=>:7>@55/.,416, +@1378_181_1684/1 +CGACTCCCGCATTCACGGTCAAGT ++ +&*#,##$#&$*$$#$#$$$#%$## +@1378_187_1407/1 +TGGCGTCCACTCGTGGGTCTATCG ++ +$#$'%#$%$%&$%#####$#$#%# +@1378_203_721/1 +CCTAAATAACCCAGGGTAAAAGAT ++ +9<1+2+1@=259@+;2.71&@+2& +@1378_206_2039/1 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +9@?8>;>>><<994;=895895-8 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_paired_F3.csfasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_paired_F3.csfasta Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,99 @@ +# Fri Jan 23 21:37:16 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/0176/0176_20090114_1/skmusc_cov_25/results.01/primary.20090124033450140 --name=0176_20090114_1_skmusc_cov_25_ --tag=F3 --minlength=25 --mask=1111111111111111111111111 --prefix=T /data/results/0176/0176_20090114_1/skmusc_cov_25/jobs/postPrimerSetPrimary.1708/rawseq +# Cwd: /home/pipeline +# Title: 0176_20090114_1_skmusc_cov_25_ +>1378_11_329_F3 +T0020112221222232212331223 +>1378_17_1788_F3 +T0321123231332130012112033 +>1378_25_2035_F3 +T0132123233223231301322223 +>1378_28_770_F3 +T0132130321122112113211113 +>1378_33_1945_F3 +T2222222222222222222222222 +>1378_34_789_F3 +T0032232213201212333201323 +>1378_35_263_F3 +T0222122222212212222222222 +>1378_43_186_F3 +T0030130233222012123323213 +>1378_51_1671_F3 +T0322230223212213133212231 +>1378_56_324_F3 +T0022133220332332121320113 +>1378_56_773_F3 +T2323123202231013303111103 +>1378_62_2027_F3 +T0133110120313213121323223 +>1378_62_2029_F3 +T0313222132313312223122323 +>1378_67_1795_F3 +T0302322213023112220313011 +>1378_68_466_F3 +T0232031231223211023111323 +>1378_68_1692_F3 +T0223133132221012221100233 +>1378_80_664_F3 +T2132133320311112232202101 +>1378_85_1786_F3 +T0030130323120313230000000 +>1378_86_1011_F3 +T0130123303321313233323113 +>1378_86_1789_F3 +T0120030311113223330200230 +>1378_91_1596_F3 +T3330212233201303132132010 +>1378_94_1595_F3 +T2123212010211103233331020 +>1378_95_1039_F3 +T0122123110313312113320203 +>1378_95_1767_F3 +T2010121011031322122130011 +>1378_96_1037_F3 +T0031111100203211323320332 +>1378_96_1764_F3 +T0301011220011332101300021 +>1378_98_1574_F3 +T0233132112232313232212221 +>1378_107_1647_F3 +T0022113013012123103320302 +>1378_111_829_F3 +T0321221013321331331230333 +>1378_111_1900_F3 +T0311113121312213132321323 +>1378_112_1483_F3 +T0323110213032122133113113 +>1378_125_1287_F3 +T0323131322222211322330223 +>1378_126_468_F3 +T2313113203302010303131123 +>1378_127_664_F3 +T0020223322323133231210213 +>1378_129_463_F3 +T3113232221100211100320002 +>1378_129_875_F3 +T0333130322133012132313211 +>1378_140_1251_F3 +T0031130212122323133222201 +>1378_141_809_F3 +T0323113110232313233222323 +>1378_144_983_F3 +T1021211122332232122131231 +>1378_153_270_F3 +T0023113323111132223333111 +>1378_155_1689_F3 +T0332220222020202013020112 +>1378_157_1580_F3 +T3322211312232111332231323 +>1378_161_317_F3 +T1332211221001111223011300 +>1378_177_735_F3 +T1023012110323033321201102 +>1378_181_1684_F3 +T0120131112103310122310023 +>1378_187_1407_F3 +T0322123110131232223130312 +>1378_203_721_F3 +T0113000300111022230000203 +>1378_206_2039_F3 +T1111111111111111111111111 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_paired_F3_QV.qualsolid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_paired_F3_QV.qualsolid Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,99 @@ +# Fri Jan 23 21:37:16 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/0176/0176_20090114_1/skmusc_cov_25/results.01/primary.20090124033450140 --name=0176_20090114_1_skmusc_cov_25_ --tag=F3 --minlength=25 --mask=1111111111111111111111111 --prefix=T /data/results/0176/0176_20090114_1/skmusc_cov_25/jobs/postPrimerSetPrimary.1708/rawseq +# Cwd: /home/pipeline +# Title: 0176_20090114_1_skmusc_cov_25_ +>1378_11_329_F3 +7 4 2 2 10 6 2 2 2 2 2 2 2 4 2 2 2 3 2 3 2 2 3 7 2 +>1378_17_1788_F3 +6 2 6 2 3 3 2 3 2 2 2 4 4 2 2 3 3 3 3 2 2 2 2 2 2 +>1378_25_2035_F3 +9 2 4 2 6 2 2 3 2 3 2 2 5 4 2 4 3 3 3 4 2 4 2 6 2 +>1378_28_770_F3 +2 4 2 2 7 2 3 3 2 4 3 2 3 4 2 2 2 3 4 4 3 2 2 3 2 +>1378_33_1945_F3 +18 10 24 26 21 19 17 23 22 22 23 23 22 20 17 22 24 21 14 20 22 21 18 20 17 +>1378_34_789_F3 +2 2 3 2 2 4 2 3 2 2 3 5 3 2 4 2 2 3 2 2 3 2 2 2 3 +>1378_35_263_F3 +3 8 11 11 2 4 6 3 8 6 12 7 4 5 4 6 4 6 11 4 4 5 5 7 5 +>1378_43_186_F3 +2 2 3 7 19 4 3 2 2 2 2 2 2 2 2 3 2 3 2 2 2 3 3 3 2 +>1378_51_1671_F3 +2 2 2 3 2 3 4 2 2 2 4 4 2 4 2 3 2 2 3 3 2 2 2 2 2 +>1378_56_324_F3 +3 14 10 2 9 9 2 2 2 4 4 2 2 4 2 2 2 2 2 3 3 3 2 3 2 +>1378_56_773_F3 +9 5 4 2 4 2 2 4 4 2 2 2 2 2 5 2 3 4 2 2 3 4 2 2 3 +>1378_62_2027_F3 +9 7 2 5 5 3 2 2 3 3 2 3 4 2 4 3 3 3 2 3 2 2 2 6 2 +>1378_62_2029_F3 +4 3 4 3 3 2 2 2 2 3 2 2 3 3 2 8 2 2 4 4 2 3 2 2 2 +>1378_67_1795_F3 +33 33 31 34 17 31 31 30 26 12 31 31 16 29 6 32 31 31 24 16 31 13 31 16 6 +>1378_68_466_F3 +4 2 7 4 8 10 2 2 3 2 3 2 4 2 10 3 4 2 2 3 2 2 2 2 2 +>1378_68_1692_F3 +3 2 2 2 8 4 6 5 4 2 2 3 2 2 2 4 2 2 2 2 2 2 2 3 2 +>1378_80_664_F3 +8 22 2 4 2 2 2 3 3 21 2 2 2 2 2 2 2 3 2 2 3 3 3 2 2 +>1378_85_1786_F3 +6 8 5 13 8 2 18 4 31 3 5 4 12 11 17 2 5 10 13 12 4 15 5 13 14 +>1378_86_1011_F3 +2 2 2 2 2 2 2 3 4 2 2 3 3 3 4 2 2 2 4 2 3 2 2 2 2 +>1378_86_1789_F3 +31 21 16 30 16 26 31 14 29 31 27 28 14 7 13 22 6 7 27 20 31 28 4 3 28 +>1378_91_1596_F3 +4 9 5 10 6 2 24 6 7 4 9 6 2 14 14 11 5 27 8 11 14 8 6 9 2 +>1378_94_1595_F3 +8 12 28 13 13 20 11 18 23 17 21 5 9 10 13 10 2 10 2 4 4 21 26 4 2 +>1378_95_1039_F3 +2 3 2 2 13 2 3 2 2 3 3 2 4 3 2 3 4 4 3 2 2 2 3 8 3 +>1378_95_1767_F3 +12 23 21 27 21 20 27 19 27 34 17 22 14 3 20 10 2 26 12 3 10 2 17 4 3 +>1378_96_1037_F3 +2 3 2 3 6 2 2 3 3 3 2 4 3 3 2 4 2 2 2 10 2 2 3 2 3 +>1378_96_1764_F3 +29 21 12 24 6 27 2 10 23 16 30 10 9 27 23 12 28 21 24 5 21 26 9 18 8 +>1378_98_1574_F3 +2 3 3 2 10 5 3 3 2 2 2 2 4 3 3 3 2 2 2 3 4 2 4 4 2 +>1378_107_1647_F3 +2 5 2 3 3 2 3 7 13 2 4 2 3 3 2 2 2 2 5 3 4 2 2 7 3 +>1378_111_829_F3 +2 4 2 4 2 2 4 2 3 4 2 3 2 4 2 2 2 3 3 2 2 5 2 3 3 +>1378_111_1900_F3 +10 3 5 4 9 3 2 7 2 8 2 2 3 2 6 2 2 4 7 2 2 3 2 3 4 +>1378_112_1483_F3 +9 4 2 3 10 2 4 2 5 2 3 2 2 2 2 2 4 2 2 2 2 4 3 2 2 +>1378_125_1287_F3 +4 3 2 2 16 18 3 6 4 2 3 2 2 2 3 3 2 2 2 3 3 3 2 5 2 +>1378_126_468_F3 +23 22 29 31 18 16 23 30 28 11 28 23 31 19 24 20 22 24 30 13 13 22 11 22 8 +>1378_127_664_F3 +9 2 2 6 2 3 2 2 2 2 2 2 3 3 4 2 2 2 2 2 2 3 3 3 2 +>1378_129_463_F3 +4 23 8 11 11 27 21 7 12 12 8 27 7 8 20 5 13 5 14 23 10 26 13 17 10 +>1378_129_875_F3 +2 2 3 7 3 2 2 4 2 2 2 2 4 3 2 3 2 2 2 2 2 3 2 2 2 +>1378_140_1251_F3 +12 2 3 4 16 2 3 3 3 2 2 3 2 2 3 2 3 2 3 2 2 3 4 3 3 +>1378_141_809_F3 +7 4 5 11 12 2 2 3 3 2 7 4 2 2 2 3 2 3 3 6 2 2 2 6 2 +>1378_144_983_F3 +11 12 3 7 5 4 9 3 2 9 2 8 8 2 3 3 3 2 4 4 3 2 3 2 2 +>1378_153_270_F3 +8 10 6 6 3 2 5 4 3 4 2 3 2 2 5 3 3 7 3 2 5 2 3 3 2 +>1378_155_1689_F3 +31 30 19 31 31 19 27 27 30 30 27 30 12 31 19 31 28 19 27 20 27 30 25 14 29 +>1378_157_1580_F3 +3 2 4 8 3 2 2 6 2 3 3 3 5 2 2 2 2 2 4 2 3 2 3 2 2 +>1378_161_317_F3 +8 22 27 11 27 6 31 8 31 29 13 8 17 31 14 6 8 6 5 7 30 14 12 27 7 +>1378_177_735_F3 +31 28 30 31 30 34 27 23 23 31 28 29 25 22 29 31 20 20 14 13 11 19 16 21 11 +>1378_181_1684_F3 +13 5 9 2 11 2 2 3 2 5 3 9 3 3 2 3 2 3 3 3 2 4 3 2 2 +>1378_187_1407_F3 +2 3 2 3 6 4 2 3 4 3 4 5 3 4 2 2 2 2 2 3 2 3 2 4 2 +>1378_203_721_F3 +33 24 27 16 10 17 10 16 31 28 17 20 24 31 10 26 17 13 22 16 5 31 10 17 5 +>1378_206_2039_F3 +26 24 31 30 23 29 26 29 29 29 27 27 24 24 19 26 28 23 24 20 23 24 20 12 23 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_paired_R3.csfasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_paired_R3.csfasta Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,99 @@ +# Mon Jan 19 06:35:55 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/0176/0176_20090114_1/skmusc_cov_25/results.01/primary.20090119120505312 --name=0176_20090114_1_skmusc_cov_25_ --tag=R3 --minlength=25 --mask=1111111111111111111111111 --prefix=G /data/results/0176/0176_20090114_1/skmusc_cov_25/jobs/postPrimerSetPrimary.1512/rawseq +# Cwd: /home/pipeline +# Title: 0176_20090114_1_skmusc_cov_25_ +>1378_11_329_R3 +G2233123221122322232333222 +>1378_17_1788_R3 +G3322232203232332312331032 +>1378_25_2035_R3 +G2232123122220222321323122 +>1378_28_770_R3 +G2223322202332212121232233 +>1378_33_1945_R3 +G2222222222222222222222222 +>1378_34_789_R3 +G3222133212330232020223323 +>1378_35_263_R3 +G2221222222222222222222222 +>1378_43_186_R3 +G3213022233322233321223222 +>1378_51_1671_R3 +G2223233233122032302123222 +>1378_56_324_R3 +G3213222320313002200323003 +>1378_56_773_R3 +G1313223122333122220232200 +>1378_62_2027_R3 +G2233221132211321123213212 +>1378_62_2029_R3 +G2221223232322321221323212 +>1378_67_1795_R3 +G1123211001201123113012202 +>1378_68_466_R3 +G1232310313202230002103323 +>1378_68_1692_R3 +G3323312033302231332113121 +>1378_80_664_R3 +G2323132123323031313223230 +>1378_85_1786_R3 +G3111302202123030112201202 +>1378_86_1011_R3

1 0

[hg] galaxy 2529: Use z-index:-1 instead of previous methods
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5003b7d10ff5 changeset: 2529:5003b7d10ff5 user: Kanwei Li <kanwei(a)gmail.com> date: Mon Aug 03 17:35:44 2009 -0400 description: Use z-index:-1 instead of previous methods 1 file(s) affected in this change: templates/base_panels.mako diffs (12 lines): diff -r 4ca7f95f854a -r 5003b7d10ff5 templates/base_panels.mako --- a/templates/base_panels.mako Mon Aug 03 17:23:52 2009 -0400 +++ b/templates/base_panels.mako Mon Aug 03 17:35:44 2009 -0400 @@ -125,7 +125,7 @@ </a> </div> - <div style="position: absolute; left: 200px; width: 60%; text-align: center"> + <div style="z-index: -1; position: absolute; left: 0px; width: 100%; text-align: center"> <table class="tab-group" border="0" cellspacing="0" style="margin: auto;"> <tr>

1 0

[hg] galaxy 2524: Tweaks to grids to make it easier to override ...
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5438f8d0a211 changeset: 2524:5438f8d0a211 user: James Taylor <james(a)jamestaylor.org> date: Mon Aug 03 17:14:12 2009 -0400 description: Tweaks to grids to make it easier to override query generation (backward compatible). 3 file(s) affected in this change: lib/galaxy/web/controllers/history.py lib/galaxy/web/framework/helpers/grids.py templates/history/grid.mako diffs (135 lines): diff -r 0431855a9ff4 -r 5438f8d0a211 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Aug 03 16:58:22 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Mon Aug 03 17:14:12 2009 -0400 @@ -13,7 +13,31 @@ # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" + class HistoryListGrid( grids.Grid ): + # Custom column types + class DatasetsByStateColumn( grids.GridColumn ): + def get_value( self, trans, grid, history ): + rval = [] + for state in ( 'ok', 'running', 'queued', 'error' ): + total = sum( 1 for d in history.active_datasets if d.state == state ) + if total: + rval.append( '<div class="count-box state-color-%s">%s</div>' % ( state, total ) ) + else: + rval.append( '' ) + return rval + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, history ): + if history.deleted: + return "deleted" + elif history.users_shared_with: + return "shared" + return "" + def get_link( self, trans, grid, item ): + if item.users_shared_with: + return dict( operation="sharing", id=item.id ) + return None + # Grid definition title = "Stored histories" model_class = model.History default_sort_key = "-create_time" @@ -21,12 +45,8 @@ grids.GridColumn( "Name", key="name", link=( lambda item: iff( item.deleted, None, dict( operation="switch", id=item.id ) ) ), attach_popup=True ), - grids.GridColumn( "Datasets (by state)", method='_build_datasets_by_state', ncells=4 ), - grids.GridColumn( "Status", method='_build_status', - link=( lambda item: iff( item.users_shared_with, - dict( operation="sharing", id=item.id ), - None ) ), - attach_popup=False ), + DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), + StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Age", key="create_time", format=time_ago ), grids.GridColumn( "Last update", key="update_time", format=time_ago ), # Valid for filtering but invisible @@ -49,21 +69,6 @@ return trans.get_history() def apply_default_filter( self, trans, query ): return query.filter_by( user=trans.user, purged=False ) - def _build_datasets_by_state( self, trans, history ): - rval = [] - for state in ( 'ok', 'running', 'queued', 'error' ): - total = sum( 1 for d in history.active_datasets if d.state == state ) - if total: - rval.append( '<div class="count-box state-color-%s">%s</div>' % ( state, total ) ) - else: - rval.append( '' ) - return rval - def _build_status( self, trans, history ): - if history.deleted: - return "deleted" - elif history.users_shared_with: - return "shared" - return "" class HistoryController( BaseController ): diff -r 0431855a9ff4 -r 5438f8d0a211 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Aug 03 16:58:22 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Aug 03 17:14:12 2009 -0400 @@ -40,16 +40,9 @@ if column.key: if "f-" + column.key in kwargs: column_filter = kwargs.get( "f-" + column.key ) - if column_filter == "True": - filter_args[column.key] = True - elif column_filter == "False": - filter_args[column.key] = False - elif column_filter == "All": - del filter_args[column.key] + query = column.filter( query, column_filter, filter_args ) # Carry filter along to newly generated urls extra_url_args[ "f-" + column.key ] = column_filter - if filter_args: - query = query.filter_by( **filter_args ) # Process sort arguments sort_key = sort_order = None if 'sort' in kwargs: @@ -143,6 +136,26 @@ if self.format: value = self.format( value ) return value + def get_link( self, trans, grid, item ): + if self.link and self.link( item ): + return self.link( item ) + return None + def filter( self, query, column_filter, filter_args ): + """ + Must modify filter_args for carrying forward, and return query + (possibly filtered). + """ + if column_filter == "True": + filter_args[self.key] = True + query = query.filter_by( **{ self.key: True } ) + elif column_filter == "False": + filter_args[self.key] = False + query = query.filter_by( **{ self.key: False } ) + elif column_filter == "All": + del filter_args[self.key] + return query + + class GridOperation( object ): def __init__( self, label, key=None, condition=None, allow_multiple=True ): diff -r 0431855a9ff4 -r 5438f8d0a211 templates/history/grid.mako --- a/templates/history/grid.mako Mon Aug 03 16:58:22 2009 -0400 +++ b/templates/history/grid.mako Mon Aug 03 17:14:12 2009 -0400 @@ -137,8 +137,9 @@ %if column.visible: <% # Link - if column.link and column.link( item ): - href = url( **column.link( item ) ) + link = column.get_link( trans, grid, item ) + if link: + href = url( **link ) else: href = None # Value (coerced to list so we can loop)

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[hg] galaxy 2525: Typos in cron/README.txt
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8dcf04f31def changeset: 2525:8dcf04f31def user: Kanwei Li <kanwei(a)gmail.com> date: Mon Aug 03 13:25:47 2009 -0400 description: Typos in cron/README.txt 1 file(s) affected in this change: cron/README.txt diffs (13 lines): diff -r aabcc797c1da -r 8dcf04f31def cron/README.txt --- a/cron/README.txt Thu Jul 30 16:23:47 2009 -0400 +++ b/cron/README.txt Mon Aug 03 13:25:47 2009 -0400 @@ -9,7 +9,7 @@ two things. First, updateucsc.sh must be edited to point towards the root galaxy directory. At the top of the file there is a variable "GALAXY" that should be edited. Second, the updates come from UCSC -via their table browsers. While the tendancy is typically to run crob +via their table browsers. While the tendency is typically to run cron jobs late at night, UCSC, like most, tend to take down their servers at odd hours for maintenance. The update scripts for UCSC are not CPU -intensive, and should be scheduled durring normal hours. +intensive, and should be scheduled during normal hours.

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[hg] galaxy 2526: Fixed CSS issue that was causing logo to becom...
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/692c384c1ca0 changeset: 2526:692c384c1ca0 user: Kanwei Li <kanwei(a)gmail.com> date: Mon Aug 03 16:07:36 2009 -0400 description: Fixed CSS issue that was causing logo to become unclickable 1 file(s) affected in this change: templates/base_panels.mako diffs (23 lines): diff -r 8dcf04f31def -r 692c384c1ca0 templates/base_panels.mako --- a/templates/base_panels.mako Mon Aug 03 13:25:47 2009 -0400 +++ b/templates/base_panels.mako Mon Aug 03 16:07:36 2009 -0400 @@ -116,16 +116,16 @@ <%def name="masthead()"> <div class="title" style="float: left;"> - <a target="_blank" href="${app.config.wiki_url}"> + <a href="/"> <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> - </a> Galaxy %if app.config.brand: <span class='brand'>/${app.config.brand}</span> %endif + </a> </div> - <div style="position: absolute; left: 0; width: 100%; text-align: center;"> + <div style="position: absolute; left: 200px; width: 500px;"> <table class="tab-group" border="0" cellspacing="0" style="margin: auto;"> <tr>

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[hg] galaxy 2519: Enhance data_source.py to take advantage of th...
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a7ba71cade35 changeset: 2519:a7ba71cade35 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Aug 03 12:02:54 2009 -0400 description: Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is greater than config.output_size_limit, no data will be retrieved and an error message will be provided to the user. Tools using this script have been updated to provide the max file size on the command line. Resolves ticket #93. 15 file(s) affected in this change: lib/galaxy/jobs/__init__.py tools/data_source/biomart.xml tools/data_source/biomart_test.xml tools/data_source/data_source.py tools/data_source/epigraph_import.xml tools/data_source/epigraph_import_test.xml tools/data_source/eupathdb.xml tools/data_source/flymine.xml tools/data_source/flymine_test.xml tools/data_source/gramene_mart.xml tools/data_source/ucsc_tablebrowser.xml tools/data_source/ucsc_tablebrowser_archaea.xml tools/data_source/ucsc_tablebrowser_test.xml tools/data_source/wormbase.xml tools/data_source/wormbase_test.xml diffs (193 lines): diff -r 07dffb2735dd -r a7ba71cade35 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri Jul 31 12:01:02 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Mon Aug 03 12:02:54 2009 -0400 @@ -595,7 +595,7 @@ self.real_path = real_path self.false_path = false_path def __str__( self ): - if false_path is None: + if self.false_path is None: return self.real_path else: return self.false_path diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/biomart.xml --- a/tools/data_source/biomart.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/biomart.xml Mon Aug 03 12:02:54 2009 -0400 @@ -9,7 +9,7 @@ --> <tool name="BioMart" id="biomart" tool_type="data_source" URL_method="get" version="1.0.1"> <description>Central server</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top"> <display>go to BioMart Central $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/biomart_test.xml --- a/tools/data_source/biomart_test.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/biomart_test.xml Mon Aug 03 12:02:54 2009 -0400 @@ -9,7 +9,7 @@ --> <tool name="BioMart" id="biomart_test" tool_type="data_source" URL_method="get" version="1.0.1"> <description>Test server</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://test.biomart.org/biomart/martview" check_values="false" method="get" target="_top"> <display>go to BioMart Central $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/data_source.py --- a/tools/data_source/data_source.py Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/data_source.py Mon Aug 03 12:02:54 2009 -0400 @@ -21,6 +21,10 @@ def __main__(): filename = sys.argv[1] + try: + max_file_size = int( sys.argv[2] ) + except: + max_file_size = 0 params = {} for line in open( filename, 'r' ): try: @@ -50,6 +54,10 @@ page = urllib.urlopen( URL, urllib.urlencode( params ) ) except Exception, e: stop_err( 'The remote data source application may be off line, please try again later. Error: %s' % str( e ) ) + if max_file_size: + file_size = int( page.info().get( 'Content-Length', 0 ) ) + if file_size > max_file_size: + stop_err( 'The size of the data (%d bytes) you have requested exceeds the maximum allowed (%d bytes) on this server.' % ( file_size, max_file_size ) ) out = open( filename, 'w' ) while 1: chunk = page.read( CHUNK_SIZE ) diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/epigraph_import.xml --- a/tools/data_source/epigraph_import.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/epigraph_import.xml Mon Aug 03 12:02:54 2009 -0400 @@ -6,7 +6,7 @@ --> <tool name="EpiGRAPH" id="epigraph_import" tool_type="data_source" URL_method="get"> <description> server</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://epigraph.mpi-inf.mpg.de/WebGRAPH/faces/Login.jsp" check_values="false" method="get"> <display>go to EpiGRAPH server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/epigraph_import_test.xml --- a/tools/data_source/epigraph_import_test.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/epigraph_import_test.xml Mon Aug 03 12:02:54 2009 -0400 @@ -6,7 +6,7 @@ --> <tool name="EpiGRAPH" id="epigraph_import_test" tool_type="data_source" URL_method="get"> <description> test server</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://epigraph.mpi-inf.mpg.de/WebGRAPH_Public_Test/faces/Login.jsp" check_values="false" method="get"> <display>go to EpiGRAPH server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import_test" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/eupathdb.xml --- a/tools/data_source/eupathdb.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/eupathdb.xml Mon Aug 03 12:02:54 2009 -0400 @@ -5,7 +5,7 @@ --> <tool name="EuPathDB" id="eupathdb" tool_type="data_source" url_method="post"> <description>server</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://galaxy.eupathdb.org/eupathdb.galaxy/queries_tools.jsp" check_values="false" method="post"> <display>go to EuPathDB server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=eupathdb" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/flymine.xml --- a/tools/data_source/flymine.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/flymine.xml Mon Aug 03 12:02:54 2009 -0400 @@ -6,7 +6,7 @@ --> <tool name="Flymine" id="flymine" tool_type="data_source" URL_method="post"> <description>server</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://www.flymine.org" check_values="false" method="get" target="_top"> <display>go to Flymine server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/flymine_test.xml --- a/tools/data_source/flymine_test.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/flymine_test.xml Mon Aug 03 12:02:54 2009 -0400 @@ -6,7 +6,7 @@ --> <tool name="Flymine test" id="flymine_test" tool_type="data_source" URL_method="post"> <description>server</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get" target="_top"> <display>go to Flymine server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/gramene_mart.xml --- a/tools/data_source/gramene_mart.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/gramene_mart.xml Mon Aug 03 12:02:54 2009 -0400 @@ -9,7 +9,7 @@ --> <tool name="GrameneMart" id="gramenemart" tool_type="data_source" URL_method="get" version="1.0.1"> <description> Central server</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://www.gramene.org/biomart/martview" check_values="false" method="get" target="_top"> <display>go to GrameneMart Central $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/ucsc_tablebrowser.xml --- a/tools/data_source/ucsc_tablebrowser.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/ucsc_tablebrowser.xml Mon Aug 03 12:02:54 2009 -0400 @@ -6,7 +6,7 @@ --> <tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source" URL_method="post"> <description>table browser</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> <display>go to UCSC Table Browser $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/ucsc_tablebrowser_archaea.xml --- a/tools/data_source/ucsc_tablebrowser_archaea.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/ucsc_tablebrowser_archaea.xml Mon Aug 03 12:02:54 2009 -0400 @@ -6,7 +6,7 @@ --> <tool name="UCSC Archaea" id="ucsc_table_direct_archaea1" tool_type="data_source" URL_method="post"> <description>table browser</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://archaea.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> <display>go to UCSC Table Browser $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/ucsc_tablebrowser_test.xml --- a/tools/data_source/ucsc_tablebrowser_test.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/ucsc_tablebrowser_test.xml Mon Aug 03 12:02:54 2009 -0400 @@ -6,7 +6,7 @@ --> <tool name="UCSC Test" id="ucsc_table_direct_test1" tool_type="data_source" URL_method="post"> <description>table browser</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://genome-test.cse.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> <display>go to UCSC Table Browser $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/wormbase.xml --- a/tools/data_source/wormbase.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/wormbase.xml Mon Aug 03 12:02:54 2009 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool name="Wormbase" id="wormbase" tool_type="data_source" URL_method="post"> <description>server</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://www.wormbase.org/db/seq/gbgff/c_elegans/" check_values="false" target="_top"> <display>go to Wormbase server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase" /> diff -r 07dffb2735dd -r a7ba71cade35 tools/data_source/wormbase_test.xml --- a/tools/data_source/wormbase_test.xml Fri Jul 31 12:01:02 2009 -0400 +++ b/tools/data_source/wormbase_test.xml Mon Aug 03 12:02:54 2009 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool name="Wormbase" id="wormbase_test" tool_type="data_source" URL_method="post"> <description>test server</description> - <command interpreter="python">data_source.py $output</command> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" target="_top"> <display>go to Wormbase test server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase_test" />

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[hg] galaxy 2521: Fix megablast wrapper never cleaning up tempfi...
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a961e11898af changeset: 2521:a961e11898af user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Aug 03 16:23:37 2009 -0400 description: Fix megablast wrapper never cleaning up tempfiles. 1 file(s) affected in this change: tools/metag_tools/megablast_wrapper.py diffs (19 lines): diff -r 7cf7b078f890 -r a961e11898af tools/metag_tools/megablast_wrapper.py --- a/tools/metag_tools/megablast_wrapper.py Mon Aug 03 15:45:26 2009 -0400 +++ b/tools/metag_tools/megablast_wrapper.py Mon Aug 03 16:23:37 2009 -0400 @@ -81,6 +81,8 @@ output.write( "%s\n" % new_line ) output.close() + os.unlink( mega_temp_output ) #remove the tempfile that we just reformated the contents of + if invalid_lines: print "Unable to parse %d lines. Keep the default format." % invalid_lines @@ -91,4 +93,4 @@ print line os.remove( './error.log' ) -if __name__ == "__main__" : __main__() \ No newline at end of file +if __name__ == "__main__" : __main__()

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