| Next changeset 1:a36c081e0043 (2013-03-20) |
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Commit message:
Uploaded tarball |
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added:
lastz_wrapper.py lastz_wrapper.xml test-data/b1.fasta test-data/lastz_census.txt test-data/lastz_diffs.txt test-data/lastz_diffs_ref_name.txt test-data/lastz_maf.txt test-data/lastz_wrapper_out2.sam test-data/lastz_wrapper_out3.tabular test-data/lastz_wrapper_out4.tabular test-data/phiX.2bit test-data/phiX.fasta test-data/phiX_split.fasta tool-data/lastz_seqs.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r 0801f8207d30 lastz_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lastz_wrapper.py Mon Nov 26 09:47:51 2012 -0500 |
| [ |
| b'@@ -0,0 +1,290 @@\n+#!/usr/bin/env python\n+\n+"""\n+Runs Lastz\n+Written for Lastz v. 1.01.88.\n+\n+usage: lastz_wrapper.py [options]\n+ --ref_name: The reference name to change all output matches to\n+ --ref_source: Whether the reference is cached or from the history\n+ --source_select: Whether to used pre-set or cached reference file\n+ --input1: The name of the reference file if using history or reference base name if using cached\n+ --input2: The reads file to align \n+ --ref_sequences: The number of sequences in the reference file if using one from history \n+ --pre_set_options: Which of the pre set options to use, if using pre-sets\n+ --strand: Which strand of the read to search, if specifying all parameters\n+ --seed: Seeding settings, if specifying all parameters\n+ --gfextend: Whether to perform gap-free extension of seed hits to HSPs (high scoring segment pairs), if specifying all parameters\n+ --chain: Whether to perform chaining of HSPs, if specifying all parameters\n+ --transition: Number of transitions to allow in each seed hit, if specifying all parameters\n+ --O: Gap opening penalty, if specifying all parameters\n+ --E: Gap extension penalty, if specifying all parameters\n+ --X: X-drop threshold, if specifying all parameters\n+ --Y: Y-drop threshold, if specifying all parameters\n+ --K: Threshold for HSPs, if specifying all parameters\n+ --L: Threshold for gapped alignments, if specifying all parameters\n+ --entropy: Whether to involve entropy when filtering HSPs, if specifying all parameters\n+ --identity_min: Minimum identity (don\'t report matches under this identity)\n+ --identity_max: Maximum identity (don\'t report matches above this identity)\n+ --coverage: The minimum coverage value (don\'t report matches covering less than this) \n+ --unmask: Whether to convert lowercase bases to uppercase\n+ --out_format: The format of the output file (sam, diffs, or tabular (general))\n+ --output: The name of the output file\n+ --lastzSeqsFileDir: Directory of local lastz_seqs.loc file\n+"""\n+import optparse, os, subprocess, shutil, sys, tempfile, threading, time\n+from Queue import Queue\n+\n+from galaxy import eggs\n+import pkg_resources\n+pkg_resources.require( \'bx-python\' )\n+from bx.seq.twobit import *\n+from bx.seq.fasta import FastaReader\n+from galaxy.util.bunch import Bunch\n+\n+STOP_SIGNAL = object()\n+WORKERS = 4\n+SLOTS = 128\n+\n+def stop_err( msg ):\n+ sys.stderr.write( "%s" % msg )\n+ sys.exit()\n+\n+def stop_queues( lastz, combine_data ):\n+ # This method should only be called if an error has been encountered.\n+ # Send STOP_SIGNAL to all worker threads\n+ for t in lastz.threads:\n+ lastz.put( STOP_SIGNAL, True )\n+ combine_data.put( STOP_SIGNAL, True )\n+\n+class BaseQueue( object ):\n+ def __init__( self, num_threads, slots=-1 ):\n+ # Initialize the queue and worker threads\n+ self.queue = Queue( slots )\n+ self.threads = []\n+ for i in range( num_threads ):\n+ worker = threading.Thread( target=self.run_next )\n+ worker.start()\n+ self.threads.append( worker )\n+ def run_next( self ):\n+ # Run the next job, waiting until one is available if necessary\n+ while True:\n+ job = self.queue.get()\n+ if job is STOP_SIGNAL:\n+ return self.shutdown()\n+ self.run_job( job )\n+ time.sleep( 1 )\n+ def run_job( self, job ):\n+ stop_err( \'Not Implemented\' )\n+ def put( self, job, block=False ):\n+ # Add a job to the queue\n+ self.queue.put( job, block )\n+ def shutdown( self ):\n+ return\n+\n+class LastzJobQueue( BaseQueue ):\n+ """\n+ A queue that runs commands in parallel. Blocking is done so the queue will\n+ not consume much memory.\n+ """\n+ def run_job( self, job ):\n+ # Execute the job\'s command\n+ proc = subprocess.Popen( args=job.command, shell=True, stderr=subprocess.PIPE, )\n+ proc.'..b' stop_err( error_msg )\n+ except:\n+ stop_queues( lastz_job_queue, combine_data_queue )\n+ stop_err( error_msg )\n+ seqs = 0\n+ fasta_reader = FastaReader( open( options.input1 ) )\n+ while True:\n+ # Read the next sequence from the reference dataset\n+ seq = fasta_reader.next()\n+ if not seq:\n+ break\n+ seqs += 1\n+ # Create a temporary file to contain the current sequence as input to lastz\n+ tmp_in_fd, tmp_in_name = tempfile.mkstemp( suffix=\'.in\' )\n+ tmp_in = os.fdopen( tmp_in_fd, \'wb\' )\n+ # Write the current sequence to the temporary input file\n+ tmp_in.write( \'>%s\\n%s\\n\' % ( seq.name, seq.text ) )\n+ tmp_in.close()\n+ # Create a 2nd temporary file to contain the output from lastz execution on the current sequence\n+ tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix=\'.out\' )\n+ os.close( tmp_out_fd )\n+ # Generate the command line for calling lastz on the current sequence\n+ command = \'lastz %s%s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s > %s\' % \\\n+ ( tmp_in_name, unmask, ref_name, input2, set_options, options.identity_min, \n+ options.identity_max, options.coverage, format, tabular_fields, tmp_out_name )\n+ # Create a job object\n+ job = Bunch()\n+ job.command = command\n+ job.output = tmp_out_name\n+ job.cleanup = [ tmp_in_name, tmp_out_name ]\n+ job.combine_data_queue = combine_data_queue\n+ # Add another job to the lastz_job_queue. Execution \n+ # will wait at this point if the queue is full.\n+ lastz_job_queue.put( job, block=True )\n+ # Make sure the value of sequences in the metadata is the same as the\n+ # number of sequences read from the dataset ( this may not be necessary ).\n+ if ref_sequences != seqs:\n+ stop_queues( lastz_job_queue, combine_data_queue )\n+ stop_err( "The value of metadata.sequences (%d) differs from the number of sequences read from the reference (%d)." % ( ref_sequences, seqs ) )\n+ else:\n+ # Reference is a locally cached 2bit file, split job across number of chroms in 2bit file\n+ tbf = TwoBitFile( open( options.input1, \'r\' ) )\n+ for chrom in tbf.keys():\n+ # Create a temporary file to contain the output from lastz execution on the current chrom\n+ tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix=\'.out\' )\n+ os.close( tmp_out_fd )\n+ command = \'lastz %s/%s%s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s >> %s\' % \\\n+ ( options.input1, chrom, unmask, ref_name, input2, set_options, options.identity_min, \n+ options.identity_max, options.coverage, format, tabular_fields, tmp_out_name )\n+ # Create a job object\n+ job = Bunch()\n+ job.command = command\n+ job.output = tmp_out_name\n+ job.cleanup = [ tmp_out_name ]\n+ job.combine_data_queue = combine_data_queue\n+ # Add another job to the lastz_job_queue. Execution \n+ # will wait at this point if the queue is full.\n+ lastz_job_queue.put( job, block=True )\n+\n+ # Stop the lastz_job_queue\n+ for t in lastz_job_queue.threads:\n+ lastz_job_queue.put( STOP_SIGNAL, True )\n+ # Although all jobs are submitted to the queue, we can\'t shut down the combine_data_queue\n+ # until we know that all jobs have been submitted to its queue. We do this by checking\n+ # whether all of the threads in the lastz_job_queue have terminated.\n+ while threading.activeCount() > 2:\n+ time.sleep( 1 )\n+ # Now it\'s safe to stop the combine_data_queue\n+ combine_data_queue.put( STOP_SIGNAL )\n+\n+if __name__=="__main__": __main__()\n' |
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| diff -r 000000000000 -r 0801f8207d30 lastz_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lastz_wrapper.xml Mon Nov 26 09:47:51 2012 -0500 |
| [ |
| b'@@ -0,0 +1,524 @@\n+<tool id="lastz_wrapper_2" name="Lastz" version="1.2.2">\n+ <requirements>\n+ <requirement type="package" version="1.02.00">lastz</requirement>\n+ </requirements>\n+ <description> map short reads against reference sequence</description>\n+ <command interpreter="python">lastz_wrapper.py\n+ #if $seq_name.how_to_name=="yes":\n+ --ref_name=$seq_name.ref_name \n+ #end if\n+ --ref_source=$source.ref_source\n+ --source_select=$params.source_select\n+ --out_format=$out_format\n+ --input2=$input2 \n+ #if $source.ref_source=="history":\n+ --input1=$source.input1\n+ --ref_sequences=$input1.metadata.sequences \n+ #else:\n+ --input1="${source.input1_2bit.fields.path}"\n+ --ref_sequences="None" \n+ #end if\n+ #if $params.source_select=="pre_set":\n+ --pre_set_options=${params.pre_set_options}\n+ #else:\n+ --strand=$params.strand\n+ --seed=$params.seed\n+ --gfextend=$params.gfextend\n+ --chain=$params.chain\n+ --transition="$params.transition"\n+ --O=$params.O\n+ --E=$params.E\n+ --X=$params.X\n+ --Y=$params.Y\n+ --K=$params.K\n+ --L=$params.L\n+ --entropy=$params.entropy \n+ #end if\n+ --identity_min=$min_ident\n+ --identity_max=$max_ident\n+ --coverage=$min_cvrg\n+ --output=$output1\n+ --unmask=$unmask\n+ --lastzSeqsFileDir=${GALAXY_DATA_INDEX_DIR}\n+ </command>\n+ <inputs>\n+ <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />\n+ <conditional name="source">\n+ <param name="ref_source" type="select" label="Against reference sequences that are">\n+ <option value="cached">locally cached</option>\n+ <option value="history">in your history</option>\n+ </param>\n+ <when value="cached">\n+ <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">\n+ <options from_data_table="lastz_seqs" />\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="input1" type="data" format="fasta" label="Select a reference dataset" />\n+ </when>\n+ </conditional>\n+ <param name="out_format" type="select" label="Output format">\n+ <option value="sam">SAM</option>\n+ <option value="diffs">Polymorphisms</option>\n+ <option value="tabular">Tabular</option>\n+ </param>\n+ <conditional name="params">\n+ <param name="source_select" type="select" label="Lastz settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">\n+ <option value="pre_set">Commonly used</option>\n+ <option value="full">Full Parameter List</option>\n+ </param>\n+ <when value="pre_set">\n+ <param name="pre_set_options" type="select" label="Select mapping mode">\n+ <option value="yasra98">Roche-454 98% identity</option>\n+ <option value="yasra95">Roche-454 95% identity</option>\n+ <option value="yasra90">Roche-454 90% identity</option>\n+ <option value="yasra85">Roche-454 85% identity</option>\n+ <option value="yasra75">Roche-454 75% identity</option>\n+ <option value="yasra95short">Illumina 95% identity</option>\n+ <option value="yasra85short">Illumina 85% identity</option>\n+ </param>\n+ </when>\n+ <when value="full">\n+ <param name="strand" type="select" label="Which strand to search?">\n+ <option value="both">Both</option>\n+ <option value="plus">Search forward strand only (the one in the reference)</option>\n+ '..b'd of words \'in\' a quantum ball\n+ --[no]entropy involve entropy in filtering high scoring pairs\n+ (default is "entropy")\n+ --[no]mirror report/use mirror image of all gap-free alignments\n+ (default is "mirror" for self-alignments only)\n+ --traceback=<bytes> space for trace-back information\n+ (default is 80.0M)\n+ --masking=<count> mask any position in target hit this many times\n+ zero indicates no masking\n+ (default is no masking)\n+ --targetcapsule=<capsule_file> the target seed word position table and seed\n+ (as well as the target sequence)are read from specified file\n+ --segments=<segment_file> read segments from a file, instead of discovering\n+ them via seeding. Replaces other seeding or gap-free extension\n+ options\n+ --[no]census[=<file>] count/report how many times each target base aligns\n+ (default is to not report census)\n+ --identity=<min>[..<max>] filter alignments by percent identity\n+ 0<=min<=max<=100; blocks (or HSPs) outside min..max\n+ are discarded\n+ (default is no identity filtering)\n+ --coverage=<min>[..<max>] filter alignments by percentage pf query covered\n+ 0<=min<=max<=100; blocks (or HSPs) outside min..max\n+ are discarded\n+ (default is no query coverage filtering)\n+ --notrivial do not output trivial self-alignment block if the target and query \n+ sequences are identical. Using --self enables this option automatically\n+ --output=<output_file> write the alignments to the specified file name instead of stdout\n+ --code=<file> give quantum code for query sequence (only for display)\n+ --format=<type> specify output format; one of lav, axt, maf, maf+, maf-, text,\n+ lav+text, cigar, text, rdplot, general, or general:<fields>\n+ (by default output is LAV)\n+ --rdotplot=<file> create an additional output file suitable for plotting the alignments \n+ with the R statistical package.\n+ --markend Just before normal completion, write "# lastz end-of-file" to output file\n+ --census[=<output_file>] count and report how many times each target base aligns, up \n+ to 255. Ns are included in the count\n+ --census16[=<output_file>] count and report how many times each target base aligns, up\n+ up 65 thousand\n+ --census32[=<output_file>] count and report how many times each target bas aligns, up\n+ to 4 billion\n+ --writecapsule=<capsule_file> just write out a target capsule file and quit; don\'t \n+ search for seeds or perform subsequent stages\n+ --verbosity=<level> set info level (0 is minimum, 10 is everything)\n+ (default is 0)\n+ --[no]runtime report runtime in the output file\n+ (default is to not report runtime)\n+ --tableonly[=count] just produce the target position table, don\'t\n+ search for seeds\n+ --[no]stats[=<file>] show search statistics (or don\'t)\n+ (not available in this build)\n+ --version report the program version and quit\n+ --help list all options\n+ --help=files list information about file specifiers\n+ --help=short[cuts] list blastz-compatible shortcuts\n+ --help=yasra list yasra-specific shortcuts\n+\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r 0801f8207d30 test-data/b1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b1.fasta Mon Nov 26 09:47:51 2012 -0500 |
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| b'@@ -0,0 +1,1000 @@\n+>HWI-EAS91_1_306UPAAXX:6:1:1503:1160\n+GGTGGTCTATAGTGTTATTAATATCAAGTTGGGGGG\n+>HWI-EAS91_1_306UPAAXX:6:1:1564:1179\n+GCGAGCAGTAGACTCCTTCTGTTGATAAGCAAGCAT\n+>HWI-EAS91_1_306UPAAXX:6:1:1704:1082\n+GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC\n+>HWI-EAS91_1_306UPAAXX:6:1:1588:1797\n+GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT\n+>HWI-EAS91_1_306UPAAXX:6:1:1304:1526\n+GTAGTTGAAATGGTAATAAGACGACCAATCTGACCT\n+>HWI-EAS91_1_306UPAAXX:6:1:1490:1582\n+GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC\n+>HWI-EAS91_1_306UPAAXX:6:1:1356:1339\n+GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC\n+>HWI-EAS91_1_306UPAAXX:6:1:1311:853\n+GGTTGGTTTATCGTTTTTGACACTCTCACGTTGTCT\n+>HWI-EAS91_1_306UPAAXX:6:1:1257:1552\n+GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC\n+>HWI-EAS91_1_306UPAAXX:6:1:1486:1402\n+GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC\n+>HWI-EAS91_1_306UPAAXX:6:1:1028:1081\n+GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT\n+>HWI-EAS91_1_306UPAAXX:6:1:1167:752\n+GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC\n+>HWI-EAS91_1_306UPAAXX:6:1:1507:1113\n+GTCAACGTTATATTTTGATAGTTTGACGGTTAATTC\n+>HWI-EAS91_1_306UPAAXX:6:1:1654:1311\n+GGATGAAAATGCTCACAATGACAAATCTGTCCACGG\n+>HWI-EAS91_1_306UPAAXX:6:1:1386:1060\n+GTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTT\n+>HWI-EAS91_1_306UPAAXX:6:1:1070:1356\n+GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG\n+>HWI-EAS91_1_306UPAAXX:6:1:787:1032\n+GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA\n+>HWI-EAS91_1_306UPAAXX:6:1:834:1017\n+GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT\n+>HWI-EAS91_1_306UPAAXX:6:1:1703:1155\n+GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT\n+>HWI-EAS91_1_306UPAAXX:6:1:1406:593\n+GTTGAGTTCGATAATGGTGATATGTATGTTTACGGC\n+>HWI-EAS91_1_306UPAAXX:6:1:1411:886\n+GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT\n+>HWI-EAS91_1_306UPAAXX:6:1:923:972\n+GCATGACAAGTAAAGGACGGTTGTCAGCGTCATAAG\n+>HWI-EAS91_1_306UPAAXX:6:1:1279:1004\n+GCCATAGCACCAGAAACAAAACTAGGGGCGGCCTCT\n+>HWI-EAS91_1_306UPAAXX:6:1:1070:840\n+GGTTGTCAGCGTCATAAGAGGTTTTACCTCCAAATG\n+>HWI-EAS91_1_306UPAAXX:6:1:1595:1040\n+GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT\n+>HWI-EAS91_1_306UPAAXX:6:1:1002:559\n+GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG\n+>HWI-EAS91_1_306UPAAXX:6:1:999:974\n+GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC\n+>HWI-EAS91_1_306UPAAXX:6:1:896:982\n+GTGGCTGGAGACAAATAATCTCTTTAATAACCTTAT\n+>HWI-EAS91_1_306UPAAXX:6:1:1366:741\n+GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC\n+>HWI-EAS91_1_306UPAAXX:6:1:749:1469\n+GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT\n+>HWI-EAS91_1_306UPAAXX:6:1:1010:592\n+GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT\n+>HWI-EAS91_1_306UPAAXX:6:1:1393:650\n+GTGACTCATATCTAAACCAGTCCTTGACGAACGTGC\n+>HWI-EAS91_1_306UPAAXX:6:1:1238:1731\n+GAGAAATAAAAGTCTGAAACATGATTAAACTCCTAA\n+>HWI-EAS91_1_306UPAAXX:6:1:1629:908\n+GATGCGGTTATCCATCTGCTTATGGAAGCCAAGCAT\n+>HWI-EAS91_1_306UPAAXX:6:1:1560:849\n+GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG\n+>HWI-EAS91_1_306UPAAXX:6:1:1029:783\n+GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT\n+>HWI-EAS91_1_306UPAAXX:6:1:1152:1324\n+GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG\n+>HWI-EAS91_1_306UPAAXX:6:1:1614:2042\n+GAAATGCCACAAGCCTCAATAGCAGGTTTAAGAGCC\n+>HWI-EAS91_1_306UPAAXX:6:1:1398:439\n+GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG\n+>HWI-EAS91_1_306UPAAXX:6:1:955:616\n+GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC\n+>HWI-EAS91_1_306UPAAXX:6:1:1672:753\n+GAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCT\n+>HWI-EAS91_1_306UPAAXX:6:1:1195:1293\n+GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC\n+>HWI-EAS91_1_306UPAAXX:6:1:1074:755\n+GCAAGAGTAAACATAGTGCCATGCTCAGGAACAAAG\n+>HWI-EAS91_1_306UPAAXX:6:1:984:499\n+GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT\n+>HWI-EAS91_1_306UPAAXX:6:1:1452:1833\n+GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT\n+>HWI-EAS91_1_306UPAAXX:6:1:863:710\n+GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT\n+>HWI-EAS91_1_306UPAAXX:6:1:885:649\n+GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC\n+>HWI-EAS91_1_306UPAAXX:6:1:917:1214\n+GACAGATGTATCCATCTGAATGCAATGAAGAAAACC\n+>HWI-EAS91_1_306UPAAXX:6:1:892:1254\n+GCTCAGGAAATGCAGCAGCAAGATAATCACGAGTAT\n+>HWI-EAS91_1_306UPAAXX:6:1:1555:1005\n+GCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCT\n+>HWI-EAS91_1_306UPAAXX:6:1:1637:1413\n+GATGCTGTTCAACCACTAATAGGTAAGAAATCATGT\n+>HWI-EAS91_1_306UPAAXX:6:1:1102:1567\n+GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA\n+>HWI-EAS91_1_306UPAAXX:6:1:799:1337\n+GTATATGCACAAAATGAGATGCTT'..b'GAAGCAATACCGCCAGCAATAGCACCAAA\n+>HWI-EAS91_1_306UPAAXX:6:1:1474:1056\n+TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC\n+>HWI-EAS91_1_306UPAAXX:6:1:105:1818\n+TTGGGGATTGAGAAAGAGTAGAAATGCCACAAGCCT\n+>HWI-EAS91_1_306UPAAXX:6:1:208:1538\n+TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA\n+>HWI-EAS91_1_306UPAAXX:6:1:1361:1623\n+AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA\n+>HWI-EAS91_1_306UPAAXX:6:1:595:1670\n+TGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACA\n+>HWI-EAS91_1_306UPAAXX:6:1:6:1885\n+TCTAATGTCGTCACTGATGCTGCTTCTGGTGTGTTT\n+>HWI-EAS91_1_306UPAAXX:6:1:706:1085\n+TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG\n+>HWI-EAS91_1_306UPAAXX:6:1:1307:825\n+AGCGGTAAAGTTAGACCAAACCATGAAACCAACATA\n+>HWI-EAS91_1_306UPAAXX:6:1:762:802\n+TGGCATTAACACCATCCTTCATGAACTTAATCCACT\n+>HWI-EAS91_1_306UPAAXX:6:1:1657:506\n+TTGCGACCCTCGGCAGCAAGAACCATACGACCAATT\n+>HWI-EAS91_1_306UPAAXX:6:1:184:811\n+TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC\n+>HWI-EAS91_1_306UPAAXX:6:1:1469:1718\n+TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTT\n+>HWI-EAS91_1_306UPAAXX:6:1:815:1640\n+TGGCGGCGATTGCGTACCCGACGACCCAAATTAGGG\n+>HWI-EAS91_1_306UPAAXX:6:1:1580:1388\n+AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG\n+>HWI-EAS91_1_306UPAAXX:6:1:1617:1554\n+TACGGGGAAGGACGTCAATAGTCACACAGTCCTTGA\n+>HWI-EAS91_1_306UPAAXX:6:1:1544:431\n+TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA\n+>HWI-EAS91_1_306UPAAXX:6:1:1604:1541\n+TCAGTGACGACATTAGAAATATCCTTTGCAGTAGCG\n+>HWI-EAS91_1_306UPAAXX:6:1:1485:741\n+ATCAAACGCTGAATAGTAAAGCCTCTACGCGATTTC\n+>HWI-EAS91_1_306UPAAXX:6:1:1226:393\n+TGCCACAAGCCTCAATAGCAGGTTTAAGAGCCTCGA\n+>HWI-EAS91_1_306UPAAXX:6:1:1506:973\n+ATTAGGGTCAACGCTACCTGTAGGAAGTGTCCGCAT\n+>HWI-EAS91_1_306UPAAXX:6:1:890:1838\n+TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC\n+>HWI-EAS91_1_306UPAAXX:6:1:453:1527\n+TAAGAGGGCGTTCAGCAGCCAGCTTGCGGCAAAACT\n+>HWI-EAS91_1_306UPAAXX:6:1:1056:570\n+ACATTGTAGCATTGTGCCAATTCATCCATTAACTTC\n+>HWI-EAS91_1_306UPAAXX:6:1:1736:74\n+TATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGT\n+>HWI-EAS91_1_306UPAAXX:6:1:169:1896\n+GTATGCAAATTAGCATAAGCAGCTTGCAGACCCATA\n+>HWI-EAS91_1_306UPAAXX:6:1:259:949\n+TGAGGATAAATTATGTCTAATATTCAAACTTGCTCC\n+>HWI-EAS91_1_306UPAAXX:6:1:1205:893\n+ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT\n+>HWI-EAS91_1_306UPAAXX:6:1:732:1335\n+TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT\n+>HWI-EAS91_1_306UPAAXX:6:1:667:664\n+TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG\n+>HWI-EAS91_1_306UPAAXX:6:1:535:587\n+TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT\n+>HWI-EAS91_1_306UPAAXX:6:1:412:446\n+GTGTGGTTGATATTTTTCATGGTATTGATAAAGCTT\n+>HWI-EAS91_1_306UPAAXX:6:1:507:1599\n+TTGCTGGCGGTTTTTCTTTTTTTTTTTTTTTTTTTT\n+>HWI-EAS91_1_306UPAAXX:6:1:575:1818\n+TAAAATGCACCGCATGGAAATGAAGACGGCCATTAG\n+>HWI-EAS91_1_306UPAAXX:6:1:1568:1428\n+ACCAGTTATATGGCTGGTTGTTTTTTTTTTTTTTTT\n+>HWI-EAS91_1_306UPAAXX:6:1:1417:982\n+AACAAGAGAATCTCTACCATGAACAAAATGTGACTC\n+>HWI-EAS91_1_306UPAAXX:6:1:280:1340\n+GGCCAAACCAGTGGCGATGGCCGCGCTGGAGGTTTT\n+>HWI-EAS91_1_306UPAAXX:6:1:966:144\n+TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT\n+>HWI-EAS91_1_306UPAAXX:6:1:1391:1987\n+TAATAATGTTTTCCGTAAATTCAGCGCCTTCCATGT\n+>HWI-EAS91_1_306UPAAXX:6:1:1280:278\n+ATGGAAATGAAGACGGCCATTAGCTGTACCATACTC\n+>HWI-EAS91_1_306UPAAXX:6:1:631:858\n+TGATATTGGTCGTATGGTTCTTGCTTCCGTGGGTCT\n+>HWI-EAS91_1_306UPAAXX:6:1:518:573\n+TTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGT\n+>HWI-EAS91_1_306UPAAXX:6:1:54:981\n+TTGACATTTTAAAAGAGCGTGGATTACTATCTGATT\n+>HWI-EAS91_1_306UPAAXX:6:1:218:1165\n+TATTGACTCTACTGTAGACATTTTTACTTTTTATTT\n+>HWI-EAS91_1_306UPAAXX:6:1:1727:1530\n+TCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCA\n+>HWI-EAS91_1_306UPAAXX:6:1:519:657\n+TGAACAGCATCGGACTCAGATAGTAATCCACGCTCT\n+>HWI-EAS91_1_306UPAAXX:6:1:939:967\n+ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC\n+>HWI-EAS91_1_306UPAAXX:6:1:299:1060\n+TATAACTGGTAGCTTTAAGCGGCTCACCTTTAGCAT\n+>HWI-EAS91_1_306UPAAXX:6:1:438:665\n+TAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTAT\n+>HWI-EAS91_1_306UPAAXX:6:1:1303:1971\n+AGCATTGTGCCAATTCATCCATTAACTTCTCAGTAA\n+>HWI-EAS91_1_306UPAAXX:6:1:214:1264\n+TCAGCACCAACAGAAACAACCTGATTAGCGGCGTTG\n+>HWI-EAS91_1_306UPAAXX:6:1:1454:1423\n+AACGGAAAACATCCTTCATAGAAATTTCACGCGGCG\n+>HWI-EAS91_1_306UPAAXX:6:1:1633:340\n+TTCCATAATAGACGCAACGCGAGCAGTAGACTCCTT\n+>HWI-EAS91_1_306UPAAXX:6:1:671:1196\n+ATACGAAAAGACAGAATCTCTTCCAAGAGCTTGATG\n' |
| b |
| diff -r 000000000000 -r 0801f8207d30 test-data/lastz_census.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lastz_census.txt Mon Nov 26 09:47:51 2012 -0500 |
| b |
| b'@@ -0,0 +1,5386 @@\n+phiX\t1\t255\n+phiX\t2\t255\n+phiX\t3\t255\n+phiX\t4\t255\n+phiX\t5\t255\n+phiX\t6\t255\n+phiX\t7\t255\n+phiX\t8\t255\n+phiX\t9\t255\n+phiX\t10\t255\n+phiX\t11\t255\n+phiX\t12\t255\n+phiX\t13\t255\n+phiX\t14\t255\n+phiX\t15\t255\n+phiX\t16\t255\n+phiX\t17\t255\n+phiX\t18\t255\n+phiX\t19\t255\n+phiX\t20\t255\n+phiX\t21\t255\n+phiX\t22\t255\n+phiX\t23\t255\n+phiX\t24\t255\n+phiX\t25\t255\n+phiX\t26\t255\n+phiX\t27\t255\n+phiX\t28\t255\n+phiX\t29\t255\n+phiX\t30\t255\n+phiX\t31\t255\n+phiX\t32\t255\n+phiX\t33\t255\n+phiX\t34\t255\n+phiX\t35\t255\n+phiX\t36\t255\n+phiX\t37\t255\n+phiX\t38\t255\n+phiX\t39\t255\n+phiX\t40\t255\n+phiX\t41\t255\n+phiX\t42\t255\n+phiX\t43\t255\n+phiX\t44\t255\n+phiX\t45\t255\n+phiX\t46\t255\n+phiX\t47\t255\n+phiX\t48\t255\n+phiX\t49\t255\n+phiX\t50\t255\n+phiX\t51\t255\n+phiX\t52\t255\n+phiX\t53\t255\n+phiX\t54\t255\n+phiX\t55\t255\n+phiX\t56\t255\n+phiX\t57\t255\n+phiX\t58\t255\n+phiX\t59\t255\n+phiX\t60\t255\n+phiX\t61\t255\n+phiX\t62\t255\n+phiX\t63\t255\n+phiX\t64\t255\n+phiX\t65\t255\n+phiX\t66\t255\n+phiX\t67\t255\n+phiX\t68\t255\n+phiX\t69\t255\n+phiX\t70\t255\n+phiX\t71\t255\n+phiX\t72\t255\n+phiX\t73\t255\n+phiX\t74\t255\n+phiX\t75\t255\n+phiX\t76\t255\n+phiX\t77\t255\n+phiX\t78\t255\n+phiX\t79\t255\n+phiX\t80\t255\n+phiX\t81\t255\n+phiX\t82\t255\n+phiX\t83\t255\n+phiX\t84\t255\n+phiX\t85\t255\n+phiX\t86\t255\n+phiX\t87\t255\n+phiX\t88\t255\n+phiX\t89\t255\n+phiX\t90\t255\n+phiX\t91\t255\n+phiX\t92\t255\n+phiX\t93\t255\n+phiX\t94\t255\n+phiX\t95\t255\n+phiX\t96\t255\n+phiX\t97\t255\n+phiX\t98\t255\n+phiX\t99\t255\n+phiX\t100\t255\n+phiX\t101\t255\n+phiX\t102\t255\n+phiX\t103\t255\n+phiX\t104\t255\n+phiX\t105\t255\n+phiX\t106\t255\n+phiX\t107\t255\n+phiX\t108\t255\n+phiX\t109\t255\n+phiX\t110\t255\n+phiX\t111\t255\n+phiX\t112\t255\n+phiX\t113\t255\n+phiX\t114\t255\n+phiX\t115\t255\n+phiX\t116\t255\n+phiX\t117\t255\n+phiX\t118\t255\n+phiX\t119\t255\n+phiX\t120\t255\n+phiX\t121\t255\n+phiX\t122\t255\n+phiX\t123\t255\n+phiX\t124\t255\n+phiX\t125\t255\n+phiX\t126\t255\n+phiX\t127\t255\n+phiX\t128\t255\n+phiX\t129\t255\n+phiX\t130\t255\n+phiX\t131\t255\n+phiX\t132\t255\n+phiX\t133\t255\n+phiX\t134\t255\n+phiX\t135\t255\n+phiX\t136\t255\n+phiX\t137\t255\n+phiX\t138\t255\n+phiX\t139\t255\n+phiX\t140\t255\n+phiX\t141\t255\n+phiX\t142\t255\n+phiX\t143\t255\n+phiX\t144\t255\n+phiX\t145\t255\n+phiX\t146\t255\n+phiX\t147\t255\n+phiX\t148\t255\n+phiX\t149\t255\n+phiX\t150\t255\n+phiX\t151\t255\n+phiX\t152\t255\n+phiX\t153\t255\n+phiX\t154\t255\n+phiX\t155\t255\n+phiX\t156\t255\n+phiX\t157\t255\n+phiX\t158\t255\n+phiX\t159\t255\n+phiX\t160\t255\n+phiX\t161\t255\n+phiX\t162\t255\n+phiX\t163\t255\n+phiX\t164\t255\n+phiX\t165\t255\n+phiX\t166\t255\n+phiX\t167\t255\n+phiX\t168\t255\n+phiX\t169\t255\n+phiX\t170\t255\n+phiX\t171\t255\n+phiX\t172\t255\n+phiX\t173\t255\n+phiX\t174\t255\n+phiX\t175\t255\n+phiX\t176\t255\n+phiX\t177\t255\n+phiX\t178\t255\n+phiX\t179\t255\n+phiX\t180\t255\n+phiX\t181\t255\n+phiX\t182\t255\n+phiX\t183\t255\n+phiX\t184\t255\n+phiX\t185\t255\n+phiX\t186\t255\n+phiX\t187\t255\n+phiX\t188\t255\n+phiX\t189\t255\n+phiX\t190\t255\n+phiX\t191\t255\n+phiX\t192\t255\n+phiX\t193\t255\n+phiX\t194\t255\n+phiX\t195\t255\n+phiX\t196\t255\n+phiX\t197\t255\n+phiX\t198\t255\n+phiX\t199\t255\n+phiX\t200\t255\n+phiX\t201\t255\n+phiX\t202\t255\n+phiX\t203\t255\n+phiX\t204\t255\n+phiX\t205\t255\n+phiX\t206\t255\n+phiX\t207\t255\n+phiX\t208\t255\n+phiX\t209\t255\n+phiX\t210\t255\n+phiX\t211\t255\n+phiX\t212\t255\n+phiX\t213\t255\n+phiX\t214\t255\n+phiX\t215\t255\n+phiX\t216\t255\n+phiX\t217\t255\n+phiX\t218\t255\n+phiX\t219\t255\n+phiX\t220\t255\n+phiX\t221\t255\n+phiX\t222\t255\n+phiX\t223\t255\n+phiX\t224\t255\n+phiX\t225\t255\n+phiX\t226\t255\n+phiX\t227\t255\n+phiX\t228\t255\n+phiX\t229\t255\n+phiX\t230\t255\n+phiX\t231\t255\n+phiX\t232\t255\n+phiX\t233\t255\n+phiX\t234\t255\n+phiX\t235\t255\n+phiX\t236\t255\n+phiX\t237\t255\n+phiX\t238\t255\n+phiX\t239\t255\n+phiX\t240\t255\n+phiX\t241\t255\n+phiX\t242\t255\n+phiX\t243\t255\n+phiX\t244\t255\n+phiX\t245\t255\n+phiX\t246\t255\n+phiX\t247\t255\n+phiX\t248\t255\n+phiX\t249\t255\n+phiX\t250\t255\n+phiX\t251\t255\n+phiX\t252\t255\n+phiX\t253\t255\n+phiX\t254\t255\n+phiX\t255\t255\n+phiX\t256\t255\n+phiX\t257\t255\n+phiX\t258\t255\n+phiX\t259\t255\n+phiX\t260\t255\n+phiX\t261\t255\n+phiX\t262\t255\n+phiX\t263\t255\n+phiX\t264\t255\n+phiX\t265\t255\n+phiX\t266\t255\n+phiX\t267\t255\n+phiX\t268\t255\n+phiX\t269\t255\n+phiX\t270\t255\n+phiX\t271\t255\n+phiX\t272\t255\n+phiX\t273\t255\n+phiX\t274\t255\n+phiX\t275\t255\n+phiX\t276\t255\n+phiX\t277\t255\n+phiX\t278\t255\n+phiX\t279\t255\n+phiX\t280\t255\n+phiX\t281\t255\n+phiX\t282\t255\n+phiX\t283\t255\n+phiX\t284\t255\n+phiX\t285\t255\n+phiX\t286\t255\n+phiX\t287\t255\n+phiX\t288\t255\n+phiX\t289\t255\n+phiX\t290\t255\n+phiX\t291\t255\n+phiX\t292\t255\n'..b'5120\t255\n+phiX\t5121\t255\n+phiX\t5122\t255\n+phiX\t5123\t255\n+phiX\t5124\t255\n+phiX\t5125\t255\n+phiX\t5126\t255\n+phiX\t5127\t255\n+phiX\t5128\t255\n+phiX\t5129\t255\n+phiX\t5130\t255\n+phiX\t5131\t255\n+phiX\t5132\t255\n+phiX\t5133\t255\n+phiX\t5134\t255\n+phiX\t5135\t255\n+phiX\t5136\t255\n+phiX\t5137\t255\n+phiX\t5138\t255\n+phiX\t5139\t255\n+phiX\t5140\t255\n+phiX\t5141\t255\n+phiX\t5142\t255\n+phiX\t5143\t255\n+phiX\t5144\t255\n+phiX\t5145\t255\n+phiX\t5146\t255\n+phiX\t5147\t255\n+phiX\t5148\t255\n+phiX\t5149\t255\n+phiX\t5150\t255\n+phiX\t5151\t255\n+phiX\t5152\t255\n+phiX\t5153\t255\n+phiX\t5154\t255\n+phiX\t5155\t255\n+phiX\t5156\t255\n+phiX\t5157\t255\n+phiX\t5158\t255\n+phiX\t5159\t255\n+phiX\t5160\t255\n+phiX\t5161\t255\n+phiX\t5162\t255\n+phiX\t5163\t255\n+phiX\t5164\t255\n+phiX\t5165\t255\n+phiX\t5166\t255\n+phiX\t5167\t255\n+phiX\t5168\t255\n+phiX\t5169\t255\n+phiX\t5170\t255\n+phiX\t5171\t255\n+phiX\t5172\t255\n+phiX\t5173\t255\n+phiX\t5174\t255\n+phiX\t5175\t255\n+phiX\t5176\t255\n+phiX\t5177\t255\n+phiX\t5178\t255\n+phiX\t5179\t255\n+phiX\t5180\t255\n+phiX\t5181\t255\n+phiX\t5182\t255\n+phiX\t5183\t255\n+phiX\t5184\t255\n+phiX\t5185\t255\n+phiX\t5186\t255\n+phiX\t5187\t255\n+phiX\t5188\t255\n+phiX\t5189\t255\n+phiX\t5190\t255\n+phiX\t5191\t255\n+phiX\t5192\t255\n+phiX\t5193\t255\n+phiX\t5194\t255\n+phiX\t5195\t255\n+phiX\t5196\t255\n+phiX\t5197\t255\n+phiX\t5198\t255\n+phiX\t5199\t255\n+phiX\t5200\t255\n+phiX\t5201\t255\n+phiX\t5202\t255\n+phiX\t5203\t255\n+phiX\t5204\t255\n+phiX\t5205\t255\n+phiX\t5206\t255\n+phiX\t5207\t255\n+phiX\t5208\t255\n+phiX\t5209\t255\n+phiX\t5210\t255\n+phiX\t5211\t255\n+phiX\t5212\t255\n+phiX\t5213\t255\n+phiX\t5214\t255\n+phiX\t5215\t255\n+phiX\t5216\t255\n+phiX\t5217\t255\n+phiX\t5218\t255\n+phiX\t5219\t255\n+phiX\t5220\t255\n+phiX\t5221\t255\n+phiX\t5222\t255\n+phiX\t5223\t255\n+phiX\t5224\t255\n+phiX\t5225\t255\n+phiX\t5226\t255\n+phiX\t5227\t255\n+phiX\t5228\t255\n+phiX\t5229\t255\n+phiX\t5230\t255\n+phiX\t5231\t255\n+phiX\t5232\t255\n+phiX\t5233\t255\n+phiX\t5234\t255\n+phiX\t5235\t255\n+phiX\t5236\t255\n+phiX\t5237\t255\n+phiX\t5238\t255\n+phiX\t5239\t255\n+phiX\t5240\t255\n+phiX\t5241\t255\n+phiX\t5242\t255\n+phiX\t5243\t255\n+phiX\t5244\t255\n+phiX\t5245\t255\n+phiX\t5246\t255\n+phiX\t5247\t255\n+phiX\t5248\t255\n+phiX\t5249\t255\n+phiX\t5250\t255\n+phiX\t5251\t255\n+phiX\t5252\t255\n+phiX\t5253\t255\n+phiX\t5254\t255\n+phiX\t5255\t255\n+phiX\t5256\t255\n+phiX\t5257\t255\n+phiX\t5258\t255\n+phiX\t5259\t255\n+phiX\t5260\t255\n+phiX\t5261\t255\n+phiX\t5262\t255\n+phiX\t5263\t255\n+phiX\t5264\t255\n+phiX\t5265\t255\n+phiX\t5266\t255\n+phiX\t5267\t255\n+phiX\t5268\t255\n+phiX\t5269\t255\n+phiX\t5270\t255\n+phiX\t5271\t255\n+phiX\t5272\t255\n+phiX\t5273\t255\n+phiX\t5274\t255\n+phiX\t5275\t255\n+phiX\t5276\t255\n+phiX\t5277\t255\n+phiX\t5278\t255\n+phiX\t5279\t255\n+phiX\t5280\t255\n+phiX\t5281\t255\n+phiX\t5282\t255\n+phiX\t5283\t255\n+phiX\t5284\t255\n+phiX\t5285\t255\n+phiX\t5286\t255\n+phiX\t5287\t255\n+phiX\t5288\t255\n+phiX\t5289\t255\n+phiX\t5290\t255\n+phiX\t5291\t255\n+phiX\t5292\t255\n+phiX\t5293\t255\n+phiX\t5294\t255\n+phiX\t5295\t255\n+phiX\t5296\t255\n+phiX\t5297\t255\n+phiX\t5298\t255\n+phiX\t5299\t255\n+phiX\t5300\t255\n+phiX\t5301\t255\n+phiX\t5302\t255\n+phiX\t5303\t255\n+phiX\t5304\t255\n+phiX\t5305\t255\n+phiX\t5306\t255\n+phiX\t5307\t255\n+phiX\t5308\t255\n+phiX\t5309\t255\n+phiX\t5310\t255\n+phiX\t5311\t255\n+phiX\t5312\t255\n+phiX\t5313\t255\n+phiX\t5314\t255\n+phiX\t5315\t255\n+phiX\t5316\t255\n+phiX\t5317\t255\n+phiX\t5318\t255\n+phiX\t5319\t255\n+phiX\t5320\t255\n+phiX\t5321\t255\n+phiX\t5322\t255\n+phiX\t5323\t255\n+phiX\t5324\t255\n+phiX\t5325\t255\n+phiX\t5326\t255\n+phiX\t5327\t255\n+phiX\t5328\t255\n+phiX\t5329\t255\n+phiX\t5330\t255\n+phiX\t5331\t255\n+phiX\t5332\t255\n+phiX\t5333\t255\n+phiX\t5334\t255\n+phiX\t5335\t255\n+phiX\t5336\t255\n+phiX\t5337\t255\n+phiX\t5338\t255\n+phiX\t5339\t255\n+phiX\t5340\t255\n+phiX\t5341\t255\n+phiX\t5342\t255\n+phiX\t5343\t255\n+phiX\t5344\t255\n+phiX\t5345\t255\n+phiX\t5346\t255\n+phiX\t5347\t255\n+phiX\t5348\t255\n+phiX\t5349\t255\n+phiX\t5350\t255\n+phiX\t5351\t255\n+phiX\t5352\t255\n+phiX\t5353\t255\n+phiX\t5354\t255\n+phiX\t5355\t255\n+phiX\t5356\t255\n+phiX\t5357\t255\n+phiX\t5358\t255\n+phiX\t5359\t255\n+phiX\t5360\t255\n+phiX\t5361\t255\n+phiX\t5362\t255\n+phiX\t5363\t255\n+phiX\t5364\t255\n+phiX\t5365\t255\n+phiX\t5366\t255\n+phiX\t5367\t255\n+phiX\t5368\t255\n+phiX\t5369\t255\n+phiX\t5370\t255\n+phiX\t5371\t255\n+phiX\t5372\t255\n+phiX\t5373\t255\n+phiX\t5374\t255\n+phiX\t5375\t255\n+phiX\t5376\t255\n+phiX\t5377\t255\n+phiX\t5378\t255\n+phiX\t5379\t255\n+phiX\t5380\t255\n+phiX\t5381\t255\n+phiX\t5382\t255\n+phiX\t5383\t255\n+phiX\t5384\t255\n+phiX\t5385\t255\n+phiX\t5386\t255\n' |
| b |
| diff -r 000000000000 -r 0801f8207d30 test-data/lastz_diffs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lastz_diffs.txt Mon Nov 26 09:47:51 2012 -0500 |
| b |
| @@ -0,0 +1,19 @@ +phiX 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC +phiX 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT +phiX 578 579 + 5386 HWI-EAS91_1_306UPAAXX:6:1:317:1411 8 9 + 36 G T GTACGCTGGACTTTGTGGGATACCCTCGCTTTCCT GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT +phiX 2992 2993 + 5386 HWI-EAS91_1_306UPAAXX:6:1:458:1629 23 24 + 36 G T GCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGT GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT +phiX 4783 4784 + 5386 HWI-EAS91_1_306UPAAXX:6:1:646:59 18 19 - 36 C T CATTTCCATGCGGTGCACTTTATGCGGACACTTCC CATTTCCATGCGGTGCATTTTATGCGGACACTTCC +phiX 1649 1650 + 5386 HWI-EAS91_1_306UPAAXX:6:1:295:694 24 25 + 36 A G GTGATTACTTCATGCAGCGTTACCATGATGTTATTT GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT +phiX 1995 1996 + 5386 HWI-EAS91_1_306UPAAXX:6:1:590:331 14 15 + 36 G T GAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGAT GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT +phiX 3261 3262 + 5386 HWI-EAS91_1_306UPAAXX:6:1:221:1238 17 18 - 36 C A AAGTCTGCCGCTGATAAAGGAAAGGATAC AAGTCTGCCGATGATAAAGGAAAGGATAC +phiX 4109 4110 + 5386 HWI-EAS91_1_306UPAAXX:6:1:478:252 12 13 - 36 C A ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC +phiX 2972 2973 + 5386 HWI-EAS91_1_306UPAAXX:6:1:836:1204 17 18 + 36 G T TTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAAT TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT +phiX 2234 2235 + 5386 HWI-EAS91_1_306UPAAXX:6:1:172:1412 13 14 - 36 C A AAATTTAATGTGACCGTTTATCGCAATCTGCCGACC AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC +phiX 2902 2903 + 5386 HWI-EAS91_1_306UPAAXX:6:1:540:1415 18 19 + 36 G T TTATTAAAGAGATTATTTGTCTCCAGCCACTTA TTATTAAAGAGATTATTTTTCTCCAGCCACTTA +phiX 2837 2838 + 5386 HWI-EAS91_1_306UPAAXX:6:1:253:1162 14 15 - 36 T A ATGGTTTGGTCTAACTTTACCGCTACTAAATGC ATGGTTTGGTCAAACTTTACCGCTACTAAATGC +phiX 4662 4663 + 5386 HWI-EAS91_1_306UPAAXX:6:1:828:754 26 27 + 36 G T TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGT TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT +phiX 4783 4784 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1566:499 9 10 + 36 C T TGCGGTGCACTTTATGCGGACACTTCCTACAGGTAG TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG +phiX 2857 2858 + 5386 HWI-EAS91_1_306UPAAXX:6:1:578:971 15 16 + 36 G T CGCTACTAAATGCCGCGGATTGGTTTCG CGCTACTAAATTCCGCGGATTGGTTTCG +phiX 3112 3113 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1721:1800 27 28 - 36 T C TCAAGGCTCTAATGTTCCTAACCC TCAAGGCTCTAATGTCCCTAACCC +phiX 4825 4826 + 5386 HWI-EAS91_1_306UPAAXX:6:1:815:1640 9 10 - 36 T G CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCA CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA +phiX 4517 4518 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1485:741 19 20 - 36 G A GAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGAT GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT |
| b |
| diff -r 000000000000 -r 0801f8207d30 test-data/lastz_diffs_ref_name.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lastz_diffs_ref_name.txt Mon Nov 26 09:47:51 2012 -0500 |
| b |
| @@ -0,0 +1,19 @@ +Ref 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC +Ref 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT +Ref 578 579 + 5386 HWI-EAS91_1_306UPAAXX:6:1:317:1411 8 9 + 36 G T GTACGCTGGACTTTGTGGGATACCCTCGCTTTCCT GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT +Ref 2992 2993 + 5386 HWI-EAS91_1_306UPAAXX:6:1:458:1629 23 24 + 36 G T GCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGT GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT +Ref 4783 4784 + 5386 HWI-EAS91_1_306UPAAXX:6:1:646:59 18 19 - 36 C T CATTTCCATGCGGTGCACTTTATGCGGACACTTCC CATTTCCATGCGGTGCATTTTATGCGGACACTTCC +Ref 1649 1650 + 5386 HWI-EAS91_1_306UPAAXX:6:1:295:694 24 25 + 36 A G GTGATTACTTCATGCAGCGTTACCATGATGTTATTT GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT +Ref 1995 1996 + 5386 HWI-EAS91_1_306UPAAXX:6:1:590:331 14 15 + 36 G T GAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGAT GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT +Ref 3261 3262 + 5386 HWI-EAS91_1_306UPAAXX:6:1:221:1238 17 18 - 36 C A AAGTCTGCCGCTGATAAAGGAAAGGATAC AAGTCTGCCGATGATAAAGGAAAGGATAC +Ref 4109 4110 + 5386 HWI-EAS91_1_306UPAAXX:6:1:478:252 12 13 - 36 C A ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC +Ref 2972 2973 + 5386 HWI-EAS91_1_306UPAAXX:6:1:836:1204 17 18 + 36 G T TTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAAT TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT +Ref 2234 2235 + 5386 HWI-EAS91_1_306UPAAXX:6:1:172:1412 13 14 - 36 C A AAATTTAATGTGACCGTTTATCGCAATCTGCCGACC AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC +Ref 2902 2903 + 5386 HWI-EAS91_1_306UPAAXX:6:1:540:1415 18 19 + 36 G T TTATTAAAGAGATTATTTGTCTCCAGCCACTTA TTATTAAAGAGATTATTTTTCTCCAGCCACTTA +Ref 2837 2838 + 5386 HWI-EAS91_1_306UPAAXX:6:1:253:1162 14 15 - 36 T A ATGGTTTGGTCTAACTTTACCGCTACTAAATGC ATGGTTTGGTCAAACTTTACCGCTACTAAATGC +Ref 4662 4663 + 5386 HWI-EAS91_1_306UPAAXX:6:1:828:754 26 27 + 36 G T TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGT TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT +Ref 4783 4784 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1566:499 9 10 + 36 C T TGCGGTGCACTTTATGCGGACACTTCCTACAGGTAG TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG +Ref 2857 2858 + 5386 HWI-EAS91_1_306UPAAXX:6:1:578:971 15 16 + 36 G T CGCTACTAAATGCCGCGGATTGGTTTCG CGCTACTAAATTCCGCGGATTGGTTTCG +Ref 3112 3113 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1721:1800 27 28 - 36 T C TCAAGGCTCTAATGTTCCTAACCC TCAAGGCTCTAATGTCCCTAACCC +Ref 4825 4826 + 5386 HWI-EAS91_1_306UPAAXX:6:1:815:1640 9 10 - 36 T G CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCA CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA +Ref 4517 4518 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1485:741 19 20 - 36 G A GAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGAT GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT |
| b |
| diff -r 000000000000 -r 0801f8207d30 test-data/lastz_maf.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lastz_maf.txt Mon Nov 26 09:47:51 2012 -0500 |
| b |
| b'@@ -0,0 +1,1982 @@\n+##maf version=1 scoring=lastz.v1.00.23\n+# lastz.v1.00.23 --yasra95short --ambiguousn --identity=0..100 --census=/Users/anton/galaxy_central/database/files/000/dataset_128.dat --coverage=0 --format=maf \n+#\n+# hsp_threshold = 10\n+# gapped_threshold = 14\n+# x_drop = 10\n+# y_drop = 14\n+# gap_open_penalty = 6\n+# gap_extend_penalty = 1\n+# A C G T\n+# A 1 -7 -7 -7\n+# C -7 1 -7 -7\n+# G -7 -7 1 -7\n+# T -7 -7 -7 1\n+a score=35\n+s phiX 4294 35 + 5386 CCCCCAACTTGATATTAATAACACTATAGACCACC\n+s read 1 35 - 36 CCCCCAACTTGATATTAATAACACTATAGACCACC\n+\n+a score=36\n+s phiX 3521 36 + 5386 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC\n+s read 0 36 - 36 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC\n+\n+a score=36\n+s phiX 228 36 + 5386 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC\n+s read 0 36 + 36 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC\n+\n+a score=36\n+s phiX 2070 36 + 5386 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT\n+s read 0 36 + 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT\n+\n+a score=35\n+s phiX 1066 35 + 5386 GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC\n+s read 1 35 - 36 GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC\n+\n+a score=36\n+s phiX 1787 36 + 5386 GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC\n+s read 0 36 + 36 GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC\n+\n+a score=36\n+s phiX 1192 36 + 5386 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC\n+s read 0 36 + 36 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC\n+\n+a score=33\n+s phiX 4562 33 + 5386 GGTTGGTTTATCGTTTTTGACACTCTCACGTTG\n+s read 0 33 + 36 GGTTGGTTTATCGTTTTTGACACTCTCACGTTG\n+\n+a score=36\n+s phiX 2667 36 + 5386 GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC\n+s read 0 36 + 36 GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC\n+\n+a score=36\n+s phiX 4247 36 + 5386 GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC\n+s read 0 36 + 36 GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC\n+\n+a score=36\n+s phiX 2862 36 + 5386 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT\n+s read 0 36 + 36 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT\n+\n+a score=36\n+s phiX 2556 36 + 5386 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC\n+s read 0 36 + 36 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC\n+\n+a score=34\n+s phiX 2510 34 + 5386 GTCAACGTTATATTTTGATAGTTTGACGGTTAAT\n+s read 0 34 + 36 GTCAACGTTATATTTTGATAGTTTGACGGTTAAT\n+\n+a score=36\n+s phiX 5151 36 + 5386 GGATGAAAATGCTCACAATGACAAATCTGTCCACGG\n+s read 0 36 + 36 GGATGAAAATGCTCACAATGACAAATCTGTCCACGG\n+\n+a score=36\n+s phiX 1589 36 + 5386 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC\n+s read 0 36 - 36 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC\n+\n+a score=36\n+s phiX 4883 36 + 5386 GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG\n+s read 0 36 + 36 GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG\n+\n+a score=36\n+s phiX 5051 36 + 5386 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA\n+s read 0 36 + 36 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA\n+\n+a score=36\n+s phiX 4908 36 + 5386 GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT\n+s read 0 36 + 36 GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT\n+\n+a score=36\n+s phiX 2862 36 + 5386 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT\n+s read 0 36 + 36 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT\n+\n+a score=30\n+s phiX 4172 30 + 5386 GTTGAGTTCGATAATGGTGATATGTATGTT\n+s read 0 30 + 36 GTTGAGTTCGATAATGGTGATATGTATGTT\n+\n+a score=36\n+s phiX 1700 36 + 5386 GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT\n+s read 0 36 + 36 GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT\n+\n+a score=36\n+s phiX 1682 36 + 5386 CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC\n+s read 0 36 - 36 CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC\n+\n+a score=35\n+s phiX 3125 35 + 5386 GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC\n+s read 1 35 - 36 GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC\n+\n+a score=36\n+s phiX 1664 36 + 5386 CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC\n+s read 0 36 - 36 CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC\n+\n+a score=36\n+s phiX 3212 36 + 5386 GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT\n+s read 0 36 + 36 GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT\n+\n+a score=36\n+s phiX 3419 36 + 5386 GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG\n+s read 0 36 + 36 GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG\n+\n+a score=36\n+s phiX 512 3'..b's read 0 36 - 36 ATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT\n+\n+a score=36\n+s phiX 1001 36 + 5386 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC\n+s read 0 36 + 36 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC\n+\n+a score=36\n+s phiX 4380 36 + 5386 AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA\n+s read 0 36 - 36 AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA\n+\n+a score=36\n+s phiX 4255 36 + 5386 GAAGTTAATGGATGAATTGGCACAATGCTACAATGT\n+s read 0 36 - 36 GAAGTTAATGGATGAATTGGCACAATGCTACAATGT\n+\n+a score=35\n+s phiX 9 35 + 5386 CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA\n+s read 1 35 - 36 CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA\n+\n+a score=36\n+s phiX 1578 36 + 5386 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC\n+s read 0 36 - 36 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC\n+\n+a score=30\n+s phiX 988 30 + 5386 TGAGGATAAATTATGTCTAATATTCAAACT\n+s read 0 30 + 36 TGAGGATAAATTATGTCTAATATTCAAACT\n+\n+a score=36\n+s phiX 3861 36 + 5386 ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT\n+s read 0 36 + 36 ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT\n+\n+a score=36\n+s phiX 3277 36 + 5386 TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT\n+s read 0 36 + 36 TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT\n+\n+a score=36\n+s phiX 348 36 + 5386 TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG\n+s read 0 36 + 36 TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG\n+\n+a score=36\n+s phiX 4607 36 + 5386 TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT\n+s read 0 36 + 36 TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT\n+\n+a score=35\n+s phiX 3807 35 + 5386 GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT\n+s read 0 35 + 36 GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT\n+\n+a score=31\n+s phiX 4752 31 + 5386 CTAATGGCCGTCTTCATTTCCATGCGGTGCA\n+s read 0 31 - 36 CTAATGGCCGTCTTCATTTCCATGCGGTGCA\n+\n+a score=36\n+s phiX 285 36 + 5386 GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT\n+s read 0 36 - 36 GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT\n+\n+a score=36\n+s phiX 2849 36 + 5386 TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT\n+s read 0 36 + 36 TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT\n+\n+a score=35\n+s phiX 679 35 + 5386 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA\n+s read 1 35 - 36 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA\n+\n+a score=36\n+s phiX 4739 36 + 5386 GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT\n+s read 0 36 - 36 GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT\n+\n+a score=25\n+s phiX 4654 25 + 5386 TGATATTGGTCGTATGGTTCTTGCT\n+s read 0 25 + 36 TGATATTGGTCGTATGGTTCTTGCT\n+\n+a score=35\n+s phiX 2466 35 + 5386 CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA\n+s read 1 35 - 36 CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA\n+\n+a score=34\n+s phiX 319 34 + 5386 TTGACATTTTAAAAGAGCGTGGATTACTATCTGA\n+s read 0 34 + 36 TTGACATTTTAAAAGAGCGTGGATTACTATCTGA\n+\n+a score=34\n+s phiX 1179 34 + 5386 TATTGACTCTACTGTAGACATTTTTACTTTTTAT\n+s read 0 34 + 36 TATTGACTCTACTGTAGACATTTTTACTTTTTAT\n+\n+a score=36\n+s phiX 520 36 + 5386 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA\n+s read 0 36 - 36 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA\n+\n+a score=36\n+s phiX 332 36 + 5386 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA\n+s read 0 36 - 36 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA\n+\n+a score=36\n+s phiX 2755 36 + 5386 ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC\n+s read 0 36 + 36 ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC\n+\n+a score=36\n+s phiX 4956 36 + 5386 ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA\n+s read 0 36 - 36 ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA\n+\n+a score=36\n+s phiX 71 36 + 5386 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA\n+s read 0 36 - 36 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA\n+\n+a score=36\n+s phiX 4248 36 + 5386 TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT\n+s read 0 36 - 36 TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT\n+\n+a score=36\n+s phiX 2591 36 + 5386 CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA\n+s read 0 36 - 36 CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA\n+\n+a score=36\n+s phiX 1973 36 + 5386 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT\n+s read 0 36 - 36 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT\n+\n+a score=36\n+s phiX 3539 36 + 5386 AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA\n+s read 0 36 - 36 AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA\n+\n+a score=36\n+s phiX 4129 36 + 5386 CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT\n+s read 0 36 - 36 CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT\n+\n' |
| b |
| diff -r 000000000000 -r 0801f8207d30 test-data/lastz_wrapper_out2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lastz_wrapper_out2.sam Mon Nov 26 09:47:51 2012 -0500 |
| b |
| b'@@ -0,0 +1,459 @@\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4295\t255\t1H35M\t*\t0\t0\tCCCCCAACTTGATATTAATAACACTATAGACCACC\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t3522\t255\t36M\t*\t0\t0\tATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t229\t255\t36M\t*\t0\t0\tGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t2071\t255\t36M\t*\t0\t0\tGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t1067\t255\t1H35M\t*\t0\t0\tGGTCAGATTGGTCGTCTTATTACCATTTCAACTAC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t1788\t255\t36M\t*\t0\t0\tGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t1193\t255\t36M\t*\t0\t0\tGTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t4563\t255\t36M\t*\t0\t0\tGGTTGGTTTATCGTTTTTGACACTCTCACGTTGTCT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t2668\t255\t36M\t*\t0\t0\tGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t4248\t255\t36M\t*\t0\t0\tGTTACTGAGAAGTTAATGGATGAATTGGCACAATGC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t2863\t255\t36M\t*\t0\t0\tGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t2557\t255\t36M\t*\t0\t0\tGGTTTTCTTCATTGCATTCAGATGGATACATCTGTC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t2511\t255\t34M2H\t*\t0\t0\tGTCAACGTTATATTTTGATAGTTTGACGGTTAAT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t5152\t255\t36M\t*\t0\t0\tGGATGAAAATGCTCACAATGACAAATCTGTCCACGG\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t1590\t255\t36M\t*\t0\t0\tAAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t4884\t255\t36M\t*\t0\t0\tGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t5052\t255\t36M\t*\t0\t0\tGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t4909\t255\t36M\t*\t0\t0\tGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t2863\t255\t36M\t*\t0\t0\tGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t4173\t255\t36M\t*\t0\t0\tGTTGAGTTCGATAATGGTGATATGTATGTTTACGGC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t1701\t255\t36M\t*\t0\t0\tGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t1683\t255\t36M\t*\t0\t0\tCTTATGACGCTGACAACCGTCCTTTACTTGTCATGC\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t3126\t255\t1H35M\t*\t0\t0\tGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t1665\t255\t36M\t*\t0\t0\tCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t3213\t255\t36M\t*\t0\t0\tGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t3420\t255\t36M\t*\t0\t0\tGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t513\t255\t36M\t*\t0\t0\tGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t2879\t255\t36M\t*\t0\t0\tATAAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t4471\t255\t36M\t*\t0\t0\tGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t1229\t255\t36M\t*\t0\t0\tGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t615\t255\t36M\t*\t0\t0\tGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t257\t255\t36M\t*\t0\t0\tGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCAC\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t2381\t255\t36M\t*\t0\t0\tTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4098\t255\t36M\t*\t0\t0\tATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t5099\t255\t36M\t*\t0\t0\tGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t4254\t255\t36M\t*\t0\t0\tGAGAAGTTAATGGATGAATTGGCACAATGCTACAAT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t3408\t255\t36M\t*\t0\t0\tGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4043\t255\t36M\t*\t0\t0\tGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t4560\t255\t36M\t*\t0\t0\tGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t1888\t255\t36M\t*\t0\t0\tGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t3434\t255\t1H35M\t*\t0\t0\tGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t4539\t255\t36M\t*\t0\t0\tGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t1828\t255\t36M\t*\t0\t0\tCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t3708\t255\t36M\t*\t0\t0\tGA'..b'iX174\t1867\t255\t36M\t*\t0\t0\tTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t3780\t255\t36M\t*\t0\t0\tTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGTTT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t3982\t255\t36M\t*\t0\t0\tTGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t2815\t255\t36M\t*\t0\t0\tTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t1242\t255\t36M\t*\t0\t0\tAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4659\t255\t1H35M\t*\t0\t0\tATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAA\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t2436\t255\t36M\t*\t0\t0\tTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t527\t255\t35M1H\t*\t0\t0\tTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4817\t255\t36M\t*\t0\t0\tCCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t2100\t255\t36M\t*\t0\t0\tAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t2762\t255\t36M\t*\t0\t0\tTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t4955\t255\t36M\t*\t0\t0\tTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t3761\t255\t36M\t*\t0\t0\tCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4499\t255\t36M\t*\t0\t0\tGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4039\t255\t36M\t*\t0\t0\tTCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4788\t255\t36M\t*\t0\t0\tATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t1002\t255\t36M\t*\t0\t0\tTGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4381\t255\t36M\t*\t0\t0\tAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4256\t255\t36M\t*\t0\t0\tGAAGTTAATGGATGAATTGGCACAATGCTACAATGT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t10\t255\t1H35M\t*\t0\t0\tCGCTTCCATGACGCAGAAGTTAACACTTTCGGATA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t1579\t255\t36M\t*\t0\t0\tTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t3862\t255\t36M\t*\t0\t0\tATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t3278\t255\t36M\t*\t0\t0\tTACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t349\t255\t36M\t*\t0\t0\tTCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t4608\t255\t36M\t*\t0\t0\tTTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t3808\t255\t35M1H\t*\t0\t0\tGTGTGGTTGATATTTTTCATGGTATTGATAAAGCT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4753\t255\t36M\t*\t0\t0\tCTAATGGCCGTCTTCATTTCCATGCGGTGCATTTTA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t286\t255\t36M\t*\t0\t0\tGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t2850\t255\t36M\t*\t0\t0\tTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t680\t255\t1H35M\t*\t0\t0\tCATGGAAGGCGCTGAATTTACGGAAAACATTATTA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4740\t255\t36M\t*\t0\t0\tGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t2467\t255\t1H35M\t*\t0\t0\tCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t320\t255\t34M2H\t*\t0\t0\tTTGACATTTTAAAAGAGCGTGGATTACTATCTGA\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t1180\t255\t34M2H\t*\t0\t0\tTATTGACTCTACTGTAGACATTTTTACTTTTTAT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t521\t255\t36M\t*\t0\t0\tTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t333\t255\t36M\t*\t0\t0\tAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA\t*\n+HWI-EAS91_1_306UPAAXX\t0\tphiX174\t2756\t255\t36M\t*\t0\t0\tATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4957\t255\t36M\t*\t0\t0\tATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t72\t255\t36M\t*\t0\t0\tATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4249\t255\t36M\t*\t0\t0\tTTACTGAGAAGTTAATGGATGAATTGGCACAATGCT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t2592\t255\t36M\t*\t0\t0\tCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t1974\t255\t36M\t*\t0\t0\tCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t3540\t255\t36M\t*\t0\t0\tAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA\t*\n+HWI-EAS91_1_306UPAAXX\t16\tphiX174\t4130\t255\t36M\t*\t0\t0\tCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT\t*\n' |
| b |
| diff -r 000000000000 -r 0801f8207d30 test-data/lastz_wrapper_out3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lastz_wrapper_out3.tabular Mon Nov 26 09:47:51 2012 -0500 |
| b |
| @@ -0,0 +1,22 @@ +phiX174 1164 1165 + 5386 HWI-EAS91_1_306UPAAXX:6:1:112:1280 26 27 + 36 G T GTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTG GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG +phiX174 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC +phiX174 2205 2206 + 5386 HWI-EAS91_1_306UPAAXX:6:1:217:737 14 15 + 36 G T GTTCAGTTGTTGCAGTGGAATA GTTCAGTTGTTGCATTGGAATA +phiX174 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT +phiX174 578 579 + 5386 HWI-EAS91_1_306UPAAXX:6:1:317:1411 8 9 + 36 G T GTACGCTGGACTTTGTGGGATACCCTCGCTTTCCT GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT +phiX174 2992 2993 + 5386 HWI-EAS91_1_306UPAAXX:6:1:458:1629 23 24 + 36 G T GCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGT GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT +phiX174 1995 1996 + 5386 HWI-EAS91_1_306UPAAXX:6:1:590:331 14 15 + 36 G T GAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGAT GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT +phiX174 3261 3262 + 5386 HWI-EAS91_1_306UPAAXX:6:1:221:1238 17 18 - 36 C A AAGTCTGCCGCTGATAAAGGAAAGGATAC AAGTCTGCCGATGATAAAGGAAAGGATAC +phiX174 4109 4110 + 5386 HWI-EAS91_1_306UPAAXX:6:1:478:252 12 13 - 36 C A ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC +phiX174 3126 3127 + 5386 HWI-EAS91_1_306UPAAXX:6:1:589:96 28 29 - 36 A G CAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCC CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC +phiX174 2569 2570 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1472:716 23 24 + 36 G T TGGTAATGGTGGTTTTCTTCATTGCATTCAG TGGTAATGGTGGTTTTCTTCATTTCATTCAG +phiX174 2972 2973 + 5386 HWI-EAS91_1_306UPAAXX:6:1:836:1204 17 18 + 36 G T TTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAAT TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT +phiX174 2234 2235 + 5386 HWI-EAS91_1_306UPAAXX:6:1:172:1412 13 14 - 36 C A AAATTTAATGTGACCGTTTATCGCAATCTGCCGACC AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC +phiX174 2902 2903 + 5386 HWI-EAS91_1_306UPAAXX:6:1:540:1415 18 19 + 36 G T TTATTAAAGAGATTATTTGTCTCCAGCCACTTA TTATTAAAGAGATTATTTTTCTCCAGCCACTTA +phiX174 2837 2838 + 5386 HWI-EAS91_1_306UPAAXX:6:1:253:1162 14 15 - 36 T A ATGGTTTGGTCTAACTTTACCGCTACTAAATGC ATGGTTTGGTCAAACTTTACCGCTACTAAATGC +phiX174 4662 4663 + 5386 HWI-EAS91_1_306UPAAXX:6:1:828:754 26 27 + 36 G T TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGT TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT +phiX174 4202 4203 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 19 20 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG +phiX174 4206 4207 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 23 24 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG +phiX174 430 431 + 5386 HWI-EAS91_1_306UPAAXX:6:1:203:667 9 10 - 36 T C AGACCGCTTTGGCCTCTATTAAGC AGACCGCCTTGGCCTCTATTAAGC +phiX174 2857 2858 + 5386 HWI-EAS91_1_306UPAAXX:6:1:578:971 15 16 + 36 G T CGCTACTAAATGCCGCGGATTGGTTTCG CGCTACTAAATTCCGCGGATTGGTTTCG +phiX174 3112 3113 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1721:1800 27 28 - 36 T C TCAAGGCTCTAATGTTCCTAACCC TCAAGGCTCTAATGTCCCTAACCC +phiX174 4825 4826 + 5386 HWI-EAS91_1_306UPAAXX:6:1:815:1640 9 10 - 36 T G CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCA CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA |
| b |
| diff -r 000000000000 -r 0801f8207d30 test-data/lastz_wrapper_out4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lastz_wrapper_out4.tabular Mon Nov 26 09:47:51 2012 -0500 |
| b |
| b'@@ -0,0 +1,491 @@\n+14\tphiX1\t+\t2310\t2192\t2191\t2213\t22\tGTTCAGTTGTTGCAGTGGAATA\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t22\t1\t0\t22\t22\tGTTCAGTTGTTGCATTGGAATA\t..............x.......\t22M\t21/22\t95.5%\t22/36\t61.1%\t0/22\t0.0%\t2191\tNA\n+16\tphiX1\t+\t2310\t424\t423\t447\t24\tAGACCGCTTTGGCCTCTATTAAGC\tHWI-EAS91_1_306UPAAXX\t-\t36\t3\t2\t26\t11\t10\t34\t24\tAGACCGCCTTGGCCTCTATTAAGC\t.......:................\t24M\t23/24\t95.8%\t24/36\t66.7%\t0/24\t0.0%\t421\tNA\n+16\tphiX2\t+\t3076\t788\t787\t811\t24\tTCAAGGCTCTAATGTTCCTAACCC\tHWI-EAS91_1_306UPAAXX\t-\t36\t13\t12\t36\t1\t0\t24\t24\tTCAAGGCTCTAATGTCCCTAACCC\t...............:........\t24M\t23/24\t95.8%\t24/36\t66.7%\t0/24\t0.0%\t775\tNA\n+18\tphiX1\t+\t2310\t657\t656\t674\t18\tAACATTCAAACGGCCTGT\tHWI-EAS91_1_306UPAAXX\t-\t36\t19\t18\t36\t1\t0\t18\t18\tAACATTCAAACGGCCTGT\t..................\t18M\t18/18\t100.0%\t18/36\t50.0%\t0/18\t0.0%\t638\tNA\n+18\tphiX2\t+\t3076\t1421\t1420\t1438\t18\tGAATCAGCGGTATGGCTC\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t18\t1\t0\t18\t18\tGAATCAGCGGTATGGCTC\t..................\t18M\t18/18\t100.0%\t18/36\t50.0%\t0/18\t0.0%\t1420\tNA\n+18\tphiX2\t+\t3076\t2625\t2624\t2642\t18\tTCTGGTTGGTTGTGGCCT\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t18\t1\t0\t18\t18\tTCTGGTTGGTTGTGGCCT\t..................\t18M\t18/18\t100.0%\t18/36\t50.0%\t0/18\t0.0%\t2624\tNA\n+19\tphiX2\t+\t3076\t1874\t1873\t1908\t35\tTAATGGTGATATGTATGTTGACGGCCATAAGGCTG\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t35\t1\t0\t35\t35\tTAATGGTGATATGTATGTTTACGTCCATAAGGCTG\t...................x...x...........\t35M\t33/35\t94.3%\t35/36\t97.2%\t0/35\t0.0%\t1873\tNA\n+20\tphiX2\t+\t3076\t537\t536\t564\t28\tCGCTACTAAATGCCGCGGATTGGTTTCG\tHWI-EAS91_1_306UPAAXX\t+\t36\t5\t4\t32\t5\t4\t32\t28\tCGCTACTAAATTCCGCGGATTGGTTTCG\t...........x................\t28M\t27/28\t96.4%\t28/36\t77.8%\t0/28\t0.0%\t532\tNA\n+20\tphiX2\t+\t3076\t628\t627\t647\t20\tGTGCTATTGCTGGCGGTATT\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t20\t1\t0\t20\t20\tGTGCTATTGCTGGCGGTATT\t....................\t20M\t20/20\t100.0%\t20/36\t55.6%\t0/20\t0.0%\t627\tNA\n+21\tphiX1\t+\t2310\t1\t0\t21\t21\tGAGTTTTATCGCTTCCATGAC\tHWI-EAS91_1_306UPAAXX\t-\t36\t16\t15\t36\t1\t0\t21\t21\tGAGTTTTATCGCTTCCATGAC\t.....................\t21M\t21/21\t100.0%\t21/36\t58.3%\t0/21\t0.0%\t-15\t-21\n+21\tphiX2\t+\t3076\t1990\t1989\t2010\t21\tAACTTGATATTAATAACACTA\tHWI-EAS91_1_306UPAAXX\t-\t36\t16\t15\t36\t1\t0\t21\t21\tAACTTGATATTAATAACACTA\t.....................\t21M\t21/21\t100.0%\t21/36\t58.3%\t0/21\t0.0%\t1974\tNA\n+21\tphiX2\t+\t3076\t942\t941\t970\t29\tAAGTCTGCCGCTGATAAAGGAAAGGATAC\tHWI-EAS91_1_306UPAAXX\t-\t36\t8\t7\t36\t1\t0\t29\t29\tAAGTCTGCCGATGATAAAGGAAAGGATAC\t..........x..................\t29M\t28/29\t96.6%\t29/36\t80.6%\t0/29\t0.0%\t934\tNA\n+22\tphiX1\t+\t2310\t2289\t2288\t2310\t22\tAGATTGAGTGTGAGGTTATAAC\tHWI-EAS91_1_306UPAAXX\t-\t36\t1\t0\t22\t15\t14\t36\t22\tAGATTGAGTGTGAGGTTATAAC\t......................\t22M\t22/22\t100.0%\t22/36\t61.1%\t0/22\t0.0%\t2288\t22\n+23\tphiX2\t+\t3076\t237\t236\t267\t31\tTGGTAATGGTGGTTTTCTTCATTGCATTCAG\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t31\t1\t0\t31\t31\tTGGTAATGGTGGTTTTCTTCATTTCATTCAG\t.......................x.......\t31M\t30/31\t96.8%\t31/36\t86.1%\t0/31\t0.0%\t236\tNA\n+24\tphiX2\t+\t3076\t1420\t1419\t1443\t24\tAGAATCAGCGGTATGGCTCTTCTC\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t24\t1\t0\t24\t24\tAGAATCAGCGGTATGGCTCTTCTC\t........................\t24M\t24/24\t100.0%\t24/36\t66.7%\t0/24\t0.0%\t1419\tNA\n+25\tphiX1\t+\t2310\t2286\t2285\t2310\t25\tAAAAGATTGAGTGTGAGGTTATAAC\tHWI-EAS91_1_306UPAAXX\t-\t36\t1\t0\t25\t12\t11\t36\t25\tAAAAGATTGAGTGTGAGGTTATAAC\t.........................\t25M\t25/25\t100.0%\t25/36\t69.4%\t0/25\t0.0%\t2285\t25\n+25\tphiX2\t+\t3076\t188\t187\t212\t25\tCTAAAGCTACATCGTCAACGTTATA\tHWI-EAS91_1_306UPAAXX\t-\t36\t12\t11\t36\t1\t0\t25\t25\tCTAAAGCTACATCGTCAACGTTATA\t.........................\t25M\t25/25\t100.0%\t25/36\t69.4%\t0/25\t0.0%\t176\tNA\n+25\tphiX2\t+\t3076\t2345\t2344\t2369\t25\tTGATATTGGTCGTATGGTTCTTGCT\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t25\t1\t0\t25\t25\tTGATATTGGTCGTATGGTTCTTGCT\t.........................\t25M\t25/25\t100.0%\t25/36\t69.4%\t0/25\t0.0%\t2344\tNA\n+25\tphiX2\t+\t3076\t517\t516\t549\t33\tATGGTTTGGTCTAACTTTACCGCTACTAAATGC\tHWI-EAS91_1_306UPAAXX\t-\t36\t4\t3\t36\t1\t0\t33\t33\tATGGTTTGGTCAAACTTTACCGCTACTAAATGC\t...........x.....................\t33M\t32/33\t97.0%\t33/36\t91.7%\t0/33\t0.0%\t513\tNA\n+25\tphiX2\t+\t3076\t575\t574\t607\t33\tTTATTAAAGAGATTATTTGTCTCCAGCCACTTA\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t33\t1\t0\t33\t33\tTTATTAAAGAGATTATTTTTCTCCAGCCACTTA\t..................x..............'..b'.0%\t0/36\t0.0%\t704\tNA\n+36\tphiX2\t+\t3076\t71\t70\t106\t36\tTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC\tHWI-EAS91_1_306UPAAXX\t-\t36\t1\t0\t36\t1\t0\t36\t36\tTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t70\tNA\n+36\tphiX2\t+\t3076\t711\t710\t746\t36\tGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t36\t1\t0\t36\t36\tGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t710\tNA\n+36\tphiX2\t+\t3076\t772\t771\t807\t36\tGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA\tHWI-EAS91_1_306UPAAXX\t-\t36\t1\t0\t36\t1\t0\t36\t36\tGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t771\tNA\n+36\tphiX2\t+\t3076\t783\t782\t818\t36\tGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t36\t1\t0\t36\t36\tGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t782\tNA\n+36\tphiX2\t+\t3076\t786\t785\t821\t36\tATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC\tHWI-EAS91_1_306UPAAXX\t-\t36\t1\t0\t36\t1\t0\t36\t36\tATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t785\tNA\n+36\tphiX2\t+\t3076\t790\t789\t825\t36\tAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCC\tHWI-EAS91_1_306UPAAXX\t-\t36\t1\t0\t36\t1\t0\t36\t36\tAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCC\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t789\tNA\n+36\tphiX2\t+\t3076\t809\t808\t844\t36\tCCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC\tHWI-EAS91_1_306UPAAXX\t-\t36\t1\t0\t36\t1\t0\t36\t36\tCCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t808\tNA\n+36\tphiX2\t+\t3076\t817\t816\t852\t36\tAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA\tHWI-EAS91_1_306UPAAXX\t-\t36\t1\t0\t36\t1\t0\t36\t36\tAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t816\tNA\n+36\tphiX2\t+\t3076\t841\t840\t876\t36\tGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t36\t1\t0\t36\t36\tGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t840\tNA\n+36\tphiX2\t+\t3076\t857\t856\t892\t36\tTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t36\t1\t0\t36\t36\tTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t856\tNA\n+36\tphiX2\t+\t3076\t903\t902\t938\t36\tGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t36\t1\t0\t36\t36\tGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t902\tNA\n+36\tphiX2\t+\t3076\t940\t939\t975\t36\tGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t36\t1\t0\t36\t36\tGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t939\tNA\n+36\tphiX2\t+\t3076\t951\t950\t986\t36\tGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t36\t1\t0\t36\t36\tGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t950\tNA\n+36\tphiX2\t+\t3076\t961\t960\t996\t36\tGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC\tHWI-EAS91_1_306UPAAXX\t-\t36\t1\t0\t36\t1\t0\t36\t36\tGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t960\tNA\n+36\tphiX2\t+\t3076\t967\t966\t1002\t36\tATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC\tHWI-EAS91_1_306UPAAXX\t-\t36\t1\t0\t36\t1\t0\t36\t36\tATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t966\tNA\n+36\tphiX2\t+\t3076\t968\t967\t1003\t36\tTACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT\tHWI-EAS91_1_306UPAAXX\t+\t36\t1\t0\t36\t1\t0\t36\t36\tTACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t967\tNA\n+36\tphiX2\t+\t3076\t974\t973\t1009\t36\tTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC\tHWI-EAS91_1_306UPAAXX\t-\t36\t1\t0\t36\t1\t0\t36\t36\tTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC\t....................................\t36M\t36/36\t100.0%\t36/36\t100.0%\t0/36\t0.0%\t973\tNA\n' |
| b |
| diff -r 000000000000 -r 0801f8207d30 test-data/phiX.2bit |
| b |
| Binary file test-data/phiX.2bit has changed |
| b |
| diff -r 000000000000 -r 0801f8207d30 test-data/phiX.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fasta Mon Nov 26 09:47:51 2012 -0500 |
| b |
| @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA + |
| b |
| diff -r 000000000000 -r 0801f8207d30 test-data/phiX_split.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX_split.fasta Mon Nov 26 09:47:51 2012 -0500 |
| b |
| @@ -0,0 +1,79 @@ +>phiX1 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +>phiX2 +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA |
| b |
| diff -r 000000000000 -r 0801f8207d30 tool-data/lastz_seqs.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/lastz_seqs.loc.sample Mon Nov 26 09:47:51 2012 -0500 |
| b |
| @@ -0,0 +1,30 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of 2bit genome files for use with Lastz. You will +#need to supply these files and then create a lastz_seqs.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The lastz_seqs.loc +#file has this format (white space characters are TAB characters): +# +#<unique_build_id> <display_name> <file_path> +# +#So, for example, if your lastz_seqs.loc began like this: +# +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +# +#then your /depot/data2/galaxy/twobit/ directory +#would need to contain the following 2bit files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit +# +#Your lastz_seqs.loc file should include an entry per line for +#each file you have stored that you want to be available. Note that +#your files should all have the extension '2bit'. +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. +# |
| b |
| diff -r 000000000000 -r 0801f8207d30 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Nov 26 09:47:51 2012 -0500 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of 2bit sequence files for use in Lastz --> + <table name="lastz_seqs" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/lastz_seqs.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 0801f8207d30 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Nov 26 09:47:51 2012 -0500 |
| b |
| @@ -0,0 +1,26 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="lastz" version="1.02.00"> + <install version="1.0"> + <actions> + <action type="download_by_url" target_filename="lastz-distrib-1.02.00.tar.gz">http://www.bx.psu.edu/miller_lab/dist/lastz-1.02.00.tar.gz</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>src/lastz</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>src/lastz_D</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. + </readme> + </package> +</tool_dependency> + |