Mercurial > repos > lparsons > sam_stats
changeset 0:b9e7569a4438 draft
Uploaded initial version with package dependency.
| author | lparsons |
|---|---|
| date | Fri, 27 Jun 2014 15:36:01 -0400 |
| parents | |
| children | a51942c74761 |
| files | README.txt sam-stats.xml test-data/test.sam test-data/testout.txt tool_dependencies.xml |
| diffstat | 5 files changed, 237 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Fri Jun 27 15:36:01 2014 -0400 @@ -0,0 +1,19 @@ +== sam-stats Galaxy Wrapper == + +This is a Galaxy wrapper for the sam-stats tool from ea-utils suite. + +** Installation ** + +Installation from a tool shed provides the necessary tool dependencies. + +Otherwise, make sure sam-stats is 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam-stats.xml Fri Jun 27 15:36:01 2014 -0400 @@ -0,0 +1,83 @@ +<tool id="sam_stats" name="sam-stats" version="1.32"> + <description> - Compute statistics from SAM or BAM files</description> + <requirements> + <requirement type="package" version="1.1.2-484">ea-utils</requirement> + </requirements> + <command> + sam-stats + $trackMultAlign + $reportAllChr + #if $rnaSeqStats: + -R $rnaSeqStatsFile + #end if + #if $input.extension == "bam": + -B + #end if + -S $histBinSize + $input + > $samStats + </command> + <inputs> + <param format="sam,bam" name="input" type="data" label="SAM/BAM File" /> + <param name="trackMultAlign" type="boolean" value="False" truevalue="-D" falsevalue="" label="Keep track of multiple alignments (slower!)" /> + <param name="reportAllChr" type="boolean" value="False" truevalue="-A" falsevalue="" label="Report all chr sigs, even if there are more than 1000" /> + <!-- <param name="numReadsSubsample" type="integer" value="1000000" min="1" max="1000000" label="Number of reads to sample for per-base statistics (max 1,000,000)" /> --> + <param name="histBinSize" type="integer" value="30" min="1" label="Number of bins per chromosome for reads by chromosome "histogram"" /> + <param name="rnaSeqStats" type="boolean" value="False" label="Output RNA-Seq statistics (coverage, 3 prime bias, etc.)" /> + </inputs> + + <outputs> + <data format="tabular" name="samStats" label="${tool.name} on ${on_string}"/> + <data format="tabular" name="rnaSeqStatsFile" label="${tool.name} on ${on_string} (RNA-Seq Stats)"> <filter>rnaSeqStats</filter> + </data> + </outputs> + + <stdio> + <exit_code range="1:" level="fatal" description="Unknown error occurred" /> + </stdio> + + <tests> + <test> + <param name="input" value="test.sam" /> + <output name="samStats" file="testout.txt" /> + </test> + </tests> + + <help> +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. + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.sam Fri Jun 27 15:36:01 2014 -0400 @@ -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<A?:AAA<B<AAA XA:i:0 MD:Z:33 NM:i:0 +GEN-SEQ-ANA_0001:1:1:4183:5576#0/1 0 PCRPRIMER1+1 1 255 38M * 0 0 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCT AA=A=7=>;<BB8;>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?<AA?A? XA:i:0 MD:Z:27 NM:i:0 +GEN-SEQ-ANA_0001:1:1:6753:19078#0/1 0 PCRPRIMER1+1 58 255 25M * 0 0 TAATGATACGGCGACCACCGAGATC A:BABA:AA<?B<<?BBBBBB@BBB XA:i:0 MD:Z:25 NM:i:0 +GEN-SEQ-ANA_0001:1:1:14641:6640#0/1 0 PCRPRIMER1+1 58 255 43M * 0 0 TAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACAC AC@CB>:CC>CCCCCC?@CCBB<?@B@BAB@ABBBBBB5:?5? XA:i:0 MD:Z:43 NM:i:0 +GEN-SEQ-ANA_0001:1:1:18498:19719#0/1 0 PCRPRIMER1+1 58 255 38M * 0 0 TAATGATACGGCGACCACCGAGATCTACACTCTTTCCC CCCCCCCCCBCCACCC@CCC@BCCCCCC@CCCCCCCCC XA:i:0 MD:Z:38 NM:i:0 +GEN-SEQ-ANA_0001:1:1:5165:8271#0/1 0 PCRPRIMER1+2 1 255 37M * 0 0 AATGATACGGCGACCACCGAGATCTACACTCTTTCCC CC=CC>CC:@CCC@C>BAB<B>AAA88?>>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 CCCCCC<CBB;;C@CC5<CABB7 XA:i:0 MD:Z:23 NM:i:0 +GEN-SEQ-ANA_0001:1:1:6236:11228#0/1 0 PCRPRIMER2+1 34 255 20M * 0 0 TAATGATACGGCGACCACCG CCCCCC8CCCCC=CC?AAAA XA:i:0 MD:Z:20 NM:i:0 +GEN-SEQ-ANA_0001:1:1:13390:7511#0/1 0 PCRPRIMER2+1 34 255 48M * 0 0 TAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGC CCACBCBBBCCCCCCC?CCC;C?CCC?CCCCCCCCCCCACCCC;=>8A 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 >===>>@@@=<89A<B:@:BAA@@ XM:i:0 +GEN-SEQ-ANA_0001:1:1:1260:17853#0/1 4 * 0 0 * * 0 0 GTACAAATTCAGGACCACGCGTAAACGTCACC CCCCCB;ACBBB6@BB@BBB=A?A>6>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<CCC@?CC;?>; 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?<C XM:i:0 +GEN-SEQ-ANA_0001:1:1:1353:17775#0/1 4 * 0 0 * * 0 0 CGATAACTTCCCAACAGTGTTGTAAAG >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@<BBB>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@<?B@C@CC@8C>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<BBB?;?6< XM:i:0 +GEN-SEQ-ANA_0001:1:1:1390:2086#0/1 4 * 0 0 * * 0 0 AATAAAACTTAAAATCTCAG BBA?B:::A6B>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@<A??CCC=C?C?C:A?A XM:i:0 +GEN-SEQ-ANA_0001:1:1:1397:15413#0/1 4 * 0 0 * * 0 0 TCTTCGAAAAAACAAGCATCTACGTCTTG 7?BA?<B?B@<:::;;<>>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<B8 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1421:18483#0/1 4 * 0 0 * * 0 0 GTACAAATTCAGAAAATATTTTATT BC?CC@CBCA@BC@AA:6B@=BAB8 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1422:15203#0/1 4 * 0 0 * * 0 0 GTACAAATTCGTGTCGAAATTGAAAAAAAAAG CCC?CCCBCACC@@@CCCACC@=C;8?;98>> 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@?B<BB?A@>BB@@>BAAB: XM:i:0 +GEN-SEQ-ANA_0001:1:1:1445:8376#0/1 4 * 0 0 * * 0 0 TGAATATGAAATTCGTAAATAGCGTGTT @@CCC@>CBCC?CCC<CCBB?B?C@?@< XM:i:0 +GEN-SEQ-ANA_0001:1:1:1449:14365#0/1 4 * 0 0 * * 0 0 TTCTCCAGGTACATCTGTCTGAAA CC<CCBCCB@@BB>@BBBBBBBB> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1451:7415#0/1 4 * 0 0 * * 0 0 CTCTTAATTCAAGTCCATATTCTCCTTGTAACCCCAAGTGATACAATATTTGATT BBA@;CCAC>@@CC>CBCC?BCCBBC<B=CBC=?7=<BABCC;@<68AA;==:=? XM:i:0 +GEN-SEQ-ANA_0001:1:1:1452:4973#0/1 4 * 0 0 * * 0 0 AGCTGAATTCTTGCTAAGCCGTGAATACAC CA<C;>AAAABCCCBCCCBC@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<B8> 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@<CCCCCCC?A@C= XM:i:0 +GEN-SEQ-ANA_0001:1:1:1464:19773#0/1 4 * 0 0 * * 0 0 TAAATTCTACTTCAAGGCGTGAT =@B>@@<BBBBB@BBBB@B=<<? XM:i:0 +GEN-SEQ-ANA_0001:1:1:1469:15650#0/1 4 * 0 0 * * 0 0 TACGTAATTCACTGCACTAATC B=>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>B<BBB:B@B7@@=A<BBB XM:i:0 +GEN-SEQ-ANA_0001:1:1:1473:13951#0/1 4 * 0 0 * * 0 0 AAATTTTTAAAAAAAATGTTTG BCCCCCCC>C=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<C=CC;C=CCCBCB8CA7C?CCC? XM:i:0 +GEN-SEQ-ANA_0001:1:1:1475:14575#0/1 4 * 0 0 * * 0 0 TACGTAATTCGAAATTTGAG ?CB@C==AA?C=CCCBB:@B XM:i:0 +GEN-SEQ-ANA_0001:1:1:1480:6616#0/1 4 * 0 0 * * 0 0 GTACAAATTCGAGCGCAAAGG C;CCCCCCC?C@C9CC?CCC: XM:i:0 +GEN-SEQ-ANA_0001:1:1:1481:5435#0/1 4 * 0 0 * * 0 0 GTACAAATTATGAATAGAGAACTTTTA B@B6BBB=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<?C@?BCCBCB@6@@AAA<<<<AB:BB@?@B6>> XM:i:0 +GEN-SEQ-ANA_0001:1:1:1487:3645#0/1 4 * 0 0 * * 0 0 CTAATTCGTGTAATAATTGTGTT >87?@@>><9C:@7<A<BB?;>B 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 <BAB?>>=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 <?A>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?A?AB XM:i:0 +GEN-SEQ-ANA_0001:1:1:1501:3386#0/1 4 * 0 0 * * 0 0 GTACAAATTCAGTAGTTTTG ?<=8?76@>;<C>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>C<?=@>BCCC:: 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<BB8B?=B>>?: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<<?6?A>AA8?A<<A6 XM:i:0 +GEN-SEQ-ANA_0001:1:1:1508:6179#0/1 4 * 0 0 * * 0 0 GTCAAAAGTAGAGAAAAAAAA ><B=9<@B?@@BAB@A@9=9= XM:i:0 +GEN-SEQ-ANA_0001:1:1:1508:8256#0/1 4 * 0 0 * * 0 0 ATTCTCGCCAGCCTTTTTAAGTCGAGTTT ABB<ABA>BAAA=?B???6BB=<BAB=B? XM:i:0 +GEN-SEQ-ANA_0001:1:1:1508:11605#0/1 4 * 0 0 * * 0 0 TACGCAATTCTTCTCAAAAATTC B==B9=:=B=CBCCCB:B5B5>> 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testout.txt Fri Jun 27 15:36:01 2014 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 27 15:36:01 2014 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ea-utils" version="1.1.2-484"> + <repository changeset_revision="ef9389074f0a" name="package_ea_utils_1_1_2_484" owner="lparsons" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>