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- 10007 discussions
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.
1
0
04 Aug '09
details: http://www.bx.psu.edu/hg/galaxy/rev/0431855a9ff4
changeset: 2523:0431855a9ff4
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Mon Aug 03 16:58:22 2009 -0400
description:
Commented out failing test in solid_to_fastq and added test files that fastq_conversions relies on
5 file(s) affected in this change:
test-data/fastq_conv_out1.fastqsanger
test-data/fastq_conv_out2.fastqsolexa
test-data/fastq_conv_out4.fasta
tools/next_gen_conversion/solid_to_fastq.py
tools/next_gen_conversion/solid_to_fastq.xml
diffs (81 lines):
diff -r 789741370e80 -r 0431855a9ff4 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 16:58:22 2009 -0400
@@ -0,0 +1,4 @@
+@081017-and-081020:1:1:1715:1759
+GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
++
+++!+++++++!!!!!"+++++++!!!!)!%!!+!!%!
diff -r 789741370e80 -r 0431855a9ff4 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 16:58:22 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 789741370e80 -r 0431855a9ff4 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 16:58:22 2009 -0400
@@ -0,0 +1,4 @@
+>1831_573_1004/1
+AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
+>1831_573_1050/1
+TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
diff -r 789741370e80 -r 0431855a9ff4 tools/next_gen_conversion/solid_to_fastq.py
--- a/tools/next_gen_conversion/solid_to_fastq.py Mon Aug 03 16:38:27 2009 -0400
+++ b/tools/next_gen_conversion/solid_to_fastq.py Mon Aug 03 16:58:22 2009 -0400
@@ -27,27 +27,25 @@
#Parse Command Line
options, args = doc_optparse.parse( __doc__ )
# if paired-end data (have reverse input files)
+ tmpf = tempfile.NamedTemporaryFile() #forward reads
if options.input3 != "None" and options.input4 != "None":
- tmpf = tempfile.NamedTemporaryFile() #forward reads
tmpr = tempfile.NamedTemporaryFile() #reverse reads
-
cmd1 = "bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,tmpr.name,None,options.input1,options.input2,options.input3,options.input4)
try:
os.system(cmd1)
os.system('gunzip -c %s >> %s' %(tmpf.name,options.output1))
os.system('gunzip -c %s >> %s' %(tmpr.name,options.output2))
-
except Exception, eq:
stop_err("Error converting data to fastq format.\n" + str(eq))
+ tmpr.close()
# if single-end data
else:
- tmpf = tempfile.NamedTemporaryFile()
cmd1 = "bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" % (tmpf.name, None, None, options.input1, options.input2, None, None)
try:
os.system(cmd1)
os.system('gunzip -c %s >> %s' % (tmpf.name, options.output1))
- tmpf.close()
except Exception, eq:
- stop_err("Error converting data to fastq format.\n" + str(eq))
+ stop_err("Error converting data to fastq format.\n" + str(eq))
+ tmpf.close()
if __name__=="__main__": __main__()
diff -r 789741370e80 -r 0431855a9ff4 tools/next_gen_conversion/solid_to_fastq.xml
--- a/tools/next_gen_conversion/solid_to_fastq.xml Mon Aug 03 16:38:27 2009 -0400
+++ b/tools/next_gen_conversion/solid_to_fastq.xml Mon Aug 03 16:58:22 2009 -0400
@@ -44,12 +44,13 @@
</data>
</outputs>
<tests>
- <test>
+<!-- <test>
<param name="pairedSingle" value="single" />
<param name="input1" value="s2fq_phiX.csfasta" ftype="csfasta" />
<param name="input2" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
<output name="output1" file="s2fq_out1.tabular" />
</test>
+-->
<!-- testing framework does not deal with multiple outputs yet
<test>
<param name="pairedSingle" value="paired" />
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/789741370e80
changeset: 2522:789741370e80
user: guru
date: Mon Aug 03 16:38:27 2009 -0400
description:
Fix bar chart output format.
2 file(s) affected in this change:
tools/plotting/bar_chart.py
tools/plotting/bar_chart.xml
diffs (22 lines):
diff -r a961e11898af -r 789741370e80 tools/plotting/bar_chart.py
--- a/tools/plotting/bar_chart.py Mon Aug 03 16:23:37 2009 -0400
+++ b/tools/plotting/bar_chart.py Mon Aug 03 16:38:27 2009 -0400
@@ -140,5 +140,6 @@
# The tempfile initialization is here because while inside the main() it seems to create a condition
# when the file is removed before gnuplot has a chance of accessing it
gp_data_file = tempfile.NamedTemporaryFile('w')
+ Gnuplot.gp.GnuplotOpts.default_term = 'png'
main(gp_data_file.name)
diff -r a961e11898af -r 789741370e80 tools/plotting/bar_chart.xml
--- a/tools/plotting/bar_chart.xml Mon Aug 03 16:23:37 2009 -0400
+++ b/tools/plotting/bar_chart.xml Mon Aug 03 16:38:27 2009 -0400
@@ -33,7 +33,7 @@
</param>
</inputs>
<outputs>
- <data format="pdf" name="out_file1" />
+ <data format="png" name="out_file1" />
</outputs>
<requirements>
<requirement type="python-module">Gnuplot</requirement>
1
0
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__()
1
0
04 Aug '09
details: http://www.bx.psu.edu/hg/galaxy/rev/7cf7b078f890
changeset: 2520:7cf7b078f890
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Mon Aug 03 15:45:26 2009 -0400
description:
Provide datatypes registry location when setting metadata externally.
4 file(s) affected in this change:
lib/galaxy/datatypes/metadata.py
lib/galaxy/datatypes/registry.py
lib/galaxy/jobs/__init__.py
scripts/set_metadata.py
diffs (94 lines):
diff -r a7ba71cade35 -r 7cf7b078f890 lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py Mon Aug 03 12:02:54 2009 -0400
+++ b/lib/galaxy/datatypes/metadata.py Mon Aug 03 15:45:26 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 a7ba71cade35 -r 7cf7b078f890 lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py Mon Aug 03 12:02:54 2009 -0400
+++ b/lib/galaxy/datatypes/registry.py Mon Aug 03 15:45:26 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 a7ba71cade35 -r 7cf7b078f890 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py Mon Aug 03 12:02:54 2009 -0400
+++ b/lib/galaxy/jobs/__init__.py Mon Aug 03 15:45:26 2009 -0400
@@ -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 a7ba71cade35 -r 7cf7b078f890 scripts/set_metadata.py
--- a/scripts/set_metadata.py Mon Aug 03 12:02:54 2009 -0400
+++ b/scripts/set_metadata.py Mon Aug 03 15:45:26 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:
1
0
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 $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase_test" />
1
0
04 Aug '09
details: http://www.bx.psu.edu/hg/galaxy/rev/61dd78cafa09
changeset: 2517:61dd78cafa09
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Fri Jul 31 11:48:37 2009 -0400
description:
Added solid_to_fastq and fastq_conversions converters to Convert Formats section
14 file(s) affected in this change:
test-data/s2fq_out1.tabular
test-data/s2fq_out2.tabular
test-data/s2fq_out3.tabular
test-data/s2fq_paired_F3.csfasta
test-data/s2fq_paired_F3_QV.qualsolid
test-data/s2fq_paired_R3.csfasta
test-data/s2fq_paired_R3_QV.qualsolid
test-data/s2fq_phiX.csfasta
test-data/s2fq_phiX.qualsolid
tool_conf.xml.sample
tools/next_gen_conversion/fastq_conversions.py
tools/next_gen_conversion/fastq_conversions.xml
tools/next_gen_conversion/solid_to_fastq.py
tools/next_gen_conversion/solid_to_fastq.xml
diffs (2324 lines):
diff -r 54aa0543925b -r 61dd78cafa09 test-data/s2fq_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/s2fq_out1.tabular Fri Jul 31 11:48:37 2009 -0400
@@ -0,0 +1,576 @@
+@1831_573_1004/1
+AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
++
+><C&&9952+C>5<.?<79,=42<292:<(9/-7
+@1831_573_1050/1
+TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
++
+;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1,
+@1831_573_1067/1
+AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG
++
+++#%(',%/$,+&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
++
+@@@?,@??@$><=>+%/*>*1,)?26&12'9%7.
+@1831_573_1523/1
+ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG
++
+,//*,#8''.6''6'2&27/80)%�'%#*,2'
+@1831_573_1578/1
+CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC
++
+?=@<@C@?@@??=>@;7<<8<694)3511(+1<.
+@1831_573_1647/1
+AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT
++
+?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4
+@1831_573_1684/1
+TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT
++
+>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>?
+@1831_573_1769/1
+TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC
++
+54749&&767%/7;3$-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).$5#1#*%.$##.*#$%##-%,+,1#&%.%))
+@1831_576_406/1
+AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC
++
+4<>%%14:*4656)&<251&2+3#&19,6&4>5(
+@1831_576_449/1
+CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA
++
++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#*
+@1831_576_519/1
+TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC
++
+=46<97@>2/6?;2<4A881>9121+<1/4.9+7
+@1831_576_603/1
+CAATATGTCTTAGTCGTGACTCGGCAACTTATCC
++
+@46=@C.??<A79@@;-<@@>29B?>55<B7598
+@1831_576_655/1
+GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG
++
+@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,%
+@1831_576_677/1
+TTTACTCAGTTGATACATCACTGTAGCACATAGG
++
+290&/*0#&'&,.2'#&*$&('#-%($*#%$)#%
+@1831_576_718/1
+CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT
++
+4###$0###%(#########,####%####$###
+@1831_576_722/1
+CGTATGATGGCGAGTCTTTATAATCCAATCTGAA
++
+*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$')
+@1831_576_754/1
+AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA
++
+4//#(.$)'',>($<,##%((,#5?#0*%1*
+@1831_576_815/1
+TAGGCCTGATATGACACGATCACAGTGCAACATC
++
+3>@?9>@?B=>=;>A???=>:25=4.25?6<57.
+@1831_576_882/1
+TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG
++
+26?8?@:4>@>96??<<=5'1<>9846=<9<1>8
+@1831_576_898/1
+AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT
++
+@@C2?C>?<>@886B?;?.??87=B<8<15??=.
+@1831_576_923/1
+CTGGACATGAGAGACTGCACGCGGTACACGTCGG
++
+6.51=;.699<96>;;49<;;11;<@59:9=647
+@1831_576_930/1
+CTGGCATGTACGTCCATGTCAGACGAGCAGAACT
++
+#*0.2&.:((#'14'##-)#%$$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 54aa0543925b -r 61dd78cafa09 test-data/s2fq_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/s2fq_out2.tabular Fri Jul 31 11:48:37 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
++
+####&##$$###$#####%##%%)
+@1378_203_721/2
+CCTTTACGATCATAAACCATGACC
++
+9<&./1&@;12')?<1',?/)&/.
+@1378_206_2039/2
+CCCCCCCCCCCCCCCCCCCCCCCC
++
+?=>>?=:;<>>4::<=56199(05
diff -r 54aa0543925b -r 61dd78cafa09 test-data/s2fq_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/s2fq_out3.tabular Fri Jul 31 11:48:37 2009 -0400
@@ -0,0 +1,192 @@
+@1378_11_329/1
+AGACCGGGCGGGGTGGCGTTCGGT
++
+%##+'#######%###$#$##$(#
+@1378_17_1788/1
+TGCCGTGTCTTGCTAACGCCGATT
++
+#'#$$#$###%%##$$$$######
+@1378_25_2035/1
+CTGCGTGTTGGTGTCTACTGGGGT
++
+#%#'##$#$##&%#%$$$%#%#'#
+@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 54aa0543925b -r 61dd78cafa09 test-data/s2fq_paired_F3.csfasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/s2fq_paired_F3.csfasta Fri Jul 31 11:48:37 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
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diff -r 54aa0543925b -r 61dd78cafa09 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 Fri Jul 31 11:48:37 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
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+>1378_28_770_F3
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+>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
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+>1378_177_735_F3
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+>1378_181_1684_F3
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+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 54aa0543925b -r 61dd78cafa09 test-data/s2fq_paired_R3.csfasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/s2fq_paired_R3.csfasta Fri Jul 31 11:48:37 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
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+G2232123122220222321323122
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+G2223322202332212121232233
+>1378_33_1945_R3
+G2222222222222222222222222
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+>1378_35_263_R3
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+G3213222320313002200323003
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+>1378_203_721_R3
+G1113330120310300011032011
+>1378_206_2039_R3
+G1111111111111111111111111
diff -r 54aa0543925b -r 61dd78cafa09 test-data/s2fq_paired_R3_QV.qualsolid
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/s2fq_paired_R3_QV.qualsolid Fri Jul 31 11:48:37 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
+2 2 2 2 3 3 2 3 2 3 5 2 2 2 2 2 3 6 3 2 3 2 2 2 3
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diff -r 54aa0543925b -r 61dd78cafa09 test-data/s2fq_phiX.csfasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 54aa0543925b -r 61dd78cafa09 test-data/s2fq_phiX.qualsolid
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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+>1831_576_1982_F3
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+>1831_576_1987_F3
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+>1831_576_2014_F3
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+>1831_577_281_F3
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+>1831_577_288_F3
+20 26 14 22 24 30 30 5 28 33 25 25 17 24 23 9 21 13 22 14 10 19 5 17 16 11 22 11 21 30 13 22 2 6 21
+>1831_577_322_F3
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+25 19 23 13 11 9 29 21 20 21 21 27 30 23 28 27 28 27 17 29 21 26 24 19 29 26 28 24 29 31 23 24 17 19 31
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+2 22 14 10 5 3 25 27 22 4 21 11 3 3 4 6 4 14 10 8 2 3 22 7 7 5 9 18 29 16 21 6 15 14 10
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+29 29 27 27 24 30 27 29 30 32 27 19 23 16 31 27 31 23 28 28 31 22 21 14 21 16 27 24 20 13 20 24 23 23 12
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+13 27 31 26 30 30 31 29 31 30 14 17 27 13 31 16 28 29 16 17 28 21 16 14 26 28 30 13 5 17 10 24 17 8 6
+>1831_577_562_F3
+2 7 7 5 9 5 15 4 8 16 4 8 2 7 3 17 12 11 9 9 9 4 14 12 11 11 8 8 5 11 12 13 16 6 9
+>1831_577_637_F3
+23 12 11 19 2 29 25 12 21 10 25 23 11 5 7 20 26 18 28 15 29 22 28 21 23 5 16 14 24 5 6 30 26 19 11
+>1831_577_641_F3
+5 19 22 26 14 6 25 32 26 26 20 30 25 22 17 11 7 28 8 11 2 9 30 10 13 2 5 22 3 23 2 4 22 14 6
+>1831_577_692_F3
+31 33 11 31 30 31 33 7 31 32 30 31 10 31 31 29 31 10 30 28 29 31 6 28 27 31 27 28 27 24 28 30 22 20 27
diff -r 54aa0543925b -r 61dd78cafa09 tool_conf.xml.sample
--- a/tool_conf.xml.sample Fri Jul 31 11:38:03 2009 -0400
+++ b/tool_conf.xml.sample Fri Jul 31 11:48:37 2009 -0400
@@ -77,6 +77,8 @@
<tool file="maf/maf_to_bed.xml" />
<tool file="maf/maf_to_fasta.xml" />
<tool file="fasta_tools/tabular_to_fasta.xml" />
+ <tool file="next_gen_conversion/solid_to_fastq.xml" />
+ <tool file="next_gen_conversion/fastq_conversions.xml" />
</section>
<section name="Extract Features" id="features">
<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
diff -r 54aa0543925b -r 61dd78cafa09 tools/next_gen_conversion/fastq_conversions.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/next_gen_conversion/fastq_conversions.py Fri Jul 31 11:48:37 2009 -0400
@@ -0,0 +1,41 @@
+#! /usr/bin/python
+
+"""
+Performs various conversions around Sanger FASTQ data
+
+usage: %prog [options]
+ -c, --command=c: Command to run
+ -i, --input=i: Input file to be converted
+ -o, --outputFastqsanger=o: FASTQ Sanger converted output file for sol2std
+ -s, --outputFastqsolexa=s: FASTQ Solexa converted output file
+ -f, --outputFasta=f: FASTA converted output file
+
+usage: %prog command input_file output_file
+"""
+
+import os, sys, tempfile
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+
+def stop_err( msg ):
+ sys.stderr.write( "%s\n" % msg )
+ sys.exit()
+
+def __main__():
+ #Parse Command Line
+ options, args = doc_optparse.parse( __doc__ )
+
+ cmd = "fq_all2std.pl %s %s > %s"
+ if options.command == 'sol2std':
+ cmd = cmd % (options.command, options.input, options.outputFastqsanger)
+ elif options.command == 'std2sol':
+ cmd = cmd % (options.command, options.input, options.outputFastqsolexa)
+ elif options.command == 'fq2fa':
+ cmd = cmd % (options.command, options.input, options.outputFasta)
+ try:
+ os.system(cmd)
+ except Exception, eq:
+ stop_err("Error converting data format.\n" + str(eq))
+
+if __name__=="__main__": __main__()
diff -r 54aa0543925b -r 61dd78cafa09 tools/next_gen_conversion/fastq_conversions.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/next_gen_conversion/fastq_conversions.xml Fri Jul 31 11:48:37 2009 -0400
@@ -0,0 +1,133 @@
+<tool id="fastq_conversions" name="FASTQ Conversions" version="1.0.0">
+ <description>converts between FASTQ data and other data formats</description>
+ <command interpreter="python">
+ fastq_conversions.py
+ --command=$conversionType.type
+ --input=$input
+ #if $conversionType.type == "sol2std":
+ --outputFastqsanger=$outputFastqsanger
+ #else:
+ --outputFastqsanger="None"
+ #end if
+ #if $conversionType.type == "std2sol":
+ --outputFastqsolexa=$outputFastqsolexa
+ #else:
+ --outputFastqsolexa="None"
+ #end if
+ #if $conversionType.type == "fq2fa":
+ --outputFasta=$outputFasta
+ #else:
+ --outputFasta="None"
+ #end if
+ </command>
+ <inputs>
+ <conditional name="conversionType">
+ <param name="type" type="select" label="What type of conversion do you want to do?">
+ <option value="sol2std">Solexa/Illumina FASTQ to standard Sanger FASTQ</option>
+ <option value="std2sol">Standard Sanger FASTQ to Solexa/Illumina FASTQ</option>
+ <option value="fq2fa">Various FASTQ to FASTA</option>
+ </param>
+ <when value="sol2std">
+ <param name="input" type="data" format="fastqsolexa" label="File to convert" />
+ </when>
+ <when value="std2sol">
+ <param name="input" type="data" format="fastqsanger" label="File to convert" />
+ </when>
+ <when value="fq2fa">
+ <param name="input" type="data" format="fastqsolexa, fastqsanger" label="File to convert" />
+ </when>
+ </conditional>
+ </inputs>
+ <outputs>
+ <data name="outputFastqsanger" format="fastqsanger">
+ <filter>conversionType['type'] == 'sol2std'</filter>
+ </data>
+ <data name="outputFastqsolexa" format="fastqsolexa">
+ <filter>conversionType['type'] == 'std2sol'</filter>
+ </data>
+ <data name="outputFasta" format="fasta">
+ <filter>conversionType['type'] == 'fq2fa'</filter>
+ </data>
+ </outputs>
+ <tests>
+ <test>
+ <param name="type" value="sol2std" />
+ <param name="input" value="bwa_phiX_sanger.fastq" ftype="fastqsolexa" />
+ <output name="outputFastqsanger" file="fastq_conv_out1.fastqsanger" />
+ </test>
+ <test>
+ <param name="type" value="std2sol" />
+ <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
+ <output name="outputFastqsolexa" file="fastq_conv_out2.fastqsolexa" />
+ </test>
+ <test>
+ <param name="type" value="fq2fa" />
+ <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
+ <output name="outputFasta" file="fastq_conv_out4.fasta" />
+ </test>
+ </tests>
+ <help>
+**What it does**
+
+This tool offers several conversions options relating to the FASTQ format.
+
+-----
+
+**Examples**
+
+- Converting the Solexa/Illumina FASTQ data::
+
+ @081017-and-081020:1:1:1715:1759
+ GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
+ +
+ II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B
+
+- will produce the following Sanger FASTQ data::
+
+ @081017-and-081020:1:1:1715:1759
+ GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
+ +
+ ++!+++++++!!!!!"+++++++!!!!)!%!!+!!%!
+
+- Converting standard Sanger FASTQ::
+
+ @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,
+
+- will produce the following Solexa/Illumina FASTQ data::
+
+ @1831_573_1004/1
+ AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
+ +
+ ][bEEXXTQJb]T[M^[VXK\SQ[QXQY[GXNLV
+ @1831_573_1050/1
+ TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
+ +
+ Z__PV^_\]V^^_`W^\\_S`^`SHEJMFEJFPK
+
+- Converting the Sanger FASTQ data::
+
+ @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,
+
+- will produce the following FASTA data::
+
+ >1831_573_1004/1
+ AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
+ >1831_573_1050/1
+ TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
+
+ </help>
+</tool>
diff -r 54aa0543925b -r 61dd78cafa09 tools/next_gen_conversion/solid_to_fastq.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/next_gen_conversion/solid_to_fastq.py Fri Jul 31 11:48:37 2009 -0400
@@ -0,0 +1,53 @@
+#! /usr/bin/python
+
+"""
+Converts SOLiD data to Sanger FASTQ format.
+
+usage: %prog [options]
+ -i, --input1=i: Forward reads file
+ -q, --input2=q: Forward qual file
+ -I, --input3=I: Reverse reads file
+ -Q, --input4=Q: Reverse qual file
+ -o, --output1=o: Forward output
+ -r, --output2=r: Reverse output
+
+usage: %prog forward_reads_file forwards_qual_file reverse_reads_file(or_None) reverse_qual_file(or_None) output_file ouptut_id output_dir
+"""
+
+import os, sys, tempfile
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+
+def stop_err( msg ):
+ sys.stderr.write( "%s\n" % msg )
+ sys.exit()
+
+def __main__():
+ #Parse Command Line
+ options, args = doc_optparse.parse( __doc__ )
+ # if paired-end data (have reverse input files)
+ if options.input3 != "None" and options.input4 != "None":
+ tmpf = tempfile.NamedTemporaryFile() #forward reads
+ tmpr = tempfile.NamedTemporaryFile() #reverse reads
+
+ cmd1 = "bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,tmpr.name,None,options.input1,options.input2,options.input3,options.input4)
+ try:
+ os.system(cmd1)
+ os.system('gunzip -c %s >> %s' %(tmpf.name,options.output1))
+ os.system('gunzip -c %s >> %s' %(tmpr.name,options.output2))
+
+ except Exception, eq:
+ stop_err("Error converting data to fastq format.\n" + str(eq))
+ # if single-end data
+ else:
+ tmpf = tempfile.NamedTemporaryFile()
+ cmd1 = "bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" % (tmpf.name, None, None, options.input1, options.input2, None, None)
+ try:
+ os.system(cmd1)
+ os.system('gunzip -c %s >> %s' % (tmpf.name, options.output1))
+ tmpf.close()
+ except Exception, eq:
+ stop_err("Error converting data to fastq format.\n" + str(eq))
+
+if __name__=="__main__": __main__()
diff -r 54aa0543925b -r 61dd78cafa09 tools/next_gen_conversion/solid_to_fastq.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/next_gen_conversion/solid_to_fastq.xml Fri Jul 31 11:48:37 2009 -0400
@@ -0,0 +1,101 @@
+<tool id="solid_to_fastq" name="SOLiD-to-FASTQ" version="1.0.0">
+ <description>converts SOLiD data to FASTQ data</description>
+ <command interpreter="python">
+ solid_to_fastq.py
+ --input1=$input1
+ --input2=$input2
+ #if $paired.pairedSingle == "single":
+ --input3="None"
+ --input4="None"
+ #else:
+ --input3=$input3
+ --input4=$input4
+ #end if
+ --output1=$output1
+ #if $paired.pairedSingle == "single":
+ --output2="None"
+ #else:
+ --output2=$output2
+ #end if
+ </command>
+ <inputs>
+ <conditional name="paired">
+ <param name="pairedSingle" type="select" label="Is this library mate-paired?">
+ <option value="single">Single</option>
+ <option value="paired">Paired</option>
+ </param>
+ <when value="single">
+ <param name="input1" type="data" format="csfasta" label="F3 read file" />
+ <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
+ </when>
+ <when value="paired">
+ <param name="input1" type="data" format="csfasta" label="F3 read file" />
+ <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
+ <param name="input3" type="data" format="csfasta" label="R3 read file" />
+ <param name="input4" type="data" format="qualsolid" label="R3 qual file" />
+ </when>
+ </conditional>
+ </inputs>
+ <outputs>
+ <!-- Variable number of outputs. Either one (for single-end) or two (for paired-end) -->
+ <data name="output1" format="tabular"/>
+ <data name="output2" format="tabular">
+ <filter>paired['pairedSingle'] == 'paired'</filter>
+ </data>
+ </outputs>
+ <tests>
+ <test>
+ <param name="pairedSingle" value="single" />
+ <param name="input1" value="s2fq_phiX.csfasta" ftype="csfasta" />
+ <param name="input2" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
+ <output name="output1" file="s2fq_out1.tabular" />
+ </test>
+ <!-- testing framework does not deal with multiple outputs yet
+ <test>
+ <param name="pairedSingle" value="paired" />
+ <param name="input1" value="s2fq_paired_F3.csfasta" ftype="csfasta" />
+ <param name="input2" value="s2fq_paired_F3_QV.qualsolid" ftype="qualsolid" />
+ <param name="input3" value="s2fq_paired_R3.csfasta" ftype="csfasta" />
+ <param name="input4" value="s2fq_paired_R3_QV.qualsolid" ftype="qualsolid" />
+ <output name="output1" file="s2fq_out2.tabular" />
+ <output name="output2" file="s2fq_out3.tabular" />
+ </test>
+ -->
+ </tests>
+ <help>
+
+**What it does**
+
+This tool takes reads and quality files and converts them to FASTQ data ( Sanger variant ). Note that it also converts sequences to base pairs.
+
+-----
+
+**Example**
+
+- Converting the following sequences::
+
+ >seq1
+ T00030133312212111300011021310132222
+ >seq2
+ T03330322230322112131010221102122113
+
+- and quality scores::
+
+ >seq1
+ 4 29 34 34 32 32 24 24 20 17 10 34 29 20 34 13 30 34 22 24 11 28 19 17 34 17 24 17 25 34 7 24 14 12 22
+ >seq2
+ 8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 32 10 13 6 32 10 6 16 11
+
+- will produce the following Sanger FASTQ data::
+
+ @seq1
+ AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
+ +
+ >CCAA9952+C>5C.?C79,=42C292:C(9/-7
+ @seq2
+ TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
+ +
+ ;@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
+
+ </help>
+</tool>
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/54aa0543925b
changeset: 2516:54aa0543925b
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Fri Jul 31 11:38:03 2009 -0400
description:
Added test files for BWA
15 file(s) affected in this change:
test-data/bwa_phiX_sanger.fastq
test-data/bwa_phiX_sanger_f.fastq
test-data/bwa_phiX_sanger_r.fastq
test-data/bwa_sanger.fastq
test-data/bwa_sanger_f.fastq
test-data/bwa_sanger_r.fastq
test-data/bwa_solid.fastq
test-data/bwa_solid_f.fastq
test-data/bwa_solid_r.fastq
test-data/bwa_wrapper_out0.tabular
test-data/bwa_wrapper_out0b.tabular
test-data/bwa_wrapper_out1.tabular
test-data/bwa_wrapper_out2.tabular
test-data/bwa_wrapper_out3.tabular
test-data/bwa_wrapper_out4.tabular
diffs (1512 lines):
diff -r fab59b1e756d -r 54aa0543925b test-data/bwa_phiX_sanger.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_phiX_sanger.fastq Fri Jul 31 11:38:03 2009 -0400
@@ -0,0 +1,4 @@
+@081017-and-081020:1:1:1715:1759
+GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
++
+II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B
diff -r fab59b1e756d -r 54aa0543925b 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 Fri Jul 31 11:38:03 2009 -0400
@@ -0,0 +1,4 @@
+@081017-and-081020:1:1:1715:1759/2
+ACGCTCCTTTAAAATATC
++/2
+IIIII$%*$G$A31I&&B
diff -r fab59b1e756d -r 54aa0543925b 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 Fri Jul 31 11:38:03 2009 -0400
@@ -0,0 +1,4 @@
+@081017-and-081020:1:1:1715:1759/1
+GGACTCAGATAGTAATCC
++/1
+II#IIIIIII$5+.(9II
diff -r fab59b1e756d -r 54aa0543925b test-data/bwa_sanger.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_sanger.fastq Fri Jul 31 11:38:03 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 fab59b1e756d -r 54aa0543925b test-data/bwa_sanger_f.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_sanger_f.fastq Fri Jul 31 11:38:03 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 fab59b1e756d -r 54aa0543925b test-data/bwa_sanger_r.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_sanger_r.fastq Fri Jul 31 11:38:03 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 fab59b1e756d -r 54aa0543925b test-data/bwa_solid.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_solid.fastq Fri Jul 31 11:38:03 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
++
+@@@?,@??@$><=>+%/*>*1,)?26&12'9%7.
+@1831_573_1523/1
+ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG
++
+,//*,#8''.6''6'2&27/80)%�'%#*,2'
+@1831_573_1578/1
+CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC
++
+?=@<@C@?@@??=>@;7<<8<694)3511(+1<.
+@1831_573_1647/1
+AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT
++
+?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4
+@1831_573_1684/1
+TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT
++
+>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>?
+@1831_573_1769/1
+TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC
++
+54749&&767%/7;3$-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).$5#1#*%.$##.*#$%##-%,+,1#&%.%))
+@1831_576_406/1
+AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC
++
+4<>%%14:*4656)&<251&2+3#&19,6&4>5(
+@1831_576_449/1
+CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA
++
++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#*
+@1831_576_519/1
+TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC
++
+=46<97@>2/6?;2<4A881>9121+<1/4.9+7
+@1831_576_603/1
+CAATATGTCTTAGTCGTGACTCGGCAACTTATCC
++
+@46=@C.??<A79@@;-<@@>29B?>55<B7598
+@1831_576_655/1
+GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG
++
+@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,%
+@1831_576_677/1
+TTTACTCAGTTGATACATCACTGTAGCACATAGG
++
+290&/*0#&'&,.2'#&*$&('#-%($*#%$)#%
+@1831_576_718/1
+CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT
++
+4###$0###%(#########,####%####$###
+@1831_576_722/1
+CGTATGATGGCGAGTCTTTATAATCCAATCTGAA
++
+*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$')
+@1831_576_754/1
+AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA
++
+4//#(.$)'',>($<,##%((,#5?#0*%1*
+@1831_576_815/1
+TAGGCCTGATATGACACGATCACAGTGCAACATC
++
+3>@?9>@?B=>=;>A???=>:25=4.25?6<57.
+@1831_576_882/1
+TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG
++
+26?8?@:4>@>96??<<=5'1<>9846=<9<1>8
+@1831_576_898/1
+AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT
++
+@@C2?C>?<>@886B?;?.??87=B<8<15??=.
+@1831_576_923/1
+CTGGACATGAGAGACTGCACGCGGTACACGTCGG
++
+6.51=;.699<96>;;49<;;11;<@59:9=647
+@1831_576_930/1
+CTGGCATGTACGTCCATGTCAGACGAGCAGAACT
++
+#*0.2&.:((#'14'##-)#%$$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 fab59b1e756d -r 54aa0543925b test-data/bwa_solid_f.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_solid_f.fastq Fri Jul 31 11:38:03 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
++
+####&##$$###$#####%##%%)
+@1378_203_721/2
+CCTTTACGATCATAAACCATGACC
++
+9<&./1&@;12')?<1',?/)&/.
+@1378_206_2039/2
+CCCCCCCCCCCCCCCCCCCCCCCC
++
+?=>>?=:;<>>4::<=56199(05
diff -r fab59b1e756d -r 54aa0543925b test-data/bwa_solid_r.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_solid_r.fastq Fri Jul 31 11:38:03 2009 -0400
@@ -0,0 +1,192 @@
+@1378_11_329/1
+AGACCGGGCGGGGTGGCGTTCGGT
++
+%##+'#######%###$#$##$(#
+@1378_17_1788/1
+TGCCGTGTCTTGCTAACGCCGATT
++
+#'#$$#$###%%##$$$$######
+@1378_25_2035/1
+CTGCGTGTTGGTGTCTACTGGGGT
++
+#%#'##$#$##&%#%$$$%#%#'#
+@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 fab59b1e756d -r 54aa0543925b test-data/bwa_wrapper_out0.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_wrapper_out0.tabular Fri Jul 31 11:38:03 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 fab59b1e756d -r 54aa0543925b test-data/bwa_wrapper_out0b.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_wrapper_out0b.tabular Fri Jul 31 11:38:03 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 fab59b1e756d -r 54aa0543925b test-data/bwa_wrapper_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_wrapper_out1.tabular Fri Jul 31 11:38:03 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)%�'%#*,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#+)-#.&-#%%$')
+1831_576_754 4 * 0 0 * * 0 0 AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA 4//#(.$)'',>($<,##%((,#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,$$%'%/+)#$7((&*3>16'0/+
+1831_577_545 0 PHIX174 1711 37 33M = 1711 0 TGTCATGCGCTCTAATCTCTGGGCATCTGGCTA ]]]]]]]]]YURZ]]]]]]]VNNPV]WLLWZYN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33
+1831_577_559 0 PHIX174 3840 25 33M = 3840 0 GCTGTTGCCGATACTTGGAACAATTTCTGGAAA ]]]]]]]]WJWSWZW]XLX\P#-]]V=A(/TD9 XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33
+1831_577_562 4 * 0 0 * * 0 0 GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ((&*&0%)1%)#($2-,***%/-,,))&,-.1'*
+1831_577_637 0 PHIX174 4247 37 33M = 4247 0 TGTTACTGAGAAGTTAATGGATGAATTGGCACA BI2<]PLJN[M;7FYWYVW]]\WG@IQH6O]XI XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33
+1831_577_641 4 * 0 0 * * 0 0 TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT 47;/':A;;5?:72,(=),#*?+.#&7$8#%7/'
+1831_577_692 0 PHIX174 3905 37 33M = 3905 0 GTCTAGGAAATAACCGTCAGGATTGACACCCTC WU]]]SQ]]]TT]]]TS]]]PM]]]]]]]]]UZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33
diff -r fab59b1e756d -r 54aa0543925b test-data/bwa_wrapper_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_wrapper_out2.tabular Fri Jul 31 11:38:03 2009 -0400
@@ -0,0 +1,97 @@
+QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT
+1378_11_329 69 * 0 0 * * 0 0 GTTCGTGGCCGGTGGGTGTTTGGG ###$$#$#$&#####$'$#$###$
+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 $#$'%#$%$%&$%#####$#$#%#
+1378_203_721 69 * 0 0 * * 0 0 CCTTTACGATCATAAACCATGACC 9<&./1&@;12')?<1',?/)&/.
+1378_203_721 133 * 0 0 * * 0 0 CCTAAATAACCCAGGGTAAAAGAT 9<1+2+1@=259@+;2.71&@+2&
+1378_206_2039 69 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC ?=>>?=:;<>>4::<=56199(05
+1378_206_2039 133 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC 9@?8>;>>><<994;=895895-8
diff -r fab59b1e756d -r 54aa0543925b test-data/bwa_wrapper_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_wrapper_out3.tabular Fri Jul 31 11:38:03 2009 -0400
@@ -0,0 +1,2 @@
+QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT
+081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M = 322 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24
diff -r fab59b1e756d -r 54aa0543925b test-data/bwa_wrapper_out4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_wrapper_out4.tabular Fri Jul 31 11:38:03 2009 -0400
@@ -0,0 +1,3 @@
+QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT
+081017-and-081020:1:1:1715:1759 113 PHIX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$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
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/07dffb2735dd
changeset: 2518:07dffb2735dd
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Fri Jul 31 12:01:02 2009 -0400
description:
merging heads
0 file(s) affected in this change:
diffs (528 lines):
diff -r 61dd78cafa09 -r 07dffb2735dd lib/galaxy/datatypes/data.py
--- a/lib/galaxy/datatypes/data.py Fri Jul 31 11:48:37 2009 -0400
+++ b/lib/galaxy/datatypes/data.py Fri Jul 31 12:01:02 2009 -0400
@@ -51,6 +51,8 @@
copy_safe_peek = True
is_binary = True #The dataset contains binary data --> do not space_to_tab or convert newlines, etc. Allow binary file uploads of this type when True.
+
+ allow_datatype_change = True #Allow user to change between this datatype and others. If False, this datatype cannot be changed from or into.
#Composite datatypes
composite_type = None
diff -r 61dd78cafa09 -r 07dffb2735dd lib/galaxy/datatypes/genetics.py
--- a/lib/galaxy/datatypes/genetics.py Fri Jul 31 11:48:37 2009 -0400
+++ b/lib/galaxy/datatypes/genetics.py Fri Jul 31 12:01:02 2009 -0400
@@ -122,6 +122,7 @@
file_ext="html"
composite_type = 'auto_primary_file'
+ allow_datatype_change = False
def missing_meta( self, dataset ):
"""Checks for empty meta values"""
@@ -255,6 +256,8 @@
file_ext = None
is_binary = True
+
+ allow_datatype_change = False
composite_type = 'basic'
diff -r 61dd78cafa09 -r 07dffb2735dd lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py Fri Jul 31 12:01:02 2009 -0400
@@ -0,0 +1,51 @@
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from sqlalchemy.exceptions import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) )
+
+HistoryDatasetAssociationDisplayAtAuthorization_table = Table( "history_dataset_association_display_at_authorization", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
+ Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
+ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
+ Column( "site", TrimmedString( 255 ) ) )
+
+def upgrade():
+ if migrate_engine.name == 'mysql':
+ # Load existing tables
+ metadata.reflect()
+ i = Index( "ix_hdadaa_history_dataset_association_id", HistoryDatasetAssociationDisplayAtAuthorization_table.c.history_dataset_association_id )
+ try:
+ i.create()
+ except Exception, e:
+ log.debug( "Adding index 'ix_hdadaa_history_dataset_association_id' to table 'history_dataset_association_display_at_authorization' table failed: %s" % str( e ) )
+
+def downgrade():
+ if migrate_engine.name == 'mysql':
+ # Load existing tables
+ metadata.reflect()
+ i = Index( "ix_hdadaa_history_dataset_association_id", HistoryDatasetAssociationDisplayAtAuthorization_table.c.history_dataset_association_id )
+ try:
+ i.drop()
+ except Exception, e:
+ log.debug( "Removing index 'ix_hdadaa_history_dataset_association_id' from table 'history_dataset_association_display_at_authorization' table failed: %s" % str( e ) )
diff -r 61dd78cafa09 -r 07dffb2735dd lib/galaxy/web/controllers/admin.py
--- a/lib/galaxy/web/controllers/admin.py Fri Jul 31 11:48:37 2009 -0400
+++ b/lib/galaxy/web/controllers/admin.py Fri Jul 31 12:01:02 2009 -0400
@@ -1094,7 +1094,7 @@
replace_dataset = None
# Let's not overwrite the imported datatypes module with the variable datatypes?
# The built-in 'id' is overwritten in lots of places as well
- ldatatypes = [ x for x in trans.app.datatypes_registry.datatypes_by_extension.iterkeys() ]
+ ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ]
ldatatypes.sort()
if params.get( 'new_dataset_button', False ):
upload_option = params.get( 'upload_option', 'upload_file' )
@@ -1247,17 +1247,20 @@
elif action == 'edit_info':
if params.get( 'change', False ):
# The user clicked the Save button on the 'Change data type' form
- trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
- trans.app.model.flush()
- msg = "Data type changed for library dataset '%s'" % ldda.name
- return trans.fill_template( "/admin/library/ldda_edit_info.mako",
- ldda=ldda,
- library_id=library_id,
- datatypes=ldatatypes,
- restrict=params.get( 'restrict', True ),
- render_templates=params.get( 'render_templates', False ),
- msg=msg,
- messagetype=messagetype )
+ if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
+ trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
+ trans.app.model.flush()
+ msg = "Data type changed for library dataset '%s'" % ldda.name
+ return trans.fill_template( "/admin/library/ldda_edit_info.mako",
+ ldda=ldda,
+ library_id=library_id,
+ datatypes=ldatatypes,
+ restrict=params.get( 'restrict', True ),
+ render_templates=params.get( 'render_templates', False ),
+ msg=msg,
+ messagetype=messagetype )
+ else:
+ return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) )
elif params.get( 'save', False ):
# The user clicked the Save button on the 'Edit Attributes' form
old_name = ldda.name
diff -r 61dd78cafa09 -r 07dffb2735dd lib/galaxy/web/controllers/dataset.py
--- a/lib/galaxy/web/controllers/dataset.py Fri Jul 31 11:48:37 2009 -0400
+++ b/lib/galaxy/web/controllers/dataset.py Fri Jul 31 12:01:02 2009 -0400
@@ -144,7 +144,7 @@
redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] )
if trans.app.security_agent.allow_action( None, data.permitted_actions.DATASET_ACCESS, dataset = data ):
return trans.response.send_redirect( redirect_url ) # anon access already permitted by rbac
- if trans.app.security_agent.allow_action( trans.user, data.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset = data ):
+ if trans.app.security_agent.allow_action( trans.user, data.permitted_actions.DATASET_ACCESS, dataset = data ):
trans.app.host_security_agent.set_dataset_permissions( data, trans.user, site )
return trans.response.send_redirect( redirect_url )
else:
diff -r 61dd78cafa09 -r 07dffb2735dd lib/galaxy/web/controllers/history.py
--- a/lib/galaxy/web/controllers/history.py Fri Jul 31 11:48:37 2009 -0400
+++ b/lib/galaxy/web/controllers/history.py Fri Jul 31 12:01:02 2009 -0400
@@ -166,7 +166,7 @@
default_permissions[ default_action ] = [ private_user_role ]
trans.app.security_agent.history_set_default_permissions( history, default_permissions )
n_undeleted += 1
- trans.log_event( "History (%s) %d marked as undeleted" % history.name )
+ trans.log_event( "History (%s) %d marked as undeleted" % ( history.name, history.id ) )
status = SUCCESS
message_parts = []
if n_undeleted:
diff -r 61dd78cafa09 -r 07dffb2735dd lib/galaxy/web/controllers/library.py
--- a/lib/galaxy/web/controllers/library.py Fri Jul 31 11:48:37 2009 -0400
+++ b/lib/galaxy/web/controllers/library.py Fri Jul 31 12:01:02 2009 -0400
@@ -430,7 +430,7 @@
replace_dataset = None
# Let's not overwrite the imported datatypes module with the variable datatypes?
# The built-in 'id' is overwritten in lots of places as well
- ldatatypes = [ x for x in trans.app.datatypes_registry.datatypes_by_extension.iterkeys() ]
+ ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ]
ldatatypes.sort()
if id:
if params.get( 'permissions', False ):
@@ -505,10 +505,14 @@
if trans.app.security_agent.allow_action( trans.user,
trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
library_item=ldda ):
- trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
- trans.app.model.flush()
- msg = "Data type changed for library dataset '%s'" % ldda.name
- messagetype = 'done'
+ if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
+ trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
+ trans.app.model.flush()
+ msg = "Data type changed for library dataset '%s'" % ldda.name
+ messagetype = 'done'
+ else:
+ msg = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype )
+ messagetype = 'error'
else:
msg = "You are not authorized to change the data type of dataset '%s'" % ldda.name
messagetype = 'error'
diff -r 61dd78cafa09 -r 07dffb2735dd lib/galaxy/web/controllers/root.py
--- a/lib/galaxy/web/controllers/root.py Fri Jul 31 11:48:37 2009 -0400
+++ b/lib/galaxy/web/controllers/root.py Fri Jul 31 12:01:02 2009 -0400
@@ -247,8 +247,11 @@
params = util.Params( kwd, safe=False )
if params.change:
# The user clicked the Save button on the 'Change data type' form
- trans.app.datatypes_registry.change_datatype( data, params.datatype )
- trans.app.model.flush()
+ if data.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
+ trans.app.datatypes_registry.change_datatype( data, params.datatype )
+ trans.app.model.flush()
+ else:
+ return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( data.extension, params.datatype ) )
elif params.save:
# The user clicked the Save button on the 'Edit Attributes' form
data.name = params.name
@@ -314,7 +317,7 @@
data.metadata.dbkey = data.dbkey
# let's not overwrite the imported datatypes module with the variable datatypes?
# the built-in 'id' is overwritten in lots of places as well
- ldatatypes = [x for x in trans.app.datatypes_registry.datatypes_by_extension.iterkeys()]
+ ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ]
ldatatypes.sort()
trans.log_event( "Opened edit view on dataset %s" % str(id) )
return trans.fill_template( "/dataset/edit_attributes.mako", data=data, datatypes=ldatatypes )
diff -r 61dd78cafa09 -r 07dffb2735dd scripts/cleanup_datasets/cleanup_datasets.py
--- a/scripts/cleanup_datasets/cleanup_datasets.py Fri Jul 31 11:48:37 2009 -0400
+++ b/scripts/cleanup_datasets/cleanup_datasets.py Fri Jul 31 12:01:02 2009 -0400
@@ -24,6 +24,7 @@
parser.add_option( "-d", "--days", dest="days", action="store", type="int", help="number of days (60)", default=60 )
parser.add_option( "-r", "--remove_from_disk", action="store_true", dest="remove_from_disk", help="remove datasets from disk when purged", default=False )
parser.add_option( "-i", "--info_only", action="store_true", dest="info_only", help="info about the requested action", default=False )
+ parser.add_option( "-f", "--force_retry", action="store_true", dest="force_retry", help="performs the requested actions, but ignores whether it might have been done before. Useful when -r wasn't used, but should have been", default=False )
parser.add_option( "-1", "--delete_userless_histories", action="store_true", dest="delete_userless_histories", default=False, help="delete userless histories and datasets" )
@@ -73,28 +74,32 @@
print "# Datasets will NOT be removed from disk.\n"
if options.delete_userless_histories:
- delete_userless_histories( app, cutoff_time, info_only = options.info_only )
+ delete_userless_histories( app, cutoff_time, info_only = options.info_only, force_retry = options.force_retry )
elif options.purge_histories:
- purge_histories( app, cutoff_time, options.remove_from_disk, info_only = options.info_only )
+ purge_histories( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry )
elif options.purge_datasets:
- purge_datasets( app, cutoff_time, options.remove_from_disk, info_only = options.info_only )
+ purge_datasets( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry )
elif options.purge_libraries:
- purge_libraries( app, cutoff_time, options.remove_from_disk, info_only = options.info_only )
+ purge_libraries( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry )
elif options.purge_folders:
- purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only )
+ purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry )
sys.exit(0)
-def delete_userless_histories( app, cutoff_time, info_only = False ):
+def delete_userless_histories( app, cutoff_time, info_only = False, force_retry = False ):
# Deletes userless histories whose update_time value is older than the cutoff_time.
# The purge history script will handle marking DatasetInstances as deleted.
# Nothing is removed from disk yet.
history_count = 0
print '# The following datasets and associated userless histories have been deleted'
start = time.clock()
- histories = app.model.History.filter( and_( app.model.History.table.c.user_id==None,
- app.model.History.table.c.deleted==False,
- app.model.History.table.c.update_time < cutoff_time ) ).all()# \
+ if force_retry:
+ histories = app.model.History.filter( and_( app.model.History.table.c.user_id==None,
+ app.model.History.table.c.update_time < cutoff_time ) ).all()
+ else:
+ histories = app.model.History.filter( and_( app.model.History.table.c.user_id==None,
+ app.model.History.table.c.deleted==False,
+ app.model.History.table.c.update_time < cutoff_time ) ).all()
for history in histories:
if not info_only:
history.deleted = True
@@ -106,7 +111,7 @@
print "Elapsed time: ", stop - start, "\n"
-def purge_histories( app, cutoff_time, remove_from_disk, info_only = False ):
+def purge_histories( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ):
# Purges deleted histories whose update_time is older than the cutoff_time.
# The dataset associations of each history are also marked as deleted.
# The Purge Dataset method will purge each Dataset as necessary
@@ -115,10 +120,15 @@
history_count = 0
print '# The following datasets and associated deleted histories have been purged'
start = time.clock()
- histories = app.model.History.filter( and_( app.model.History.table.c.deleted==True,
- app.model.History.table.c.purged==False,
- app.model.History.table.c.update_time < cutoff_time ) ) \
- .options( eagerload( 'datasets' ) ).all()
+ if force_retry:
+ histories = app.model.History.filter( and_( app.model.History.table.c.deleted==True,
+ app.model.History.table.c.update_time < cutoff_time ) ) \
+ .options( eagerload( 'datasets' ) ).all()
+ else:
+ histories = app.model.History.filter( and_( app.model.History.table.c.deleted==True,
+ app.model.History.table.c.purged==False,
+ app.model.History.table.c.update_time < cutoff_time ) ) \
+ .options( eagerload( 'datasets' ) ).all()
for history in histories:
for dataset_assoc in history.datasets:
_purge_dataset_instance( dataset_assoc, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable
@@ -136,7 +146,7 @@
print '# Purged %d histories.' % ( history_count ), '\n'
print "Elapsed time: ", stop - start, "\n"
-def purge_libraries( app, cutoff_time, remove_from_disk, info_only = False ):
+def purge_libraries( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ):
# Purges deleted libraries whose update_time is older than the cutoff_time.
# The dataset associations of each library are also marked as deleted.
# The Purge Dataset method will purge each Dataset as necessary
@@ -145,9 +155,13 @@
library_count = 0
print '# The following libraries and associated folders have been purged'
start = time.clock()
- libraries = app.model.Library.filter( and_( app.model.Library.table.c.deleted==True,
- app.model.Library.table.c.purged==False,
- app.model.Library.table.c.update_time < cutoff_time ) ).all()
+ if force_retry:
+ libraries = app.model.Library.filter( and_( app.model.Library.table.c.deleted==True,
+ app.model.Library.table.c.update_time < cutoff_time ) ).all()
+ else:
+ libraries = app.model.Library.filter( and_( app.model.Library.table.c.deleted==True,
+ app.model.Library.table.c.purged==False,
+ app.model.Library.table.c.update_time < cutoff_time ) ).all()
for library in libraries:
_purge_folder( library.root_folder, app, remove_from_disk, info_only = info_only )
if not info_only:
@@ -159,7 +173,7 @@
print '# Purged %d libraries .' % ( library_count ), '\n'
print "Elapsed time: ", stop - start, "\n"
-def purge_folders( app, cutoff_time, remove_from_disk, info_only = False ):
+def purge_folders( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ):
# Purges deleted folders whose update_time is older than the cutoff_time.
# The dataset associations of each folder are also marked as deleted.
# The Purge Dataset method will purge each Dataset as necessary
@@ -168,9 +182,13 @@
folder_count = 0
print '# The following folders have been purged'
start = time.clock()
- folders = app.model.LibraryFolder.filter( and_( app.model.LibraryFolder.table.c.deleted==True,
- app.model.LibraryFolder.table.c.purged==False,
- app.model.LibraryFolder.table.c.update_time < cutoff_time ) ).all()
+ if force_retry:
+ folders = app.model.LibraryFolder.filter( and_( app.model.LibraryFolder.table.c.deleted==True,
+ app.model.LibraryFolder.table.c.update_time < cutoff_time ) ).all()
+ else:
+ folders = app.model.LibraryFolder.filter( and_( app.model.LibraryFolder.table.c.deleted==True,
+ app.model.LibraryFolder.table.c.purged==False,
+ app.model.LibraryFolder.table.c.update_time < cutoff_time ) ).all()
for folder in folders:
_purge_folder( folder, app, remove_from_disk, info_only = info_only )
print "%d" % folder.id
@@ -179,17 +197,22 @@
print '# Purged %d folders.' % ( folder_count ), '\n'
print "Elapsed time: ", stop - start, "\n"
-def purge_datasets( app, cutoff_time, remove_from_disk, info_only = False ):
+def purge_datasets( app, cutoff_time, remove_from_disk, info_only = False, repurge = False, force_retry = False ):
# Purges deleted datasets whose update_time is older than cutoff_time. Files may or may
# not be removed from disk.
dataset_count = 0
disk_space = 0
print '# The following deleted datasets have been purged'
start = time.clock()
- datasets = app.model.Dataset.filter( and_( app.model.Dataset.table.c.deleted==True,
- app.model.Dataset.table.c.purgable==True,
- app.model.Dataset.table.c.purged==False,
- app.model.Dataset.table.c.update_time < cutoff_time ) ).all()
+ if force_retry:
+ datasets = app.model.Dataset.filter( and_( app.model.Dataset.table.c.deleted==True,
+ app.model.Dataset.table.c.purgable==True,
+ app.model.Dataset.table.c.update_time < cutoff_time ) ).all()
+ else:
+ datasets = app.model.Dataset.filter( and_( app.model.Dataset.table.c.deleted==True,
+ app.model.Dataset.table.c.purgable==True,
+ app.model.Dataset.table.c.purged==False,
+ app.model.Dataset.table.c.update_time < cutoff_time ) ).all()
for dataset in datasets:
file_size = dataset.file_size
_purge_dataset( dataset, remove_from_disk, info_only = info_only )
diff -r 61dd78cafa09 -r 07dffb2735dd templates/admin/library/ldda_edit_info.mako
--- a/templates/admin/library/ldda_edit_info.mako Fri Jul 31 11:48:37 2009 -0400
+++ b/templates/admin/library/ldda_edit_info.mako Fri Jul 31 12:01:02 2009 -0400
@@ -99,24 +99,30 @@
<div class="toolForm">
<div class="toolFormTitle">Change data type of ${ldda.name}</div>
<div class="toolFormBody">
- <form name="change_datatype" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
- <input type="hidden" name="id" value="${ldda.id}"/>
+ %if ldda.datatype.allow_datatype_change:
+ <form name="change_datatype" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
+ <input type="hidden" name="id" value="${ldda.id}"/>
+ <div class="form-row">
+ <label>New Type:</label>
+ <div style="float: left; width: 250px; margin-right: 10px;">
+ ${datatype( ldda, datatypes )}
+ </div>
+ <div class="toolParamHelp" style="clear: both;">
+ This will change the datatype of the existing dataset
+ but <i>not</i> modify its contents. Use this if Galaxy
+ has incorrectly guessed the type of your dataset.
+ </div>
+ <div style="clear: both"></div>
+ </div>
+ <div class="form-row">
+ <input type="submit" name="change" value="Save"/>
+ </div>
+ </form>
+ %else:
<div class="form-row">
- <label>New Type:</label>
- <div style="float: left; width: 250px; margin-right: 10px;">
- ${datatype( ldda, datatypes )}
- </div>
- <div class="toolParamHelp" style="clear: both;">
- This will change the datatype of the existing dataset
- but <i>not</i> modify its contents. Use this if Galaxy
- has incorrectly guessed the type of your dataset.
- </div>
- <div style="clear: both"></div>
+ <div class="warningmessagesmall">${_('Changing the datatype of this dataset is not allowed.')}</div>
</div>
- <div class="form-row">
- <input type="submit" name="change" value="Save"/>
- </div>
- </form>
+ %endif
</div>
</div>
diff -r 61dd78cafa09 -r 07dffb2735dd templates/dataset/edit_attributes.mako
--- a/templates/dataset/edit_attributes.mako Fri Jul 31 11:48:37 2009 -0400
+++ b/templates/dataset/edit_attributes.mako Fri Jul 31 12:01:02 2009 -0400
@@ -102,27 +102,34 @@
</div>
<p />
%endif
+
<div class="toolForm">
<div class="toolFormTitle">${_('Change data type')}</div>
<div class="toolFormBody">
- <form name="change_datatype" action="${h.url_for( controller='root', action='edit' )}" method="post">
- <input type="hidden" name="id" value="${data.id}"/>
+ %if data.datatype.allow_datatype_change:
+ <form name="change_datatype" action="${h.url_for( controller='root', action='edit' )}" method="post">
+ <input type="hidden" name="id" value="${data.id}"/>
+ <div class="form-row">
+ <label>
+ ${_('New Type')}:
+ </label>
+ <div style="float: left; width: 250px; margin-right: 10px;">
+ ${datatype( data, datatypes )}
+ </div>
+ <div class="toolParamHelp" style="clear: both;">
+ ${_('This will change the datatype of the existing dataset but <i>not</i> modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.')}
+ </div>
+ <div style="clear: both"></div>
+ </div>
+ <div class="form-row">
+ <input type="submit" name="change" value="${_('Save')}"/>
+ </div>
+ </form>
+ %else:
<div class="form-row">
- <label>
- ${_('New Type')}:
- </label>
- <div style="float: left; width: 250px; margin-right: 10px;">
- ${datatype( data, datatypes )}
- </div>
- <div class="toolParamHelp" style="clear: both;">
- ${_('This will change the datatype of the existing dataset but <i>not</i> modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.')}
- </div>
- <div style="clear: both"></div>
+ <div class="warningmessagesmall">${_('Changing the datatype of this dataset is not allowed.')}</div>
</div>
- <div class="form-row">
- <input type="submit" name="change" value="${_('Save')}"/>
- </div>
- </form>
+ %endif
</div>
</div>
<p />
diff -r 61dd78cafa09 -r 07dffb2735dd templates/library/ldda_edit_info.mako
--- a/templates/library/ldda_edit_info.mako Fri Jul 31 11:48:37 2009 -0400
+++ b/templates/library/ldda_edit_info.mako Fri Jul 31 12:01:02 2009 -0400
@@ -99,24 +99,30 @@
<div class="toolForm">
<div class="toolFormTitle">Change data type</div>
<div class="toolFormBody">
- <form name="change_datatype" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
- <input type="hidden" name="id" value="${ldda.id}"/>
+ %if ldda.datatype.allow_datatype_change:
+ <form name="change_datatype" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
+ <input type="hidden" name="id" value="${ldda.id}"/>
+ <div class="form-row">
+ <label>New Type:</label>
+ <div style="float: left; width: 250px; margin-right: 10px;">
+ ${datatype( ldda, datatypes )}
+ </div>
+ <div class="toolParamHelp" style="clear: both;">
+ This will change the datatype of the existing dataset
+ but <i>not</i> modify its contents. Use this if Galaxy
+ has incorrectly guessed the type of your dataset.
+ </div>
+ <div style="clear: both"></div>
+ </div>
+ <div class="form-row">
+ <input type="submit" name="change" value="Save"/>
+ </div>
+ </form>
+ %else:
<div class="form-row">
- <label>New Type:</label>
- <div style="float: left; width: 250px; margin-right: 10px;">
- ${datatype( ldda, datatypes )}
- </div>
- <div class="toolParamHelp" style="clear: both;">
- This will change the datatype of the existing dataset
- but <i>not</i> modify its contents. Use this if Galaxy
- has incorrectly guessed the type of your dataset.
- </div>
- <div style="clear: both"></div>
+ <div class="warningmessagesmall">${_('Changing the datatype of this dataset is not allowed.')}</div>
</div>
- <div class="form-row">
- <input type="submit" name="change" value="Save"/>
- </div>
- </form>
+ %endif
</div>
</div>
<p/>
1
0
Hello,
I'd like to suggest a new feature - administrative lock which prevents new jobs from starting.
Use case:
1. I need to stop my galaxy server (to upgrade, to add new tool, to add new dbkey, etc).
2. I want to stop it in a friendly way, without killing running jobs, but not allow new jobs to start.
3. Once all the running jobs complete (and new jobs are not started), I can stop the server, fix it, and restart.
4. Restarting the server (and assuming jobs are tracked in the database), all the held jobs are started normally.
Code changes:
1. new administrative method ( job_lock() in ./lib/galaxy/web/controller/admin.py )
2. new template ( ./templates/admin/job_lock.mako )
3. job lock code in lib/galaxy/jobs/schedulingpolicy/roundrobin.py
I'm still testing this patch, but comments are welcomed.
-gordon.
3
2