| Next changeset 1:e1c59c194b7b (2013-04-01) |
|
Commit message:
Uploaded tarball |
|
added:
bowtie_wrapper.py bowtie_wrapper.xml test-data/bowtie_in2.fastqsanger test-data/bowtie_in5.fastqillumina test-data/bowtie_in5.fastqsanger test-data/bowtie_in5.fastqsolexa test-data/bowtie_in6.fastqillumina test-data/bowtie_in6.fastqsanger test-data/bowtie_in6.fastqsolexa test-data/bowtie_out10.sam test-data/bowtie_out6.sam test-data/bowtie_out7.sam test-data/bowtie_out8_1.fastq test-data/bowtie_out8_1.fastqillumina.sorted test-data/bowtie_out8_1.fastqsolexa.sorted test-data/bowtie_out8_2.fastq test-data/bowtie_out8_2.fastqillumina.sorted test-data/bowtie_out8_2.fastqsolexa.sorted test-data/bowtie_out9.sam test-data/phiX.fasta tool-data/bowtie_indices.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c bowtie_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bowtie_wrapper.py Mon Nov 26 09:43:28 2012 -0500 |
| [ |
| b'@@ -0,0 +1,469 @@\n+#!/usr/bin/env python\n+\n+"""\n+Runs Bowtie on single-end or paired-end data.\n+For use with Bowtie v. 0.12.7\n+\n+usage: bowtie_wrapper.py [options]\n+ -t, --threads=t: The number of threads to run\n+ -o, --output=o: The output file\n+ --output_unmapped_reads=: File name for unmapped reads (single-end)\n+ --output_unmapped_reads_l=: File name for unmapped reads (left, paired-end)\n+ --output_unmapped_reads_r=: File name for unmapped reads (right, paired-end)\n+ --output_suppressed_reads=: File name for suppressed reads because of max setting (single-end)\n+ --output_suppressed_reads_l=: File name for suppressed reads because of max setting (left, paired-end)\n+ --output_suppressed_reads_r=: File name for suppressed reads because of max setting (right, paired-end)\n+ -i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format\n+ -I, --input2=I: The reverse reads file in Sanger FASTQ format\n+ -4, --dataType=4: The type of data (SOLiD or Solexa)\n+ -2, --paired=2: Whether the data is single- or paired-end\n+ -g, --genomeSource=g: The type of reference provided\n+ -r, --ref=r: The reference genome to use or index\n+ -s, --skip=s: Skip the first n reads\n+ -a, --alignLimit=a: Only align the first n reads\n+ -T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment\n+ -L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment\n+ -m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed\n+ -M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions\n+ -l, --seedLen=l: Seed length\n+ -n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30\n+ -P, --maqSoapAlign=P: Choose MAQ- or SOAP-like alignment policy\n+ -w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist\n+ -v, --valAlign=v: Report up to n valid arguments per read\n+ -V, --allValAligns=V: Whether or not to report all valid alignments per read\n+ -G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist\n+ -b, --best=b: Whether or not to make Bowtie guarantee that reported singleton alignments are \'best\' in terms of stratum and in terms of the quality values at the mismatched positions\n+ -B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read\n+ -R, --strata=R: Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable\n+ -j, --minInsert=j: Minimum insert size for valid paired-end alignments\n+ -J, --maxInsert=J: Maximum insert size for valid paired-end alignments\n+ -O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand\n+ -A, --maxAlignAttempt=A: Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate\n+ -f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand\n+ -E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand\n+ -F, --offrate=F: Override the offrate of the index to n\n+ -8, --snpphred=8: SNP penalty on Phred scale\n+ -6, --snpfrac=6: Fraction of sites expected to be SNP sites\n+ -7, --keepends=7: Keep extreme-end nucleotides and qualities\n+ -S, --seed=S: Seed for pseudo-random number generator\n+ -C, --params=C: Whether to use default or specified parameters\n+ -u, --iautoB=u: Automatic or specified behavior\n+ -K, --ipacked=K: Whether or not to use a packed representation for DNA strings\n+ -Q, --ibmax=Q: Maximum number of suffixes allowed in a block\n+ -Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference\n+ -D, --idcv=D: The period for the difference-cover sample\n+ -U, '..b'smatchSeed, mismatchQual, seedLen, rounding, minInsert, \n+ maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,\n+ tryHard, valAlign, allValAligns, suppressAlign, best,\n+ strata, offrate, seed, snpphred, snpfrac, keepends,\n+ output_unmapped_reads, output_suppressed_reads,\n+ quality_score_encoding )\n+ except ValueError, e:\n+ # clean up temp dir\n+ if os.path.exists( tmp_index_dir ):\n+ shutil.rmtree( tmp_index_dir )\n+ stop_err( \'Something is wrong with the alignment parameters and the alignment could not be run\\n\' + str( e ) )\n+ try:\n+ # have to nest try-except in try-finally to handle 2.4\n+ try:\n+ # prepare actual mapping commands\n+ if options.paired == \'paired\':\n+ cmd2 = \'bowtie %s %s -1 %s -2 %s > %s\' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )\n+ else:\n+ cmd2 = \'bowtie %s %s %s > %s\' % ( aligning_cmds, ref_file_name, options.input1, options.output )\n+ # align\n+ tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name\n+ tmp_stderr = open( tmp, \'wb\' )\n+ proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )\n+ returncode = proc.wait()\n+ tmp_stderr.close()\n+ # get stderr, allowing for case where it\'s very large\n+ tmp_stderr = open( tmp, \'rb\' )\n+ stderr = \'\'\n+ buffsize = 1048576\n+ try:\n+ while True:\n+ stderr += tmp_stderr.read( buffsize )\n+ if not stderr or len( stderr ) % buffsize != 0:\n+ break\n+ except OverflowError:\n+ pass\n+ tmp_stderr.close()\n+ if returncode != 0:\n+ raise Exception, stderr\n+ # get suppressed and unmapped reads output files in place if appropriate\n+ if options.paired == \'paired\' and tmp_suppressed_file_name and \\\n+ options.output_suppressed_reads_l and options.output_suppressed_reads_r:\n+ try:\n+ left = tmp_suppressed_file_name.replace( \'.fastq\', \'_1.fastq\' )\n+ right = tmp_suppressed_file_name.replace( \'.fastq\', \'_1.fastq\' )\n+ shutil.move( left, options.output_suppressed_reads_l )\n+ shutil.move( right, options.output_suppressed_reads_r )\n+ except Exception, e:\n+ sys.stdout.write( \'Error producing the suppressed output file.\\n\' )\n+ if options.paired == \'paired\' and tmp_unmapped_file_name and \\\n+ options.output_unmapped_reads_l and options.output_unmapped_reads_r:\n+ try:\n+ left = tmp_unmapped_file_name.replace( \'.fastq\', \'_1.fastq\' )\n+ right = tmp_unmapped_file_name.replace( \'.fastq\', \'_2.fastq\' )\n+ shutil.move( left, options.output_unmapped_reads_l )\n+ shutil.move( right, options.output_unmapped_reads_r )\n+ except Exception, e:\n+ sys.stdout.write( \'Error producing the unmapped output file.\\n\' )\n+ # check that there are results in the output file\n+ if os.path.getsize( options.output ) == 0:\n+ raise Exception, \'The output file is empty, there may be an error with your input file or settings.\'\n+ except Exception, e:\n+ stop_err( \'Error aligning sequence. \' + str( e ) )\n+ finally:\n+ # clean up temp dir\n+ if os.path.exists( tmp_index_dir ):\n+ shutil.rmtree( tmp_index_dir )\n+ stdout += \'Sequence file aligned.\\n\'\n+ sys.stdout.write( stdout )\n+\n+if __name__=="__main__": __main__()\n' |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c bowtie_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bowtie_wrapper.xml Mon Nov 26 09:43:28 2012 -0500 |
| [ |
| b'@@ -0,0 +1,839 @@\n+<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.2">\n+ <requirements>\n+ <requirement type=\'package\' version="0.12.7">bowtie</requirement>\n+ </requirements>\n+ <description></description>\n+ <parallelism method="basic"></parallelism>\n+ <command interpreter="python">\n+ bowtie_wrapper.py\n+ ## Hackish setting of number of threads\n+ --threads="4"\n+ ## Outputs\n+ --output=$output\n+ #if str( $singlePaired.sPaired ) == "single"\n+ #if $output_unmapped_reads_l\n+ --output_unmapped_reads=$output_unmapped_reads_l\n+ #end if\n+ #if $output_suppressed_reads_l\n+ --output_suppressed_reads=$output_suppressed_reads_l\n+ #end if\n+ --galaxy_input_format="${singlePaired.sInput1.ext}"\n+ #else\n+ #if $output_unmapped_reads_l and $output_unmapped_reads_r\n+ --output_unmapped_reads_l=$output_unmapped_reads_l\n+ --output_unmapped_reads_r=$output_unmapped_reads_r\n+ #end if\n+ #if $output_suppressed_reads_l and $output_suppressed_reads_l\n+ --output_suppressed_reads_l=$output_suppressed_reads_l\n+ --output_suppressed_reads_r=$output_suppressed_reads_r\n+ #end if\n+ --galaxy_input_format="${singlePaired.pInput1.ext}"\n+ #end if\n+ ## Inputs\n+ --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper\n+ --suppressHeader=$suppressHeader\n+ --genomeSource=$refGenomeSource.genomeSource\n+ #if $refGenomeSource.genomeSource == "history":\n+ ##index already exists\n+ #if $refGenomeSource.ownFile.extension.startswith( \'bowtie_\' ):\n+ ##user previously built\n+ --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"\n+ --do_not_build_index\n+ #else:\n+ ##build index on the fly\n+ --ref=$refGenomeSource.ownFile\n+ --indexSettings=$refGenomeSource.indexParams.indexSettings\n+ #if $refGenomeSource.indexParams.indexSettings == "indexFull":\n+ --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB\n+ #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":\n+ --ipacked=$refGenomeSource.indexParams.autoBehavior.packed\n+ --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax\n+ --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn\n+ --idcv=$refGenomeSource.indexParams.autoBehavior.dcv\n+ #end if\n+ --inodc=$refGenomeSource.indexParams.nodc\n+ --inoref=$refGenomeSource.indexParams.noref\n+ --ioffrate=$refGenomeSource.indexParams.offrate\n+ --iftab=$refGenomeSource.indexParams.ftab\n+ --intoa=$refGenomeSource.indexParams.ntoa\n+ --iendian=$refGenomeSource.indexParams.endian\n+ --iseed=$refGenomeSource.indexParams.seed\n+ --icutoff=$refGenomeSource.indexParams.cutoff \n+ #end if\n+ #end if\n+ #else\n+ ##use pre-built index\n+ --ref="${refGenomeSource.index.fields.path}"\n+ #end if\n+ --paired=$singlePaired.sPaired\n+ #if $singlePaired.sPaired == "single":\n+ --input1=$singlePaired.sInput1\n+ --params=$singlePaired.sParams.sSettingsType\n+ #if $singlePaired.sParams.sSettingsType == "full":\n+ --skip=$singlePaired.sParams.sSkip\n+ --alignLimit=$singlePaired.sParams.sAlignLimit\n+ --trimH=$singlePaired.sParams.sTrimH\n+ --trimL=$singlePaired.sParams.sTrimL\n+ --mismatchSeed=$singlePaired.sParams.sMismatchSeed\n+ --mismatchQual=$singlePaired.sParams.sMismatchQual\n+ --seedLen=$singlePaired.sParams.sSeedLen\n+ --rounding=$singlePaired.sParams.sRounding\n+ --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign\n+ --tryHard=$singlePaired.sParams.sTryHard\n+ --valAlign=$singlePaired.sParams.sValAlign\n+ '..b'-n ceiling applies. Must be at least 5. [28]\n+ --nomaqround Suppress MAQ rounding. Values are internally rounded to the nearest 10 and \n+ saturate at 30. This options turns off that rounding. [off] \n+ -v INT MAQ- or SOAP-like alignment policy. This option turns off the default \n+ MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments \n+ with at most INT mismatches. [off]\n+ -I INT Minimum insert. The minimum insert size for valid paired-end alignments. \n+ Does checking on untrimmed reads if -5 or -3 is used. [0]\n+ -X INT Maximum insert. The maximum insert size for valid paired-end alignments. \n+ Does checking on untrimmed reads if -5 or -3 is used. [250]\n+ --fr Mate orientation. The upstream/downstream mate orientations for a valid \n+ paired-end alignment against the forward reference strand. [--fr]\n+ --rf Mate orientation. [off]\n+ --ff Mate orientation. [off]\n+ --pairtries INT Maximum alignment attempts for paired-end data. [100] \n+ --nofw No forward aligning. Choosing this option means that Bowtie will not attempt \n+ to align against the forward reference strand. [off]\n+ --norc No reverse-complement aligning. Setting this will mean that Bowtie will not \n+ attempt to align against the reverse-complement reference strand. [off]\n+ --un FILENAME Write all reads that could not be aligned to file [off]\n+ --max FILENAME Write all reads with a number of valid alignments exceeding the limit\n+ set with the -m option to file [off]\n+ --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning \n+ a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]\n+ -y Try hard. Try as hard as possible to find valid alignments when they exist, \n+ including paired-end alignments. [off]\n+ --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to \n+ store path descriptors in --best mode. [32]\n+ -k INT Valid alignments. The number of valid alignments per read or pair. [off] \n+ -a All valid alignments. Choosing this means that all valid alignments per read \n+ or pair will be reported. [off]\n+ -m INT Suppress alignments. Suppress all alignments for a particular read or pair \n+ if more than INT reportable alignments exist for it. [no limit]\n+ --best Best mode. Make Bowtie guarantee that reported singleton alignments are \n+ "best" in terms of stratum (the number of mismatches) and quality values at \n+ mismatched position. [off]\n+ --strata Best strata. When running in best mode, report alignments that fall into the \n+ best stratum if there are ones falling into more than one. [off]\n+ -o INT Offrate override. Override the offrate of the index with INT. Some row \n+ markings are discarded when index read into memory. INT must be greater than \n+ the value used to build the index (default: 5). [off]\n+ --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]\n+ --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of \n+ SNPs per base in the subject genome. [see --snpfrac]\n+ --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace \n+ alignments. [0.001]\n+ --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace \n+ alignments. [off]\n+\n+ </help>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_in2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in2.fastqsanger Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,104 @@ +@HWI-EAS91_1_30788AAXX:1:1:1513:715/1 +GTTTTTTGGGCATAGATGTTTAGTTGTGGTAGTCAG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I +@HWI-EAS91_1_30788AAXX:1:1:1698:516/1 +GTTGTTAGGGAGAGGAGTTGAACCTCTGAGTGTAAA ++ +IIIIIII""IIIIIIIIIIIIIIIIIII5IIIII9I +@HWI-EAS91_1_30788AAXX:1:1:1491:637/1 +GCTAGCAGGATGGATCCGGCAATTGGGGCTTCTACA ++ +IIIIIII""IIIIIIIIIIIIFIIIIIIIIIIIABD +@HWI-EAS91_1_30788AAXX:1:1:1711:249/1 +GGAAGTAGGGGCCTGCGTTCAGGCGTTCTGTTTGGT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1634:211/1 +GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF +@HWI-EAS91_1_30788AAXX:1:1:1218:141/1 +GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I +@HWI-EAS91_1_30788AAXX:1:1:1398:854/1 +GTGAAGAGGAGGGGATTTATTAGTACGGGAAGGGTG ++ +IIIIIII""IIIIIBIIIIIIIIIIIIIIA=IIIII +@HWI-EAS91_1_30788AAXX:1:1:1310:991/1 +GAATAGTGGTAGTATTATTCCTTCTAGGCATAGGAG ++ +IIIIIII""IIIIIIIIII4IIIIIIDII:IEI2:I +@HWI-EAS91_1_30788AAXX:1:1:1716:413/1 +GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1630:59/1 +GGAGCGGGGGGTTGGTAAGGTTGGGGTCGAGTATGA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIII;IIHIIF +@HWI-EAS91_1_30788AAXX:1:1:1601:805/1 +GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III +@HWI-EAS91_1_30788AAXX:1:1:1663:724/1 +GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA ++ +IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3 +@HWI-EAS91_1_30788AAXX:1:1:1454:975/1 +GCTAGGCGGGAGTGGTAAAAGGCTCAGAAGAAGCCA ++ +IIIIIII""IIIIIIIIIIIIIIIIEIG;IIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1461:255/1 +GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT ++ +IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I +@HWI-EAS91_1_30788AAXX:1:1:1775:764/1 +GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC ++ +IIIIIII""III@IIII+IIIIII8H8IIIIIIICI +@HWI-EAS91_1_30788AAXX:1:1:1269:520/1 +GGAGTATGGAATAAGTGATTTTAGATCGGTTTGTCG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1303:1162/1 +GAGCAAGGGCAGGAGGAGGAGTCCTAGGATGTCTTT ++ +IIIIIII""IIIIFII4*IGIAI(IAII49',3I6I +@HWI-EAS91_1_30788AAXX:1:1:1090:409/1 +GTTTGTTGGGAATGGAGCGTAGGATGGCGTAGGCAA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIII:IIA8I +@HWI-EAS91_1_30788AAXX:1:1:1336:1000/1 +GGTAAATGGGAAATATTAAGTTTCTGTTTCTAGATC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIII9II +@HWI-EAS91_1_30788AAXX:1:1:1199:1376/1 +GTTTTCTGGAAAACCTTCACCTATTTATGGGGGTTT ++ +IIIIIII""IIIIIIIIIIIII;III3IIG&:/III +@HWI-EAS91_1_30788AAXX:1:1:1598:1148/1 +GATCAATGGTTTGGATCAATAAGTGATTATATATTT ++ +IIIIIII""IIIIIDIIIIII?IIICII=IHIIIII +@HWI-EAS91_1_30788AAXX:1:1:1723:1459/1 +GAAACCCGGACGTTTGGATGGGCCCGGAGCGAGGAT ++ +IIIIIII""IIIIIIIIDIIIIIIIII9HII-II=I +@HWI-EAS91_1_30788AAXX:1:1:1442:1346/1 +TATCAAGGGGCTGCTTCGAATCCGAAGTGGTGGCTG ++ +IIIIIII""IIIIIDIIIII1I(I4II<?<-II*,& +@HWI-EAS91_1_30788AAXX:1:1:850:117/1 +GTATGACGGTAAAGAAAATTATTACGAATGCATGGG ++ +IIIIIII""IIIIIIEIEIIIIIIIIEBIDD9I;:? +@HWI-EAS91_1_30788AAXX:1:1:795:325/1 +GGGTACTGGGAAGTGGAATGGTGTGAGTCCAAGTTT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIII65IIII +@HWI-EAS91_1_30788AAXX:1:1:873:453/1 +GAGTAGGGGGATTGCTAGAGTTACTTCGTATGAGAT ++ +IIIIIII""IIIIIIIIIIIIIIIII@IIIIIII=I |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_in5.fastqillumina --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in5.fastqillumina Mon Nov 26 09:43:28 2012 -0500 |
| [ |
| @@ -0,0 +1,72 @@ +@Dummy:1:1:1761:343/1 +TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA ++ +hhhhhhhAAhhhhhhhhhhh^hOhhhhghhhfhhhhhOhh^hAAhhhhhh +@Dummy:1:1:1578:331/1 +TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh +@Dummy:1:1:1647:512/1 +TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh +@Dummy:1:1:1570:620/1 +GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG ++ +hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhhAhhhhhhhOOOhhhh +@Dummy:1:1:1599:330/1 +AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhh[hhh_hhAhhhhhhhOOOhhhh +@Dummy:1:1:1652:270/1 +AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhhAhhhhhhhOOOhhhh +@Dummy:1:1:1746:351/1 +CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh +@Dummy:1:1:1582:633/1 +CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh +@Dummy:1:1:1598:534/1 +GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh +@Dummy:1:1:1572:324/1 +AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOThAhhhhhhhOOOhhhh +@Dummy:1:1:1749:466/1 +TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh +@Dummy:1:1:1629:446/1 +AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh +@Dummy:1:1:1763:587/1 +AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh +@Dummy:1:1:1616:363/1 +TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhchhhAhhhhhhhOOOhhhh +@Dummy:1:1:1768:715/1 +ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT ++ +hhhhhhhAAhhhhhhhhhhhhhchhhhhhhhhhhhAhhhhhhhOOOhhhh +@Dummy:1:1:1572:270/1 +TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh +@Dummy:1:1:1673:514/1 +ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhPAhhhhhhhOOOhhhh +@Dummy:1:1:1634:330/1 +GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhWhhAhhhhhhhOOOhhhh |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_in5.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in5.fastqsanger Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,72 @@ +@Dummy:1:1:1761:343/1 +TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA ++ +IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII +@Dummy:1:1:1578:331/1 +TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII +@Dummy:1:1:1647:512/1 +TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII +@Dummy:1:1:1570:620/1 +GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG ++ +IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII +@Dummy:1:1:1599:330/1 +AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC ++ +IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII +@Dummy:1:1:1652:270/1 +AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII +@Dummy:1:1:1746:351/1 +CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII +@Dummy:1:1:1582:633/1 +CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII +@Dummy:1:1:1598:534/1 +GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII +@Dummy:1:1:1572:324/1 +AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII +@Dummy:1:1:1749:466/1 +TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII +@Dummy:1:1:1629:446/1 +AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII +@Dummy:1:1:1763:587/1 +AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII +@Dummy:1:1:1616:363/1 +TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII +@Dummy:1:1:1768:715/1 +ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT ++ +IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII +@Dummy:1:1:1572:270/1 +TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII +@Dummy:1:1:1673:514/1 +ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII +@Dummy:1:1:1634:330/1 +GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_in5.fastqsolexa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in5.fastqsolexa Mon Nov 26 09:43:28 2012 -0500 |
| [ |
| @@ -0,0 +1,72 @@ +@Dummy:1:1:1761:343/1 +TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA ++ +hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhhhOhh^h;;hhhhhh +@Dummy:1:1:1578:331/1 +TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh +@Dummy:1:1:1647:512/1 +TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh +@Dummy:1:1:1570:620/1 +GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG ++ +hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh;hhhhhhhOOOhhhh +@Dummy:1:1:1599:330/1 +AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhh[hhh_hh;hhhhhhhOOOhhhh +@Dummy:1:1:1652:270/1 +AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh;hhhhhhhOOOhhhh +@Dummy:1:1:1746:351/1 +CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh +@Dummy:1:1:1582:633/1 +CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh +@Dummy:1:1:1598:534/1 +GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh +@Dummy:1:1:1572:324/1 +AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh;hhhhhhhOOOhhhh +@Dummy:1:1:1749:466/1 +TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh +@Dummy:1:1:1629:446/1 +AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh +@Dummy:1:1:1763:587/1 +AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh +@Dummy:1:1:1616:363/1 +TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhchhh;hhhhhhhOOOhhhh +@Dummy:1:1:1768:715/1 +ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT ++ +hhhhhhh;;hhhhhhhhhhhhhchhhhhhhhhhhh;hhhhhhhOOOhhhh +@Dummy:1:1:1572:270/1 +TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh +@Dummy:1:1:1673:514/1 +ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhP;hhhhhhhOOOhhhh +@Dummy:1:1:1634:330/1 +GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhWhh;hhhhhhhOOOhhhh |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_in6.fastqillumina --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in6.fastqillumina Mon Nov 26 09:43:28 2012 -0500 |
| [ |
| @@ -0,0 +1,72 @@ +@Dummy:1:1:1761:343/2 +TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG ++ +hhhhhhhAAhhhhhhhOhh^hAAhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1578:331/2 +AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1647:512/2 +TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1570:620/2 +CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT ++ +hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1599:330/2 +TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhh[hhh_hh^hOhhhhghhhfhhh +@Dummy:1:1:1652:270/2 +GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh +@Dummy:1:1:1746:351/2 +CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh +@Dummy:1:1:1582:633/2 +TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1598:534/2 +TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1572:324/2 +GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh +@Dummy:1:1:1749:466/2 +GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1629:446/2 +CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1763:587/2 +CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1616:363/2 +GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhchhh^hOhhhhghhhfhhh +@Dummy:1:1:1768:715/2 +AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA ++ +hhhhhhhAAhhhhhhhhhhhhhchhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1572:270/2 +ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1673:514/2 +GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhP^hOhhhhghhhfhhh +@Dummy:1:1:1634:330/2 +TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT ++ +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhWhh^hOhhhhghhhfhhh |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_in6.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in6.fastqsanger Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,72 @@ +@Dummy:1:1:1761:343/2 +TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG ++ +IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII +@Dummy:1:1:1578:331/2 +AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII +@Dummy:1:1:1647:512/2 +TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII +@Dummy:1:1:1570:620/2 +CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT ++ +IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII +@Dummy:1:1:1599:330/2 +TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA ++ +IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII +@Dummy:1:1:1652:270/2 +GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII +@Dummy:1:1:1746:351/2 +CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT ++ +IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII +@Dummy:1:1:1582:633/2 +TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII +@Dummy:1:1:1598:534/2 +TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII +@Dummy:1:1:1572:324/2 +GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII +@Dummy:1:1:1749:466/2 +GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII +@Dummy:1:1:1629:446/2 +CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII +@Dummy:1:1:1763:587/2 +CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII +@Dummy:1:1:1616:363/2 +GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII +@Dummy:1:1:1768:715/2 +AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA ++ +IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII +@Dummy:1:1:1572:270/2 +ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII +@Dummy:1:1:1673:514/2 +GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII +@Dummy:1:1:1634:330/2 +TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_in6.fastqsolexa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in6.fastqsolexa Mon Nov 26 09:43:28 2012 -0500 |
| [ |
| @@ -0,0 +1,72 @@ +@Dummy:1:1:1761:343/2 +TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG ++ +hhhhhhh;;hhhhhhhOhh^h;;hhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1578:331/2 +AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1647:512/2 +TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1570:620/2 +CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT ++ +hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1599:330/2 +TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhh[hhh_hh^hOhhhhghhhfhhh +@Dummy:1:1:1652:270/2 +GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh +@Dummy:1:1:1746:351/2 +CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh +@Dummy:1:1:1582:633/2 +TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1598:534/2 +TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1572:324/2 +GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh +@Dummy:1:1:1749:466/2 +GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1629:446/2 +CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1763:587/2 +CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1616:363/2 +GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhchhh^hOhhhhghhhfhhh +@Dummy:1:1:1768:715/2 +AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA ++ +hhhhhhh;;hhhhhhhhhhhhhchhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1572:270/2 +ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh +@Dummy:1:1:1673:514/2 +GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhP^hOhhhhghhhfhhh +@Dummy:1:1:1634:330/2 +TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT ++ +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhWhh^hOhhhhghhhfhhh |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_out10.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out10.sam Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,36 @@ +Dummy:1:1:1570:620 141 * 0 0 * * 0 0 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII XM:i:0 +Dummy:1:1:1570:620 77 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +Dummy:1:1:1572:270 131 phiX174 3577 255 50M = 3518 -109 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1572:270 67 phiX174 3518 255 50M = 3577 109 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1572:324 141 * 0 0 * * 0 0 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII XM:i:0 +Dummy:1:1:1572:324 77 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 +Dummy:1:1:1578:331 131 phiX174 268 255 50M = 209 -109 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1578:331 67 phiX174 209 255 50M = 268 109 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1582:633 141 * 0 0 * * 0 0 TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XM:i:0 +Dummy:1:1:1582:633 77 * 0 0 * * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +Dummy:1:1:1598:534 131 phiX174 1772 255 50M = 1717 -105 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1598:534 67 phiX174 1717 255 50M = 1772 105 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1599:330 131 phiX174 868 255 50M = 803 -115 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1599:330 67 phiX174 803 255 50M = 868 115 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1616:363 131 phiX174 2773 255 50M = 2718 -105 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1616:363 67 phiX174 2718 255 50M = 2773 105 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1629:446 131 phiX174 2355 255 50M = 2301 -104 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1629:446 67 phiX174 2301 255 50M = 2355 104 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1634:330 131 phiX174 4473 255 50M = 4418 -105 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1634:330 67 phiX174 4418 255 50M = 4473 105 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1647:512 131 phiX174 451 255 50M = 401 -100 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1647:512 67 phiX174 401 255 50M = 451 100 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1652:270 141 * 0 0 * * 0 0 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII XM:i:0 +Dummy:1:1:1652:270 77 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 +Dummy:1:1:1673:514 131 phiX174 4072 255 50M = 4018 -104 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1673:514 67 phiX174 4018 255 50M = 4072 104 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1746:351 141 * 0 0 * * 0 0 CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII XM:i:0 +Dummy:1:1:1746:351 77 * 0 0 * * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +Dummy:1:1:1749:466 131 phiX174 2251 255 50M = 2201 -100 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1749:466 67 phiX174 2201 255 50M = 2251 100 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1761:343 131 phiX174 69 255 50M = 5 -114 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1761:343 67 phiX174 5 255 50M = 69 114 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1763:587 131 phiX174 2566 255 50M = 2501 -115 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1763:587 67 phiX174 2501 255 50M = 2566 115 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1768:715 131 phiX174 3173 255 50M = 3118 -105 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1768:715 67 phiX174 3118 255 50M = 3173 105 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_out6.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out6.sam Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,26 @@ +HWI-EAS91_1_30788AAXX:1:1:1090:409/1 16 chrM 15014 255 36M * 0 0 TTGCCTACGCCATCCTACGCTCCATTCCCAACAAAC I8AII:IIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1199:1376/1 16 chrM 14023 255 36M * 0 0 AAACCCCCATAAATAGGTGAAGGTTTTCCAGAAAAC III/:&GII3III;IIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27G0A7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1218:141/1 4 * 0 0 * * 0 0 GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1269:520/1 16 chrM 11036 255 36M * 0 0 CGACAAACCGATCTAAAATCACTTATTCCATACTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27G8 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1303:1162/1 16 chrM 14866 255 36M * 0 0 AAAGACATCCTAGGACTCCTCCTCCTGCCCTTGCTC I6I3,'94IIAI(IAIGI*4IIFIIII""IIIIIII XA:i:2 MD:Z:27A0T7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1310:991/1 16 chrM 10002 255 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTACCACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1336:1000/1 16 chrM 11616 255 36M * 0 0 GATCTAGAAACAGAAACTTAATATTTCCCATTTACC II9IIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27T0T7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1398:854/1 16 chrM 3921 255 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTCCTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII XA:i:2 MD:Z:27T0A7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1442:1346/1 16 chrM 9331 255 36M * 0 0 CAGCCACCACTTCGGATTCGAAGCAGCCCCTTGATA &,*II-<?<II4I(I1IIIIIDIIIII""IIIIIII XA:i:1 MD:Z:28G7 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1454:975/1 16 chrM 8929 255 36M * 0 0 TGGCTTCTTCTGAGCCTTTTACCACTCCCGCCTAGC IIIIIII;GIEIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0A7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1461:255/1 0 chrM 12988 255 36M * 0 0 GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I XA:i:2 MD:Z:7A0A27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1491:637/1 16 chrM 10864 255 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATCCTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1513:715/1 16 chrM 9563 255 36M * 0 0 CTGACTACCACAACTAAACATCTATGCCCAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1598:1148/1 16 chrM 2334 255 36M * 0 0 AAATATATAATCACTTATTGATCCAAACCATTGATC IIIIIHI=IICIII?IIIIIIDIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1601:805/1 0 chrM 12584 255 36M * 0 0 GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III XA:i:2 MD:Z:7A0C27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1630:59/1 16 chrM 12387 255 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCCCCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1634:211/1 0 chrM 9350 255 36M * 0 0 GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF XA:i:2 MD:Z:7C0C27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1663:724/1 0 chrM 15012 255 36M * 0 0 GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3 XA:i:2 MD:Z:7T0A27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1698:516/1 16 chrM 2735 255 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCCCTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1711:249/1 16 chrM 10617 255 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCCCTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1716:413/1 0 chrM 6040 255 36M * 0 0 GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII XA:i:2 MD:Z:7T0C27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1723:1459/1 16 chrM 15787 255 36M * 0 0 ATCCTCGCTCCGGGCCCATCCAAACGTCCGGGTTTC I=II-IIH9IIIIIIIIIDIIIIIIII""IIIIIII XA:i:2 MD:Z:27G0G7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1775:764/1 0 chrM 16613 255 36M * 0 0 GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC IIIIIII""III@IIII+IIIIII8H8IIIIIIICI XA:i:2 MD:Z:7C0C27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:795:325/1 16 chrM 4249 255 36M * 0 0 AAACTTGGACTCACACCATTCCACTTCCCAGTACCC IIII56IIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27T0G7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:850:117/1 16 chrM 5540 255 36M * 0 0 CCCATGCATTCGTAATAATTTTCTTTACCGTCATAC ?:;I9DDIBEIIIIIIIIEIEIIIIII""IIIIIII XA:i:2 MD:Z:27T0G7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:873:453/1 16 chrM 3188 255 36M * 0 0 ATCTCATACGAAGTAACTCTAGCAATCCCCCTACTC I=IIIIIII@IIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0T7 NM:i:2 |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_out7.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out7.sam Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,36 @@ +Dummy:1:1:1570:620 141 * 0 0 * * 0 0 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII XM:i:0 +Dummy:1:1:1570:620 77 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +Dummy:1:1:1572:270 131 phiX174 3577 255 50M = 3518 -109 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1572:270 67 phiX174 3518 255 50M = 3577 109 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1572:324 141 * 0 0 * * 0 0 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII XM:i:0 +Dummy:1:1:1572:324 77 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 +Dummy:1:1:1578:331 131 phiX174 268 255 50M = 209 -109 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1578:331 67 phiX174 209 255 50M = 268 109 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1582:633 141 * 0 0 * * 0 0 TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XM:i:0 +Dummy:1:1:1582:633 77 * 0 0 * * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +Dummy:1:1:1598:534 131 phiX174 1772 255 50M = 1717 -105 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1598:534 67 phiX174 1717 255 50M = 1772 105 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1599:330 131 phiX174 868 255 50M = 803 -115 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1599:330 67 phiX174 803 255 50M = 868 115 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1616:363 131 phiX174 2773 255 50M = 2718 -105 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1616:363 67 phiX174 2718 255 50M = 2773 105 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1629:446 131 phiX174 2355 255 50M = 2301 -104 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1629:446 67 phiX174 2301 255 50M = 2355 104 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1634:330 131 phiX174 4473 255 50M = 4418 -105 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1634:330 67 phiX174 4418 255 50M = 4473 105 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1647:512 131 phiX174 451 255 50M = 401 -100 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1647:512 67 phiX174 401 255 50M = 451 100 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1652:270 141 * 0 0 * * 0 0 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII XM:i:0 +Dummy:1:1:1652:270 77 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 +Dummy:1:1:1673:514 131 phiX174 4072 255 50M = 4018 -104 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1673:514 67 phiX174 4018 255 50M = 4072 104 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1746:351 141 * 0 0 * * 0 0 CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII XM:i:0 +Dummy:1:1:1746:351 77 * 0 0 * * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +Dummy:1:1:1749:466 131 phiX174 2251 255 50M = 2201 -100 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1749:466 67 phiX174 2201 255 50M = 2251 100 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1761:343 131 phiX174 69 255 50M = 5 -114 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1761:343 67 phiX174 5 255 50M = 69 114 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1763:587 131 phiX174 2566 255 50M = 2501 -115 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1763:587 67 phiX174 2501 255 50M = 2566 115 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1768:715 131 phiX174 3173 255 50M = 3118 -105 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 +Dummy:1:1:1768:715 67 phiX174 3118 255 50M = 3173 105 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_out8_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out8_1.fastq Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,20 @@ ++ ++ ++ ++ ++ +@Dummy:1:1:1570:620/1 +@Dummy:1:1:1572:324/1 +@Dummy:1:1:1582:633/1 +@Dummy:1:1:1652:270/1 +@Dummy:1:1:1746:351/1 +AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC +AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG +CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC +CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT +GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG +IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII +IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_out8_1.fastqillumina.sorted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out8_1.fastqillumina.sorted Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,20 @@ ++ ++ ++ ++ ++ +@Dummy:1:1:1570:620/1 +@Dummy:1:1:1572:324/1 +@Dummy:1:1:1582:633/1 +@Dummy:1:1:1652:270/1 +@Dummy:1:1:1746:351/1 +AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC +AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG +CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC +CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT +GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG +hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhhAhhhhhhhOOOhhhh +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOThAhhhhhhhOOOhhhh +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhhAhhhhhhhOOOhhhh +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_out8_1.fastqsolexa.sorted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out8_1.fastqsolexa.sorted Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,20 @@ ++ ++ ++ ++ ++ +@Dummy:1:1:1570:620/1 +@Dummy:1:1:1572:324/1 +@Dummy:1:1:1582:633/1 +@Dummy:1:1:1652:270/1 +@Dummy:1:1:1746:351/1 +AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC +AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG +CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC +CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT +GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG +hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh;hhhhhhhOOOhhhh +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh;hhhhhhhOOOhhhh +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh;hhhhhhhOOOhhhh +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_out8_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out8_2.fastq Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,20 @@ ++ ++ ++ ++ ++ +@Dummy:1:1:1570:620/2 +@Dummy:1:1:1572:324/2 +@Dummy:1:1:1582:633/2 +@Dummy:1:1:1652:270/2 +@Dummy:1:1:1746:351/2 +CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT +CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT +GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT +GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG +IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII +IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII +IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII +TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_out8_2.fastqillumina.sorted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out8_2.fastqillumina.sorted Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,20 @@ ++ ++ ++ ++ ++ +@Dummy:1:1:1570:620/2 +@Dummy:1:1:1572:324/2 +@Dummy:1:1:1582:633/2 +@Dummy:1:1:1652:270/2 +@Dummy:1:1:1746:351/2 +CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT +CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT +GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT +GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG +TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT +hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh +hhhhhhhAAhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh +hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_out8_2.fastqsolexa.sorted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out8_2.fastqsolexa.sorted Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,20 @@ ++ ++ ++ ++ ++ +@Dummy:1:1:1570:620/2 +@Dummy:1:1:1572:324/2 +@Dummy:1:1:1582:633/2 +@Dummy:1:1:1652:270/2 +@Dummy:1:1:1746:351/2 +CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT +CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT +GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT +GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG +TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT +hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh +hhhhhhh;;hhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh +hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/bowtie_out9.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out9.sam Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,26 @@ +HWI-EAS91_1_30788AAXX:1:1:1090:409/1 16 chrM 15014 255 36M * 0 0 TTGCCTACGCCATCCTACGCTCCATTCCCAACAAAC I8AII:IIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1199:1376/1 16 chrM 14023 255 36M * 0 0 AAACCCCCATAAATAGGTGAAGGTTTTCCAGAAAAC III/:&GII3III;IIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27G0A7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1218:141/1 4 * 0 0 * * 0 0 GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1269:520/1 16 chrM 11036 255 36M * 0 0 CGACAAACCGATCTAAAATCACTTATTCCATACTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27G8 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1303:1162/1 16 chrM 14866 255 36M * 0 0 AAAGACATCCTAGGACTCCTCCTCCTGCCCTTGCTC I6I3,'94IIAI(IAIGI*4IIFIIII""IIIIIII XA:i:2 MD:Z:27A0T7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1310:991/1 16 chrM 10002 255 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTACCACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1336:1000/1 16 chrM 11616 255 36M * 0 0 GATCTAGAAACAGAAACTTAATATTTCCCATTTACC II9IIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27T0T7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1398:854/1 16 chrM 3921 255 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTCCTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII XA:i:2 MD:Z:27T0A7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1442:1346/1 16 chrM 9331 255 36M * 0 0 CAGCCACCACTTCGGATTCGAAGCAGCCCCTTGATA &,*II-<?<II4I(I1IIIIIDIIIII""IIIIIII XA:i:1 MD:Z:28G7 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1454:975/1 16 chrM 8929 255 36M * 0 0 TGGCTTCTTCTGAGCCTTTTACCACTCCCGCCTAGC IIIIIII;GIEIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0A7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1461:255/1 0 chrM 12988 255 36M * 0 0 GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I XA:i:2 MD:Z:7A0A27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1491:637/1 16 chrM 10864 255 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATCCTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1513:715/1 16 chrM 9563 255 36M * 0 0 CTGACTACCACAACTAAACATCTATGCCCAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1598:1148/1 16 chrM 2334 255 36M * 0 0 AAATATATAATCACTTATTGATCCAAACCATTGATC IIIIIHI=IICIII?IIIIIIDIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1601:805/1 0 chrM 12584 255 36M * 0 0 GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III XA:i:2 MD:Z:7A0C27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1630:59/1 16 chrM 12387 255 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCCCCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1634:211/1 0 chrM 9350 255 36M * 0 0 GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF XA:i:2 MD:Z:7C0C27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1663:724/1 0 chrM 15012 255 36M * 0 0 GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3 XA:i:2 MD:Z:7T0A27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1698:516/1 16 chrM 2735 255 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCCCTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1711:249/1 16 chrM 10617 255 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCCCTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1716:413/1 0 chrM 6040 255 36M * 0 0 GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII XA:i:2 MD:Z:7T0C27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1723:1459/1 16 chrM 15787 255 36M * 0 0 ATCCTCGCTCCGGGCCCATCCAAACGTCCGGGTTTC I=II-IIH9IIIIIIIIIDIIIIIIII""IIIIIII XA:i:2 MD:Z:27G0G7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:1775:764/1 0 chrM 16613 255 36M * 0 0 GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC IIIIIII""III@IIII+IIIIII8H8IIIIIIICI XA:i:2 MD:Z:7C0C27 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:795:325/1 16 chrM 4249 255 36M * 0 0 AAACTTGGACTCACACCATTCCACTTCCCAGTACCC IIII56IIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27T0G7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:850:117/1 16 chrM 5540 255 36M * 0 0 CCCATGCATTCGTAATAATTTTCTTTACCGTCATAC ?:;I9DDIBEIIIIIIIIEIEIIIIII""IIIIIII XA:i:2 MD:Z:27T0G7 NM:i:2 +HWI-EAS91_1_30788AAXX:1:1:873:453/1 16 chrM 3188 255 36M * 0 0 ATCTCATACGAAGTAACTCTAGCAATCCCCCTACTC I=IIIIIII@IIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0T7 NM:i:2 |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c test-data/phiX.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fasta Mon Nov 26 09:43:28 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 0c7e4eadfb3c tool-data/bowtie_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie_indices.loc.sample Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,37 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Bowtie indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie/hg18/, +#then the bowtie_indices.loc entry would look like this: +# +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +# +#and your /depot/data2/galaxy/bowtie/hg18/ directory +#would contain hg18.*.ebwt files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt +#...etc... +# +#Your bowtie_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#...etc... +# +#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. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c 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 09:43:28 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 indexes in the Bowtie mapper format --> + <table name="bowtie_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 0c7e4eadfb3c tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Nov 26 09:43:28 2012 -0500 |
| b |
| @@ -0,0 +1,30 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bowtie" version="0.12.7"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>bowtie</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bowtie-build</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bowtie-inspect</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> +Compiling Bowtie requires libpthread to be present on your system. + </readme> + </package> +</tool_dependency> + |