# HG changeset patch # User lparsons # Date 1353444854 18000 # Node ID cf4b5125a8356d69788a2c0abb81cc5685afcafc # Parent e6f1c31279dbcc884f902fb7fafc8b9f2535b4bd Uploaded diff -r e6f1c31279db -r cf4b5125a835 .hgignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.hgignore Tue Nov 20 15:54:14 2012 -0500 @@ -0,0 +1,3 @@ +^package$ +syntax: glob +*.pyc diff -r e6f1c31279db -r cf4b5125a835 .hgtags --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.hgtags Tue Nov 20 15:54:14 2012 -0500 @@ -0,0 +1,1 @@ +d7b1bb0ab083311487138fd8f0f7561091f7e74e 0.1 diff -r e6f1c31279db -r cf4b5125a835 README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Tue Nov 20 15:54:14 2012 -0500 @@ -0,0 +1,19 @@ +== ea-utils Galaxy Wrapper == + +This is a Galaxy wrapper for some ea-utils tools, fastq-join and sam-stats. + +** Installation ** + +Installation from a tool shed provides the necessary tool dependencies. + +Otherwise, make sure fastq-join and sam-stats are in the path. +Move the test data files to your galaxy root test-data. +Move the xml files to a subdirectory of your tools directory and add lines in tool_conf.xml to point to them. +Restart the Galaxy server. + +** Attribution ** + +The ea-utils package and associated documentation can be found at: http://code.google.com/p/ea-utils/ + +The galaxy wrapper code was written by Lance Parsons (lparsons@princeton.edu), Lewis-Sigler Institute for Integrative Genomics, Princeton University. +The code is housed on BitBucket at: https://bitbucket.org/lance_parsons/ea_utils_galaxy_wrapper diff -r e6f1c31279db -r cf4b5125a835 fastq-join.xml --- a/fastq-join.xml Thu Sep 20 18:59:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ - - - Joins two paired-end reads on the overlapping ends - - ea-utils - - - fastq-join - -v '$splitChar' - -p $pctMaxDiff - -m $minOverlap - #if $stitchLengthReport: - -r $outputStitchLengthReport - #end if - $read1 - $read2 - -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined - - - - - - - - - - - - - - - - stitchLengthReport - - - - - - - - - - - - - - - - - - -Overview --------- -fastq-join joins two paired-end reads on the overlapping ends. - -Split read ids character: Verifies that the 2 files probe id's match up to char C. Use ' ' for Illumina reads. - -Maximum difference is the maximum allowed percentage of bases that differ in the matching region. - -Minimum overlap is the minimum number of bases that must overlap (with no more than the maximum difference) for reads to be joined. - -Verbose stitch length report is a report for each joined paired of reads showing how large the overlapping section was. - -This tool uses sqr(distance)/len for anchored alignment quality algorithm. It's a good measure of anchored alignment quality, akin to squared-deviation for means. This tool uses the fastq-join program that is part of the ea-utils suite. See http://code.google.com/p/ea-utils/wiki/FastqJoin for details. - - diff -r e6f1c31279db -r cf4b5125a835 sam-stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam-stats.xml Tue Nov 20 15:54:14 2012 -0500 @@ -0,0 +1,83 @@ + + - Compute statistics from SAM or BAM files + + ea-utils + + + sam-stats + $trackMultAlign + $reportAllChr + #if $rnaSeqStats: + -R $rnaSeqStatsFile + #end if + #if $input.extension == "bam": + -B + #end if + -S $histBinSize + $input + > $samStats + + + + + + + + + + + + + rnaSeqStats + + + + + + + + + + + + + + + +Overview +-------- +sam-stats computes varius statics on SAM/BAM alignment files. + +Complete Stats:: + + <STATS> : mean, max, stdev, median, Q1 (25 percentile), Q3 + reads : # of entries in the sam file, might not be # reads + phred : phred scale used + bsize : # reads used for qual stats + mapped reads : number of aligned reads (unique probe id sequences) + mapped bases : total of the lengths of the aligned reads + forward : number of forward-aligned reads + reverse : number of reverse-aligned reads + snp rate : mismatched bases / total bases + ins rate : insert bases / total bases + del rate : deleted bases / total bases + pct mismatch : percent of reads that have mismatches + len <STATS> : read length stats, ignored if fixed-length + mapq <STATS> : stats for mapping qualities + insert <STATS> : stats for insert sizes + <CHR> : percentage of mapped bases per chr, followed by a signature + +Subsampled stats (1M reads max):: + + base qual <STATS> : stats for base qualities + A,T,C,G : base percentages + +Meaning of the per-chromosome signature: + + A ascii-histogram of mapped reads by chromosome position. It is only output if the original SAM/BAM has a header. The values are the log2 of the # of mapped reads at each position + ascii '0'. + +See http://code.google.com/p/ea-utils/wiki/SamStatsDetails for more information on each stat, how it's calculated and what it means. + +This tool uses the sam-stats program that is part of the ea-utils suite. See http://code.google.com/p/ea-utils/wiki/SamStats for details. + + diff -r e6f1c31279db -r cf4b5125a835 test-data/test.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.sam Tue Nov 20 15:54:14 2012 -0500 @@ -0,0 +1,100 @@ +GEN-SEQ-ANA_0001:1:1:17434:14109#0/1 0 PCRPRIMER1 5 255 33M * 0 0 ATACGGCGACCACCGAGATCTACACTCTTTCCC ?>BB>>A5AAA;;9:B;5>>?:B>BAABBBBBBBBABBB; XA:i:0 MD:Z:38 NM:i:0 +GEN-SEQ-ANA_0001:1:1:16837:9043#0/1 0 PCRPRIMER1+1 14 255 27M * 0 0 CCACCGAGATCTACACTCTTTCCCTAC ?BB?ABB?BBB<7A5?7??A?:CC>CCCCCC?@CCBBCC:@CCC@C>BABAAA88?>>ABBB:AA XA:i:0 MD:Z:37 NM:i:0 +GEN-SEQ-ANA_0001:1:1:3890:20139#0/1 0 PCRPRIMER2+1 34 255 23M * 0 0 TAATGATACGGCGACCACCGAGA CCCCCC8A XA:i:0 MD:Z:48 NM:i:0 +GEN-SEQ-ANA_0001:1:1:16810:9063#0/1 0 PCRPRIMER2+1 34 255 45M * 0 0 TAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA CCCCCCCCBCCCBBCCCCCCCCCCCCCCBA=@CCCCBC5B@9@@@ XA:i:0 MD:Z:45 NM:i:0 +GEN-SEQ-ANA_0001:1:1:1127:14386#0/1 4 * 0 0 * * 0 0 TGAATTCATGAATGGAAAAA ?ACC<@>69@6>@BB?@:== XM:i:0 +GEN-SEQ-ANA_0001:1:1:1210:17845#0/1 4 * 0 0 * * 0 0 GAGATAATTCAAAATCTTGCCGAT >===>>@@@=<89A6>AB?>B XM:i:0 +GEN-SEQ-ANA_0001:1:1:1227:4069#0/1 4 * 0 0 * * 0 0 TCGAGAATTCTTTATCAACCTCGTT =CCCCCBC6@BCCC=9BA7A>>BB> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1309:16895#0/1 4 * 0 0 * * 0 0 GTACAAATTCCCTCATTCTTGGATTTGTA CA>CC@BBC8C@C>=C5; XM:i:0 +GEN-SEQ-ANA_0001:1:1:1290:1939#0/1 4 * 0 0 * * 0 0 TACGTAATTCCGTGTCGGAGCCCGT ??B:6>B;>AB=>B>B:BB>?A<6? XM:i:0 +GEN-SEQ-ANA_0001:1:1:1311:12611#0/1 4 * 0 0 * * 0 0 AAATTCGTTTATTTTTGTATTT BBBBB@@@@@@@B:====:BBA XM:i:0 +GEN-SEQ-ANA_0001:1:1:1312:13847#0/1 4 * 0 0 * * 0 0 CGATAAATTCCTTGCTTCAACGATGCA ?BB>=8CC@??CCCC@B?>CC:CCC:8 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1327:14127#0/1 4 * 0 0 * * 0 0 ATAAATTCAGAATAGTTTCACT =A:??B>=;B@A;97C>B@=6B XM:i:0 +GEN-SEQ-ANA_0001:1:1:1328:16612#0/1 4 * 0 0 * * 0 0 GAGATAATTCTTCTCATCGG @@@8@;C@C@CC=BC=>=AA XM:i:0 +GEN-SEQ-ANA_0001:1:1:1339:13574#0/1 4 * 0 0 * * 0 0 TTCTGTGATAATTTCAATATTGCC CB8B>=B=ABBBB:=BABBB@>=6 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1343:12008#0/1 4 * 0 0 * * 0 0 TTCGGCACTTTTCAGCACAATTTTCA CA=ACC@CC@BB=?AC??CC?CC?5CBC?8?C=?ACBC>CCBB@=CAA8: XM:i:0 +GEN-SEQ-ANA_0001:1:1:1358:3384#0/1 4 * 0 0 * * 0 0 AACAAACCATGTTTTGCCCTCAAACAG B8:BBBBB:BBB=BBBA@BB:9 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1361:15054#0/1 4 * 0 0 * * 0 0 ATGCTAATTCAGTAGCTATTGTTCTCCAAAT BCC:?CA?C?=CC?ABC@C XM:i:0 +GEN-SEQ-ANA_0001:1:1:1362:13972#0/1 4 * 0 0 * * 0 0 GTAATTCTTCGCGAGTCTTTG @>C?CA?:@??@@@@CC?C?B XM:i:0 +GEN-SEQ-ANA_0001:1:1:1363:2154#0/1 4 * 0 0 * * 0 0 AGCTGAATTCTAGAAATGAAGAATATTTTTATTTATTTTCAG CB@C?B;CC=CAAC@@>:C?@:???CCBB>8>>>>?C>6>A? XM:i:0 +GEN-SEQ-ANA_0001:1:1:1373:2799#0/1 4 * 0 0 * * 0 0 GAGATAATTCAAAACTACTACTGTAGAGGGGTACTG ?BABACCCC@B=<=@@?8B><@B@>BAAB9<@<>@B XM:i:0 +GEN-SEQ-ANA_0001:1:1:1374:3530#0/1 4 * 0 0 * * 0 0 GAGATAATTCTTCCTCCTTAA AAAC8A=CA>CC@CC:B7ACC XM:i:0 +GEN-SEQ-ANA_0001:1:1:1379:7364#0/1 4 * 0 0 * * 0 0 CGCCAACCAAACCGATTGGCC =???A;CCC?CCABCB8>CCC XM:i:0 +GEN-SEQ-ANA_0001:1:1:1382:18005#0/1 4 * 0 0 * * 0 0 GTAGCGAGTGACTCCAGTATGGAT ?CBB>=BBB:@B;>><<><@>@?7 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1385:14548#0/1 4 * 0 0 * * 0 0 TTCCTATTCAACTCCTCAATT 8=9=AA:A@=?AA@@@:@?AA XM:i:0 +GEN-SEQ-ANA_0001:1:1:1387:6982#0/1 4 * 0 0 * * 0 0 ATTCGCGCCGATTGGGATTTTTG 6B?>:A=:A?7:A>B=B=BB XM:i:0 +GEN-SEQ-ANA_0001:1:1:1392:4030#0/1 4 * 0 0 * * 0 0 AGCTGAATTCGAGCCCATTGATGA ?@6C@C@>BB<<<;95BA XM:i:0 +GEN-SEQ-ANA_0001:1:1:1403:14145#0/1 4 * 0 0 * * 0 0 ATGCTAATTCTCGTGGAACTCG CA>C=CC@CA?8???7C7@=?? XM:i:0 +GEN-SEQ-ANA_0001:1:1:1404:13576#0/1 4 * 0 0 * * 0 0 CGATAAATTCTCTGAAAATGCATA >BB=:BBBB@B@=B@BB=BBAB;B XM:i:0 +GEN-SEQ-ANA_0001:1:1:1408:13430#0/1 4 * 0 0 * * 0 0 GAACAATAAAACCTCCTGTC @8B5@AA?@A==AAA=AA6@ XM:i:0 +GEN-SEQ-ANA_0001:1:1:1410:6288#0/1 4 * 0 0 * * 0 0 TCCGAAAACCAAATTTTACTG 9?>B5:CBC:@C@CCB?CCCB XM:i:0 +GEN-SEQ-ANA_0001:1:1:1420:17657#0/1 4 * 0 0 * * 0 0 TTCAATGAGAGAATCCGCGACGAAAATGG CC?CCC?BB?C:CAAB5AB>BB>BA8> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1423:18328#0/1 4 * 0 0 * * 0 0 ATAAATTCATCGACAGGTACCTTCTAT <@@<>?B>>AB=>BBB>B=BBBA7>>6 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1426:4162#0/1 4 * 0 0 * * 0 0 GCTAATTCCTATGGTTATAACTCTAAAACGGGTC 7==8<>@9B@?=5ACACA>>BCC?>C=?B>9@8; XM:i:0 +GEN-SEQ-ANA_0001:1:1:1426:18217#0/1 4 * 0 0 * * 0 0 TCCTTCAAAAATCATCACTGAAA >7:>@>@AA=@A:A@6@7A;>55 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1428:17122#0/1 4 * 0 0 * * 0 0 GTACAAATTCATCTAATGGTCTAACTTTATA C?CC8CCCBA@@=C>AAABC8BC:CCBACCC XM:i:0 +GEN-SEQ-ANA_0001:1:1:1434:13892#0/1 4 * 0 0 * * 0 0 GTACAAATTCGCCAAGCGTTGGATTG A???88@:;=>=?@@>BBB6A>AA5> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1441:16403#0/1 4 * 0 0 * * 0 0 TGAATTCTGGCACTTCGGCGATT B>B@?BBB@@>BAAB: XM:i:0 +GEN-SEQ-ANA_0001:1:1:1445:8376#0/1 4 * 0 0 * * 0 0 TGAATATGAAATTCGTAAATAGCGTGTT @@CCC@>CBCC?CCC@BBBBBBBB> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1451:7415#0/1 4 * 0 0 * * 0 0 CTCTTAATTCAAGTCCATATTCTCCTTGTAACCCCAAGTGATACAATATTTGATT BBA@;CCAC>@@CC>CBCC?BCCBBCAAAABCCCBCCCBC@CACAC;CC< XM:i:0 +GEN-SEQ-ANA_0001:1:1:1455:18050#0/1 4 * 0 0 * * 0 0 AGCTGAATTCCAGACATTATAGAAAA BCCCC@=B@>>?C>CCCC?:CC:C=> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1455:12928#0/1 4 * 0 0 * * 0 0 TCGAGAATTCCACATCACTTCTAT @?@@;CCCC@B:C:CBBB=6 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1456:13493#0/1 4 * 0 0 * * 0 0 TTCATATTGGGTTTCTACCGCGAC AB>B=?AA>B@BB>=BAAB=BBB> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1456:4776#0/1 4 * 0 0 * * 0 0 ATGCTAATTCACATTCATGATT CCCA=A@C@@@C@C5C???BCCBCCC@?CC XM:i:0 +GEN-SEQ-ANA_0001:1:1:1469:15421#0/1 4 * 0 0 * * 0 0 CGATAAATTCTGCCGGCAGAACTACGCATTT AC;>CACCB8?CCA;ACBCBBC?CCAC=CCC XM:i:0 +GEN-SEQ-ANA_0001:1:1:1472:17572#0/1 4 * 0 0 * * 0 0 TTCTACCCGGAACTCTTAAACAGAAGCGAGGC CC>B@@:BB>>>B>BC=CBC@8>CCC=C XM:i:0 +GEN-SEQ-ANA_0001:1:1:1473:13352#0/1 4 * 0 0 * * 0 0 TCTGTGGAATTAACAATCACAATAACTAAAG C?@BC@B@@=@=@@BBBB>B?>B= XM:i:0 +GEN-SEQ-ANA_0001:1:1:1481:5276#0/1 4 * 0 0 * * 0 0 GTACAAATTCGAATGAAATCATA CCCCBBCDB@C=CDACCC=C?C> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1482:10064#0/1 4 * 0 0 * * 0 0 CGATAAATTCAATTTGAAAA CC=CCC6C@;CCCBCAB?9B XM:i:0 +GEN-SEQ-ANA_0001:1:1:1484:2325#0/1 4 * 0 0 * * 0 0 AATTCCAACCACCATTGGAA @A@=>@C??@C7CB@B6?:? XM:i:0 +GEN-SEQ-ANA_0001:1:1:1487:6701#0/1 4 * 0 0 * * 0 0 CTCATTCATCTAGATATTTCTGATTTATCGTTGTTC @9> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1487:3645#0/1 4 * 0 0 * * 0 0 CTAATTCGTGTAATAATTGTGTT >87?@@>><9C:@7B XM:i:0 +GEN-SEQ-ANA_0001:1:1:1488:9645#0/1 4 * 0 0 * * 0 0 ATGCTAATTCGAAGTGCGTATCTCTCGGT ACCCCC8C@>>BBB=BB=A>BBBBB6B?> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1489:3252#0/1 4 * 0 0 * * 0 0 TAAATTCTGAAAAATGTATTT @<@@B@@=?C:C>>>B@A6A8 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1492:14525#0/1 4 * 0 0 * * 0 0 AACTTCGAATATTAACAACA @7:@>@@5C@>@@@C@@?B@ XM:i:0 +GEN-SEQ-ANA_0001:1:1:1493:11409#0/1 4 * 0 0 * * 0 0 CGAAACGGGCGTTGAGGCGTTTT >=B6BBBBAB@=BB>BB XM:i:0 +GEN-SEQ-ANA_0001:1:1:1494:17779#0/1 4 * 0 0 * * 0 0 TTTTCCTGAAAAATGTTCAACCTGATTATT :;A;:?:A>A8A:A=?AAA@@:=55AA6@@ XM:i:0 +GEN-SEQ-ANA_0001:1:1:1495:12537#0/1 4 * 0 0 * * 0 0 GTACAAATTCACAATAATTA BCCCBCCBCA;CCCBB@>>8 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1495:14319#0/1 4 * 0 0 * * 0 0 ATTCGCCAAATTTGGCGTTAG CCCCACBBCB@CCCACA XM:i:0 +GEN-SEQ-ANA_0001:1:1:1496:18187#0/1 4 * 0 0 * * 0 0 AGGCGCGGCCAGCGGCTGGG <:B<<6B6<>A?BBB:5A6A XM:i:0 +GEN-SEQ-ANA_0001:1:1:1496:10780#0/1 4 * 0 0 * * 0 0 GAAATTCCCAAGAAACCCAAG C:?7@??CACCBCCC=8AA:6 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1497:8211#0/1 4 * 0 0 * * 0 0 CGATAAATTCCAAAGTTTGTGAATTT BCCCCC?C@?<::A:?AA?AB?:B@< XM:i:0 +GEN-SEQ-ANA_0001:1:1:1498:13789#0/1 4 * 0 0 * * 0 0 ATGCTAATTCTTTCGGAAACGAGACCATCTGA >C8C>CC>B@==C@AC?C8@B?:6;AA@BBA@ XM:i:0 +GEN-SEQ-ANA_0001:1:1:1502:11211#0/1 4 * 0 0 * * 0 0 ATTCGTACTCGTGATTTTCGAACAATCCAGT @AB=CCCCCCCBBA;CACCCB@A@C==C@CA XM:i:0 +GEN-SEQ-ANA_0001:1:1:1506:3772#0/1 4 * 0 0 * * 0 0 CCATAAAATTATTGTCAATTTTCAAT ??:@?:BC:C?CC>CBCCC:: XM:i:0 +GEN-SEQ-ANA_0001:1:1:1506:13304#0/1 4 * 0 0 * * 0 0 AATTCGACATCGCAAGTGAG AAA?>?CC>CBB?CBCBCA> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1506:17897#0/1 4 * 0 0 * * 0 0 TGAATTCCGCCTTGGAGACAATGTTCT B:6>?:B=B=BB>=?BBA XM:i:0 +GEN-SEQ-ANA_0001:1:1:1507:13225#0/1 4 * 0 0 * * 0 0 TGCTAATTCTAATTTTCATGTATACTAAACCCCCAC @?C>B8@<9B?C=CB5B66A<AA8?A<BAAA=?B???6BB=> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1510:9250#0/1 4 * 0 0 * * 0 0 AAAAACTGAAAAATTAAGATTAAAAGC A=?A6AA@?AAA@@AA:A8A@:>8AA5 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1510:4740#0/1 4 * 0 0 * * 0 0 CTCTTAATTCATTTTTTTTTCAGTTTTAAAGGTG BC;BBCCCC@>CC;CCB>8>=BBB6BBBB=B?=B XM:i:0 +GEN-SEQ-ANA_0001:1:1:1511:8709#0/1 4 * 0 0 * * 0 0 TTCACTTTCTATGGTTATTTT CC@=ACCCCCB?CCBBCCC=> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1513:14094#0/1 4 * 0 0 * * 0 0 AGCTGAATTCCAATTCTCTATCACGATT BC8CCBCC@;CCC8CCCCCACCCAB@@@ XM:i:0 +GEN-SEQ-ANA_0001:1:1:1515:16388#0/1 4 * 0 0 * * 0 0 AGCTGAATTCGCCAAGCGTTGGAT BC;CCC@C?;=CCCCCCC@C;C@C XM:i:0 +GEN-SEQ-ANA_0001:1:1:1516:14913#0/1 4 * 0 0 * * 0 0 CTAATTCGTCCAGATTTCCA C:BCCB?CCBBACCBBCCCC XM:i:0 +GEN-SEQ-ANA_0001:1:1:1517:17176#0/1 4 * 0 0 * * 0 0 CGATAAATTCTAATTTTGCCA >C<@CBA9B?BB?CBCABCCB XM:i:0 +GEN-SEQ-ANA_0001:1:1:1520:6860#0/1 4 * 0 0 * * 0 0 GTACAAATTCTTGAGAGACAGAATT C??C;CCCC?CCCCCCC@BC@C?AC XM:i:0 diff -r e6f1c31279db -r cf4b5125a835 test-data/test_read1.fastq --- a/test-data/test_read1.fastq Thu Sep 20 18:59:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -@JLK5VL1:222:D1888ACXX:1:1101:1656:2143 1:N:0: -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT -+ -?+:BDDDAD8BDD?@4+5;6?;;@A;AABA>A@>AAAD;A>A>5=5>>>BBAA###### -@JLK5VL1:222:D1888ACXX:1:1101:1613:2167 1:N:0: -GTGATAGAGATACTGAGCACAGAGCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT -+ -@?BDFFFFHBHHHJJJGFEHHEIHEGHJJJJDI@DHIIHGGGGGEHIHGIIIIJJJGIB?AACBEDDFCDCCCCCEDC>@CD>CC@BA>CDEECD=BDDB> -@JLK5VL1:222:D1888ACXX:1:1101:1927:2121 1:N:0: -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT -+ -@B@DFFFFHHHHHJJIHJIJJJJJJJJJJJJIJHJJIJIJIHHGIJIIJGIIJJJIIII?EEEDFFFFEEEEEDECDDDEDDDDCCBACDEDECC@BB9CCCCCACDDEEDCA9>BBDC -@JLK5VL1:222:D1888ACXX:1:1101:1763:2172 1:N:0: -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAAGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT -+ -@?@DDDBDHDFDHBFB3CCGFFHDHHIIIIIIG@<>BD? -@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 1:N:0: -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTCGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT -+ -@?BFFFFFHHHHHJJJGIGIJIIJJJIGJJJJJJIIIIHGHIIGIJGIIIJJIJIIJJJEHDBDCDEEEEDDDDD@CCCDAA@CA@A:@CADD>C9<@B9C -@JLK5VL1:222:D1888ACXX:1:1101:2236:2214 1:N:0: -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT -+ -@=@DFDFFHAHDHGFEE@FFHGGEDEGHGIJ@GFGHAGFIIGBDGHIIJIGJJJJJIIIACEBDEFDFDEEEEDEDDCCDCD;CDCB@CF@DD@C?B<@DC -@JLK5VL1:222:D1888ACXX:1:1101:2090:2240 1:N:0: -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT -+ -@:?DDDDDFABCCDCFFCA:9BBBC diff -r e6f1c31279db -r cf4b5125a835 test-data/test_read3.fastq --- a/test-data/test_read3.fastq Thu Sep 20 18:59:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -@JLK5VL1:222:D1888ACXX:1:1101:1656:2143 3:N:0: -TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA -+ -BB8=4ADDHHHHACG(;(;@C@C:<:>>@>>;B>B(44?>C@B9<<8 -@JLK5VL1:222:D1888ACXX:1:1101:1613:2167 3:N:0: -TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA -+ -@?=DDDFFDFHHHIGGHHIGGFEGIJJFAFEGGGH@AFFHGIIIGEFHBF>@FCGAE@DD=D'9@DCC@;C@C@CDDCD>CCD@>>:@@C@CDDACA<28? -@JLK5VL1:222:D1888ACXX:1:1101:1927:2121 3:N:0: -TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA -+ -CCCFFFFFHHHHHJIIJJJJJJIJJJJIJJJJJJJIJJJJJJJJJJJJJJIHIJJIJEEHHF>BBDEFEDDDDDDDCDDDDCDDDEEEEDDDDDDDBDBDD -@JLK5VL1:222:D1888ACXX:1:1101:2000:2166 3:N:0: -TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA -+ -B@@DDFFFGHHHDIFHIJIIIJJJJIJJJJJIJJIIJIJIGIIJGIJJJJDFGGGII:DHFF3>C>CCCC(5(;>CDECCAC>@AB08AB -@JLK5VL1:222:D1888ACXX:1:1101:1832:2198 3:N:0: -TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATGCTTGTGAACAATGTGTATTCACTAACAACGTCA -+ -C@@FFFFFHHHHHJJJJJIJIJJJJIIJJIJIIFIGIJGHIDGIIIGIJJIHGHIIJGIIHF<<@DDDDEEDDCCCDDDCCCDDDEDDEDDCCDDCBB?AB -@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 3:N:0: -TTTGCCCTATTTATAGGACCCTAGAAAGAAAAAACCTCAAATAAAATAAAAGTGATTGGCGGGATATACTTGTGAACAATGTGTATTTACTTACCACCACC -+ -##################################################################################################### -@JLK5VL1:222:D1888ACXX:1:1101:2236:2214 3:N:0: -TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA -+ -@@@DDFFFHHHHFEEGIEHIJJGGFGIGIHCHJJJJJJIJIJGIGGIJIJGCDGEGG>EGHF=ABC@BDDCDDA@CCCCDCDE@CCD>CC@CDDDDBD?<< -@JLK5VL1:222:D1888ACXX:1:1101:2090:2240 3:N:0: -TGGATCCTATTAATAGGACCCTAGAAAGATAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA -+ -CC@FFFFFGFHDDHH>@FHHCHIIGIIEGGHIJIIBEEHIGGGGJIJJJJGBFGIGGCAHEA,9?B>B@@C>@@ACACCCC@C@@CDCDC@>CCCDD@(8? -@JLK5VL1:222:D1888ACXX:1:1101:2952:2161 3:N:0: -TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA -+ -CCCFFFFFHHHGHJJJJJIJJJJJIJJJHIJJIJJIIGIIIJEIIJIIJIG@FHIJJJIJHFCCDCCDDDDDDCDCCDDEACA@CDDDDDABB diff -r e6f1c31279db -r cf4b5125a835 test-data/testout.join.fastq --- a/test-data/testout.join.fastq Thu Sep 20 18:59:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -@JLK5VL1:222:D1888ACXX:1:1101:1656:2143 -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA -+ -?+:BDDDAD8BDD?@4+?;;@B>BABA@A@>AACDCA>A>5>@CC>BBDEA;7@;@@DFCIGGCCABB?3GED@0FDC;CEEACIIIIIGGIHFFBHFEGIIIGHFFA@HGGGEFAFJJIGEFGGIHHGGIHHHFDFFDDD=?@ -@JLK5VL1:222:D1888ACXX:1:1101:1927:2121 -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA -+ -@B@DFFFFHHHHHJJIHJIJJJJJJJJJJJJIJHJJIJIJIHHGIJIIJGIIJJJIIIIDEEEDFFFFEEEEEDEDDDDEDDDDDDEFEDEDEFHHEEJIJJIHIJJJJJJJJJJJJJJIJJJJJJJIJJJJIJJJJJJIIJHHHHHFFFFFCCC -@JLK5VL1:222:D1888ACXX:1:1101:2000:2166 -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACGTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA -+ -B?@DFFFFHHHHHGIIJIIJJJJJJIJJJJJIIHIJJIJJIIGGJJGHGHIGGIIJHIGDEEEDFFEEEEFEEDDDDDDDCCCCDDEDDEEEDFFHDBIIGGGFDJJJJIGJIIGIJIJIIJJIJJJJJIJJJJIIIJIHFIDHHHGFFFDD@@B -@JLK5VL1:222:D1888ACXX:1:1101:1763:2172 -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAAGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA -+ -@?@DDDBDHDFDHBFB3CCGFFHDHHIIIIIIG@GGEGDCGJIJIGGIGJIJIJJJJJJHCHIGIGFGGJJIHEIGEEFHHHHFFFDD@@@ -@JLK5VL1:222:D1888ACXX:1:1101:2090:2240 -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTATCTTTCTAGGGTCCTATTAATAGGATCCA -+ -@:?DDDDDFHHDDHFGFFFFF@CC -@JLK5VL1:222:D1888ACXX:1:1101:2952:2161 -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA -+ -@@@DFFFFHFHHGIJIJJJJJIJJJJIIIJJIIJJIJIEHIHIEHHIGJEHIIJIJDDGDEDCFFFDFEDDEEEDDDDDDDDDCCACCCDCFFFHJIJJJIHF@GIJIIJIIEJIIIGIIJJIJJIHJJJIJJJJJIJJJJJHGHHHFFFFFCCC diff -r e6f1c31279db -r cf4b5125a835 test-data/testout.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testout.txt Tue Nov 20 15:54:14 2012 -0500 @@ -0,0 +1,29 @@ +reads 100 +version 1.32 +mapped reads 11 +mapped bases 377 +phred 33 +forward 0 +reverse 11 +len max 48 +len mean 34.2727 +len stdev 9.4137 +mapq mean 255.0000 +mapq stdev 0.0000 +mapq Q1 255.00 +mapq median 255.00 +mapq Q3 255.00 +snp rate 0.000000 +pct mismatch 0.0000 +base qual mean 31.5650 +base qual stdev 3.2627 +%A 27.5862 +%C 34.4828 +%G 16.7109 +%T 21.2202 +%PCRPRIMER1 8.753316 +%PCRPRIMER1+1 45.358090 +%PCRPRIMER1+2 9.814324 +%PCRPRIMER2+1 36.074271 +num ref seqs 4 +num ref aligned 4 diff -r e6f1c31279db -r cf4b5125a835 test-data/testout.un1.fastq --- a/test-data/testout.un1.fastq Thu Sep 20 18:59:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 1:N:0: -GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTCGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT -+ -@?BFFFFFHHHHHJJJGIGIJIIJJJIGJJJJJJIIIIHGHIIGIJGIIIJJIJIIJJJEHDBDCDEEEEDDDDD@CCCDAA@CA@A:@CADD>C9<@B9C diff -r e6f1c31279db -r cf4b5125a835 test-data/testout.un2.fastq --- a/test-data/testout.un2.fastq Thu Sep 20 18:59:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 3:N:0: -TTTGCCCTATTTATAGGACCCTAGAAAGAAAAAACCTCAAATAAAATAAAAGTGATTGGCGGGATATACTTGTGAACAATGTGTATTTACTTACCACCACC -+ -##################################################################################################### diff -r e6f1c31279db -r cf4b5125a835 tool_dependencies.xml --- a/tool_dependencies.xml Thu Sep 20 18:59:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ - - - - - - http://ea-utils.googlecode.com/files/ea-utils.1.1.2-469.tar.gz - - sed -i.bak 's/sam-stats varcall$//' Makefile - PREFIX=$INSTALL_DIR make install - - $INSTALL_DIR/bin - - - - - - -