| Next changeset 1:f73f13641bb6 (2018-01-10) |
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Commit message:
planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36 |
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added:
macros.xml test-data/group_in1.sam test-data/group_in2.bam test-data/group_in3.bam test-data/group_in4.bam test-data/group_in5.bam test-data/group_in6.bam test-data/group_out1.bam test-data/group_out2.bam test-data/group_out3.bam test-data/group_out3.tab test-data/group_out4.bam test-data/group_out4.tab test-data/group_out5.bam test-data/group_out6.bam test-data/out_R1.fastq.gz test-data/out_R2.fastq.gz test-data/out_SE.fastq test-data/out_paired.log test-data/out_single.log test-data/t_R1.fastq test-data/t_R1.fastq.gz test-data/t_R2.fastq.gz umi-tools_group.xml |
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| diff -r 000000000000 -r 860bc357b678 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Aug 29 17:37:21 2017 -0400 |
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| @@ -0,0 +1,23 @@ +<?xml version="1.0"?> +<macros> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.209601.116</citation> + <citation type="bibtex"> + @misc{githubUMI-tools, + title = {UMI-tools}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/CGATOxford/UMI-tools}, + } + </citation> + </citations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">umi_tools</requirement> + <yield /> + </requirements> + </xml> + <token name="@VERSION@">0.5.0</token> +</macros> |
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| diff -r 000000000000 -r 860bc357b678 test-data/group_in1.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group_in1.sam Tue Aug 29 17:37:21 2017 -0400 |
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| b'@@ -0,0 +1,666 @@\n+@HD\tVN:1.0\tSO:coordinate\n+@PG\tID:Bowtie\tVN:1.1.2\tCL:"bowtie --wrapper basic-0 --threads 4 -v 2 -m 10 -a /ifs/mirror/genomes/bowtie/mm9 /dev/fd/63 --sam"\n+@SQ\tSN:chr10\tLN:129993255\n+@SQ\tSN:chr11\tLN:121843856\n+@SQ\tSN:chr12\tLN:121257530\n+@SQ\tSN:chr13\tLN:120284312\n+@SQ\tSN:chr14\tLN:125194864\n+@SQ\tSN:chr15\tLN:103494974\n+@SQ\tSN:chr16\tLN:98319150\n+@SQ\tSN:chr17\tLN:95272651\n+@SQ\tSN:chr18\tLN:90772031\n+@SQ\tSN:chr19\tLN:61342430\n+@SQ\tSN:chr1\tLN:197195432\n+@SQ\tSN:chr2\tLN:181748087\n+@SQ\tSN:chr3\tLN:159599783\n+@SQ\tSN:chr4\tLN:155630120\n+@SQ\tSN:chr5\tLN:152537259\n+@SQ\tSN:chr6\tLN:149517037\n+@SQ\tSN:chr7\tLN:152524553\n+@SQ\tSN:chr8\tLN:131738871\n+@SQ\tSN:chr9\tLN:124076172\n+@SQ\tSN:chrM\tLN:16299\n+@SQ\tSN:chrX\tLN:166650296\n+@SQ\tSN:chrY\tLN:15902555\n+SRR2057595.10000392_AAGTA\t16\tchr19\t31326011\t255\t57M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:23A33\tNM:i:1\tUG:i:512\tBX:Z:AAGTA\n+SRR2057595.10000468_GCTAT\t16\tchr19\t61240267\t255\t28M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:11C16\tNM:i:1\tUG:i:706\tBX:Z:GCTAT\n+SRR2057595.10000704_TGATG\t16\tchr19\t3544146\t255\t39M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:39\tNM:i:0\tUG:i:1\tBX:Z:TGATG\n+SRR2057595.10000838_TAGTA\t0\tchr19\t10274608\t255\t34M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:34\tNM:i:0\tUG:i:324\tBX:Z:TAGTA\n+SRR2057595.10001118_TCTCA\t16\tchr19\t4078298\t255\t50M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:43A6\tNM:i:1\tUG:i:36\tBX:Z:TCTCA\n+SRR2057595.10001329_CGGTC\t16\tchr19\t28083193\t255\t60M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:60\tNM:i:0\tUG:i:497\tBX:Z:CGGTC\n+SRR2057595.10001382_CTGCC\t16\tchr19\t3957282\t255\t22M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:17C1G2\tNM:i:2\tUG:i:9\tBX:Z:CTGCC\n+SRR2057595.10001382_CTGCC\t16\tchr19\t3970897\t255\t22M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:17C1G2\tNM:i:2\tUG:i:10\tBX:Z:CTGCC\n+SRR2057595.10002047_ATTAT\t16\tchr19\t7546213\t255\t27M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:27\tNM:i:0\tUG:i:278\tBX:Z:ATTAT\n+SRR2057595.10002219_ATCAG\t16\tchr19\t5796783\t255\t34M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:34\tNM:i:0\tUG:i:234\tBX:Z:ATCAG\n+SRR2057595.10002597_AATTA\t16\tchr19\t50733887\t255\t64M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:58C0C4\tNM:i:2\tUG:i:645\tBX:Z:AATTA\n+SRR2057595.10003084_GTCTA\t16\tchr19\t4078420\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:2T19A44\tNM:i:2\tUG:i:124\tBX:Z:GTCTA\n+SRR2057595.10003230_ACATT\t0\tchr19\t8799370\t255\t64M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:64\tNM:i:0\tUG:i:297\tBX:Z:ACATT\n+SRR2057595.10003317_CGGCC\t16\tchr19\t52641725\t255\t20M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:1C13A4\tNM:i:2\tUG:i:648\tBX:Z:CGGCC\n+SRR2057595.10003567_ATGTC\t0\tchr19\t37052811\t255\t64M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:11C52\tNM:i:1\tUG:i:542\tBX:Z:ATGTC\n+SRR2057595.10003576_AATCG\t16\tchr19\t4078303\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:38A21A6\tNM:i:2\tUG:i:88\tBX:Z:AATCG\n+SRR2057595.10003630_GTGTT\t16\tchr19\t4078298\t255\t52M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:42G0A8\tNM:i:2\tUG:i:45\tBX:Z:GTGTT\n+SRR2057595.10003869_TCTTG\t16\tchr19\t4078423\t255\t67M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:19A47\tNM:i:1\tUG:i:111\tBX:Z:TCTTG\n+SRR2057595.1000404_AACTT\t16\tchr19\t4078420\t255\t64M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:2T19A41\tNM:i:2\tUG:i:55\tBX:Z:AACTT\n+SRR2057595.10004161_TTCGC\t16\tchr19\t4078428\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:14A24T27\tNM:i:2\tUG:i:74\tBX:Z:TTCGC\n+SRR2057595.1000475_TCTGG\t0\tchr19\t13129234\t255\t28M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:22T5\tNM:i:1\tUG:i:383\tBX:Z:TCTGG\n+SRR2057595.10004845_GGATA\t0\tchr19\t24394180\t255\t29M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:11C15T1\tNM:i:2\tUG:i:481\tBX:Z:GGATA\n+SRR2057595.10005100_TTAAA\t16\tchr19\t4785463\t255\t21M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:21\tNM:i:0\tUG:i:196\tBX:Z:TTAAA\n+SRR2057595.10005761_CTAGA\t16\tchr19\t4078299\t255\t50M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:41G0A7\tNM:i:2\tUG:i:43\tBX:Z:CTAGA\n+SRR2057595.10005808_CAGTA\t16\tchr19\t7545872\t255\t24M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:24\tNM:i:0\tUG:i:276\tBX:Z:CAGTA\n+SRR2057595.10005955_GACAT\t16\tchr19\t4078302\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:39A21A5\tNM:i:2\tUG:i:82\tBX:Z:GACAT\n+SRR2057595.10006011_TCTCA\t16\tchr19\t4078298\t255\t50M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:43A6\tNM:i:1\tUG:i:36\tBX:Z:TCTCA\n+SRR2057595.10006546_GCTAC\t16\tchr19\t4078446\t255\t67M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:67\tNM:i:0\tUG:i:97\tBX:Z:GCTAC\n+SRR2057595.1000663_ACGCA\t16\tchr19\t51217013\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:3A46A16\tNM:i:2\tUG:i:647\tBX:Z:ACGCA\n+SRR2057595.10006870_GTCCA\t16\tchr19\t4078431\t255\t67M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:11A55\tNM:i:1\tUG:i:107\tBX:Z:GTCCA\n+SRR2057595.10006926_GGATA\t0\tchr19\t24394180\t255\t29M\t*\t0\t0\t*\t*\tXA:'..b'\tchr19\t55501486\t255\t31M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:8A22\tNM:i:1\tUG:i:659\tBX:Z:GATTG\n+SRR2057595.1013616_ATAGA\t0\tchr19\t38795805\t255\t62M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:46A15\tNM:i:1\tUG:i:553\tBX:Z:ATAGA\n+SRR2057595.10136267_TTCGC\t16\tchr19\t4078428\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:14A24T27\tNM:i:2\tUG:i:74\tBX:Z:TTCGC\n+SRR2057595.10136714_ATCCG\t16\tchr19\t37369602\t255\t35M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:35\tNM:i:0\tUG:i:544\tBX:Z:ATCCG\n+SRR2057595.10136765_GCTAT\t0\tchr19\t57701750\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:34T1T30\tNM:i:2\tUG:i:677\tBX:Z:GCTAT\n+SRR2057595.10137151_ATTCT\t0\tchr19\t3576314\t255\t23M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:16T5T0\tNM:i:2\tUG:i:5\tBX:Z:ATTCT\n+SRR2057595.10137262_ACAAA\t16\tchr19\t4078298\t255\t49M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:43A5\tNM:i:1\tUG:i:27\tBX:Z:ACAAA\n+SRR2057595.10137317_GATTG\t0\tchr19\t8799830\t255\t67M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:67\tNM:i:0\tUG:i:314\tBX:Z:GATTG\n+SRR2057595.10137603_GCTAT\t16\tchr19\t61240267\t255\t28M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:11C16\tNM:i:1\tUG:i:706\tBX:Z:GCTAT\n+SRR2057595.10137788_TAGTA\t0\tchr19\t10274608\t255\t34M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:34\tNM:i:0\tUG:i:324\tBX:Z:TAGTA\n+SRR2057595.1013793_GCGCA\t0\tchr19\t8798523\t255\t30M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:30\tNM:i:0\tUG:i:295\tBX:Z:GCGCA\n+SRR2057595.10138029_GTTGT\t16\tchr19\t12564367\t255\t21M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:0A12A7\tNM:i:2\tUG:i:380\tBX:Z:GTTGT\n+SRR2057595.10138656_CTAGC\t16\tchr19\t4078298\t255\t62M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:43A18\tNM:i:1\tUG:i:63\tBX:Z:CTAGC\n+SRR2057595.10138697_GCCGT\t0\tchr19\t30861987\t255\t20M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:3C2T13\tNM:i:2\tUG:i:511\tBX:Z:GCCGT\n+SRR2057595.10138764_GATGG\t0\tchr19\t44417644\t255\t23M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:15T4C2\tNM:i:2\tUG:i:601\tBX:Z:GATGG\n+SRR2057595.10138897_TGATT\t16\tchr19\t4078299\t255\t50M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:41G0A7\tNM:i:2\tUG:i:41\tBX:Z:TGATT\n+SRR2057595.10139239_GAGTG\t0\tchr19\t8798502\t255\t51M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:51\tNM:i:0\tUG:i:289\tBX:Z:GAGTG\n+SRR2057595.10139499_AGTCT\t0\tchr19\t13129558\t255\t37M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:21A15\tNM:i:1\tUG:i:398\tBX:Z:AGTCT\n+SRR2057595.10139596_GCTAC\t16\tchr19\t4078446\t255\t67M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:67\tNM:i:0\tUG:i:97\tBX:Z:GCTAC\n+SRR2057595.10139652_GGATG\t0\tchr19\t13129322\t255\t27M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:27\tNM:i:0\tUG:i:402\tBX:Z:GGATG\n+SRR2057595.10139674_ATGAA\t16\tchr19\t4078298\t255\t37M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:37\tNM:i:0\tUG:i:175\tBX:Z:ATAAA\n+SRR2057595.10139952_TAGTA\t16\tchr19\t61240268\t255\t27M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:10C16\tNM:i:1\tUG:i:702\tBX:Z:TAGTA\n+SRR2057595.10140058_ATATA\t0\tchr19\t13129330\t255\t22M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:0T21\tNM:i:1\tUG:i:422\tBX:Z:ATATA\n+SRR2057595.10141122_GTCCC\t0\tchr19\t12347657\t255\t32M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:32\tNM:i:0\tUG:i:372\tBX:Z:GTCCC\n+SRR2057595.10141122_GTCCC\t0\tchr19\t12348043\t255\t32M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:32\tNM:i:0\tUG:i:374\tBX:Z:GTCCC\n+SRR2057595.10141122_GTCCC\t16\tchr19\t15035071\t255\t32M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:29T2\tNM:i:1\tUG:i:428\tBX:Z:GTCCC\n+SRR2057595.10141295_TAGTA\t0\tchr19\t10274608\t255\t34M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:34\tNM:i:0\tUG:i:324\tBX:Z:TAGTA\n+SRR2057595.10142441_GTCTA\t16\tchr19\t4078420\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:2T19A44\tNM:i:2\tUG:i:124\tBX:Z:GTCTA\n+SRR2057595.10142482_GCCGA\t16\tchr19\t7389994\t255\t48M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:47C0\tNM:i:1\tUG:i:274\tBX:Z:GCCGA\n+SRR2057595.10143102_AAGTA\t16\tchr19\t31326011\t255\t57M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:23A33\tNM:i:1\tUG:i:512\tBX:Z:AAGTA\n+SRR2057595.10143387_GCATA\t16\tchr19\t4078298\t255\t57M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:42G0A13\tNM:i:2\tUG:i:53\tBX:Z:GCATA\n+SRR2057595.10143631_ATTTT\t0\tchr19\t45095257\t255\t57M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:57\tNM:i:0\tUG:i:606\tBX:Z:ATTTT\n+SRR2057595.10143687_CGCTT\t0\tchr19\t13129322\t255\t26M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:26\tNM:i:0\tUG:i:406\tBX:Z:CGCTT\n+SRR2057595.10143772_TGATT\t16\tchr19\t4078299\t255\t50M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:41G0A7\tNM:i:2\tUG:i:41\tBX:Z:TGATT\n+SRR2057595.10143909_CAGAC\t0\tchr19\t5493782\t255\t41M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:41\tNM:i:0\tUG:i:218\tBX:Z:CAGAC\n+SRR2057595.10143972_CTTAC\t16\tchr19\t4078298\t255\t54M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:42G0A10\tNM:i:2\tUG:i:49\tBX:Z:CTTAC\n+SRR2057595.10144216_CATAA\t0\tchr19\t13129322\t255\t35M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:33C1\tNM:i:1\tUG:i:401\tBX:Z:CATAA\n+SRR2057595.10144367_ATGAT\t16\tchr19\t61240306\t255\t36M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:16A4T14\tNM:i:2\tUG:i:716\tBX:Z:ATGAT\n' 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| diff -r 000000000000 -r 860bc357b678 test-data/group_out3.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group_out3.tab Tue Aug 29 17:37:21 2017 -0400 |
| b |
| b'@@ -0,0 +1,498 @@\n+read_id\tcontig\tposition\tgene\tumi\tumi_count\tfinal_umi\tfinal_umi_count\tunique_id\n+chrM_81_583_3:0:0_2:0:0_f4/1_TT\tchrM\t80\tNA\tTT\t1\tTT\t1\t0\n+chrM_110_732_3:0:0_2:0:0_160/1_CC\tchrM\t109\tNA\tCC\t1\tCC\t1\t1\n+chrM_118_613_6:0:0_4:0:0_169/1_AG\tchrM\t117\tNA\tAG\t1\tAG\t1\t2\n+chrM_149_684_2:0:0_2:0:0_6e/1_TA\tchrM\t148\tNA\tTA\t1\tTA\t1\t3\n+chrM_152_616_6:0:0_2:0:0_84/1_GC\tchrM\t151\tNA\tGC\t1\tGC\t1\t4\n+chrM_247_748_8:0:0_1:0:0_1b7/1_GC\tchrM\t246\tNA\tGC\t1\tGC\t1\t5\n+chrM_280_772_1:0:0_9:0:0_31/1_CG\tchrM\t279\tNA\tCG\t1\tCG\t1\t6\n+chrM_292_819_2:0:0_1:0:0_18d/1_CA\tchrM\t291\tNA\tCA\t1\tCA\t1\t7\n+chrM_390_890_3:0:0_6:0:0_bf/1_CA\tchrM\t389\tNA\tCA\t1\tCA\t1\t8\n+chrM_447_921_2:0:0_3:0:0_1cc/1_AC\tchrM\t446\tNA\tAC\t1\tAC\t1\t9\n+chrM_469_983_2:0:0_1:0:0_121/1_AC\tchrM\t468\tNA\tAC\t1\tAC\t1\t10\n+chrM_541_1074_3:0:0_8:1:0_22/1_AC\tchrM\t540\tNA\tAC\t1\tAC\t1\t11\n+chrM_8_556_3:0:0_2:0:0_1b1/1_AC\tchrM\t556\tNA\tAC\t1\tAC\t1\t12\n+chrM_112_577_2:0:0_4:0:0_17b/1_CG\tchrM\t577\tNA\tCG\t1\tCG\t1\t13\n+chrM_627_1063_6:0:0_4:1:0_12a/1_AA\tchrM\t626\tNA\tAA\t1\tAA\t1\t14\n+chrM_164_650_5:0:0_3:0:0_164/1_AC\tchrM\t650\tNA\tAC\t1\tAC\t1\t15\n+chrM_200_695_6:0:0_2:0:0_5a/1_TA\tchrM\t695\tNA\tTA\t3\tTA\t3\t16\n+chrM_168_695_5:0:0_2:0:0_1af/1_TA\tchrM\t695\tNA\tTA\t3\tTA\t3\t16\n+chrM_170_695_1:0:0_6:0:0_1e3/1_TA\tchrM\t695\tNA\tTA\t3\tTA\t3\t16\n+chrM_209_705_3:0:0_2:0:0_1b3/1_TA\tchrM\t705\tNA\tTA\t1\tTA\t1\t17\n+chrM_288_807_3:0:0_5:0:0_8e/1_AG\tchrM\t807\tNA\tAG\t1\tAG\t1\t18\n+chrM_818_1274_1:1:0_4:0:0_124/1_TC\tchrM\t817\tNA\tTC\t1\tTC\t1\t19\n+chrM_442_872_4:0:0_6:0:0_146/1_AT\tchrM\t872\tNA\tAT\t1\tAT\t1\t20\n+chrM_460_919_3:0:0_1:0:0_0/1_GA\tchrM\t919\tNA\tGA\t1\tGA\t1\t21\n+chrM_384_950_5:0:0_2:0:0_34/1_GG\tchrM\t950\tNA\tGG\t1\tGG\t1\t22\n+chrM_476_980_5:0:0_2:0:0_133/1_TA\tchrM\t980\tNA\tTA\t1\tTA\t1\t23\n+chrM_552_999_4:0:0_5:0:0_bb/1_AT\tchrM\t999\tNA\tAT\t1\tAT\t1\t24\n+chrM_512_1030_5:0:0_7:1:0_a5/1_AC\tchrM\t1030\tNA\tAC\t1\tAC\t1\t25\n+chrM_1103_1634_5:0:0_3:0:0_36/1_TA\tchrM\t1102\tNA\tTA\t1\tTA\t1\t26\n+chrM_648_1148_3:0:0_3:1:0_1d1/1_TT\tchrM\t1148\tNA\tTT\t1\tTT\t1\t27\n+chrM_1167_1797_8:0:0_2:1:0_14e/1_GT\tchrM\t1166\tNA\tGT\t1\tGT\t1\t28\n+chrM_619_1169_3:0:0_5:1:0_33/1_CC\tchrM\t1169\tNA\tCC\t1\tCC\t1\t29\n+chrM_668_1248_0:0:0_4:0:0_fa/1_TT\tchrM\t1248\tNA\tTT\t1\tTT\t1\t30\n+chrM_1288_1759_4:0:0_2:1:0_a1/1_TA\tchrM\t1287\tNA\tTA\t1\tTA\t1\t31\n+chrM_1327_1786_4:0:0_3:1:0_1ad/1_CA\tchrM\t1326\tNA\tCA\t1\tCA\t1\t32\n+chrM_866_1351_5:1:0_6:0:0_1c9/1_TA\tchrM\t1351\tNA\tTA\t1\tTA\t1\t33\n+chrM_853_1366_6:1:0_4:0:0_13b/1_TC\tchrM\t1366\tNA\tTC\t1\tTC\t1\t34\n+chrM_1399_1851_2:0:0_11:1:0_85/1_AT\tchrM\t1398\tNA\tAT\t1\tAT\t1\t35\n+chrM_946_1444_4:1:0_6:0:0_113/1_TT\tchrM\t1444\tNA\tTT\t1\tTT\t1\t36\n+chrM_943_1485_2:1:0_5:0:0_1e2/1_AT\tchrM\t1485\tNA\tAT\t1\tAT\t1\t37\n+chrM_1022_1501_4:0:0_5:0:0_132/1_GA\tchrM\t1501\tNA\tGA\t1\tGA\t1\t38\n+chrM_1504_2013_4:1:0_3:0:0_10b/1_AT\tchrM\t1503\tNA\tAT\t1\tAT\t1\t39\n+chrM_1505_1934_1:1:0_5:0:0_157/1_TC\tchrM\t1504\tNA\tTC\t1\tTC\t1\t40\n+chrM_997_1511_2:1:0_1:0:0_1d8/1_AT\tchrM\t1511\tNA\tAT\t1\tAT\t1\t41\n+chrM_1521_2070_5:1:0_3:0:0_1a/1_TA\tchrM\t1520\tNA\tTA\t1\tTA\t1\t42\n+chrM_1575_2126_5:1:0_2:1:0_18c/1_TA\tchrM\t1574\tNA\tTA\t1\tTA\t1\t43\n+chrM_1063_1598_5:0:0_5:0:0_f5/1_TG\tchrM\t1598\tNA\tTG\t1\tTG\t1\t44\n+chrM_1605_2128_3:1:0_4:1:0_1ea/1_TT\tchrM\t1604\tNA\tTT\t1\tTT\t1\t45\n+chrM_1065_1609_3:0:0_5:0:0_18e/1_TA\tchrM\t1609\tNA\tTA\t1\tTA\t1\t46\n+chrM_1140_1619_1:0:0_4:0:0_74/1_TT\tchrM\t1619\tNA\tTT\t1\tTT\t1\t47\n+chrM_1111_1626_4:0:0_2:0:0_186/1_AC\tchrM\t1626\tNA\tAC\t1\tAC\t1\t48\n+chrM_1664_2135_0:1:0_3:1:0_179/1_TT\tchrM\t1663\tNA\tTT\t1\tTT\t1\t49\n+chrM_1699_2147_1:0:0_7:0:0_10c/1_AA\tchrM\t1698\tNA\tAA\t1\tAA\t1\t50\n+chrM_1706_2240_3:0:0_6:0:0_99/1_GT\tchrM\t1705\tNA\tGT\t1\tGT\t1\t51\n+chrM_1756_2309_0:0:0_3:0:0_c3/1_AT\tchrM\t1755\tNA\tAT\t1\tAT\t1\t52\n+chrM_1344_1758_4:0:0_3:1:0_75/1_TT\tchrM\t1758\tNA\tTT\t1\tTT\t1\t53\n+chrM_1223_1777_5:0:0_6:1:0_42/1_TG\tchrM\t1777\tNA\tTG\t1\tTG\t1\t54\n+chrM_1790_2351_4:0:0_4:0:0_f3/1_CC\tchrM\t1789\tNA\tCC\t1\tCC\t1\t55\n+chrM_1308_1807_4:0:0_4:1:0_45/1_TA\tchrM\t1807\tNA\tTA\t1\tTA\t1\t56\n+chrM_1814_2315_6:0:0_3:0:0_12d/1_AA\tchrM\t1813\tNA\tAA\t1\tAA\t1\t57\n+chrM_1862_2304_4:0:0_1:0:0_19d/1_AA\tchrM\t1861\tNA\tAA\t1\tAA\t1\t58\n+chrM_1363_1869_5:0:0_3:1:0_aa/1_TA\tchrM\t1869\tNA\tTA\t1\tTA\t1\t59\n+chrM_1363_1887_2:0:0_3:0:0_d3/1_CA\tchrM\t1887\tNA\tCA\t1\tCA\t1\t60\n+chrM_1428_1904_7:0:0_1:0:0_1b0/1_AC\tchrM\t1904\tNA\tAC\t1\tAC\t1\t6'..b'\tTA\t1\t431\n+chrM_14135_14581_5:0:0_5:0:0_1de/1_AT\tchrM\t14581\tNA\tAT\t1\tAT\t1\t432\n+chrM_14612_15169_2:0:0_5:0:0_e4/1_TT\tchrM\t14611\tNA\tTT\t1\tTT\t1\t433\n+chrM_14668_15109_2:0:0_3:0:0_3d/1_TG\tchrM\t14667\tNA\tTG\t1\tTG\t1\t434\n+chrM_14696_15126_2:0:0_2:0:0_a7/1_AA\tchrM\t14695\tNA\tAA\t1\tAA\t1\t435\n+chrM_14727_15156_4:0:0_4:0:0_178/1_GA\tchrM\t14726\tNA\tGA\t1\tGA\t1\t436\n+chrM_14245_14783_3:0:0_1:0:0_9d/1_GG\tchrM\t14783\tNA\tGG\t1\tGG\t1\t437\n+chrM_14314_14802_5:0:0_3:0:0_191/1_GG\tchrM\t14802\tNA\tGG\t1\tGG\t1\t438\n+chrM_14817_15261_5:0:0_4:0:0_65/1_AT\tchrM\t14816\tNA\tAT\t1\tAT\t1\t439\n+chrM_14863_15320_2:0:0_4:0:0_d8/1_AA\tchrM\t14862\tNA\tAA\t1\tAA\t1\t440\n+chrM_14869_15387_2:0:0_7:0:0_1f/1_AC\tchrM\t14868\tNA\tAC\t1\tAC\t1\t441\n+chrM_14888_15340_3:0:0_3:0:0_112/1_GG\tchrM\t14887\tNA\tGG\t1\tGG\t1\t442\n+chrM_14368_14894_6:0:0_5:0:0_40/1_TC\tchrM\t14894\tNA\tTC\t1\tTC\t1\t443\n+chrM_14410_14941_6:0:0_3:0:0_e5/1_TA\tchrM\t14941\tNA\tTA\t1\tTA\t1\t444\n+chrM_14962_15543_5:0:0_8:0:0_46/1_CA\tchrM\t14961\tNA\tCA\t1\tCA\t1\t445\n+chrM_14456_14987_3:0:0_5:0:0_ab/1_GT\tchrM\t14987\tNA\tGT\t1\tGT\t1\t446\n+chrM_15070_15569_5:0:0_5:0:0_cf/1_CA\tchrM\t15069\tNA\tCA\t1\tCA\t1\t447\n+chrM_15140_15686_2:0:0_5:0:0_185/1_CC\tchrM\t15139\tNA\tCC\t1\tCC\t1\t448\n+chrM_15142_15661_7:0:0_3:0:0_11e/1_CT\tchrM\t15141\tNA\tCT\t1\tCT\t1\t449\n+chrM_15192_15694_5:0:0_2:0:0_f7/1_CA\tchrM\t15191\tNA\tCA\t1\tCA\t1\t450\n+chrM_15211_15685_5:0:0_2:0:0_1d7/1_AC\tchrM\t15210\tNA\tAC\t1\tAC\t1\t451\n+chrM_15225_15786_3:0:0_6:0:0_17e/1_TT\tchrM\t15224\tNA\tTT\t1\tTT\t1\t452\n+chrM_15258_15810_4:0:0_6:0:0_5f/1_TT\tchrM\t15257\tNA\tTT\t1\tTT\t1\t453\n+chrM_14817_15317_5:0:0_2:0:0_59/1_GC\tchrM\t15317\tNA\tGC\t1\tGC\t1\t454\n+chrM_15324_15836_4:0:0_3:0:0_94/1_AC\tchrM\t15323\tNA\tAC\t1\tAC\t1\t455\n+chrM_15365_15880_4:1:0_3:0:0_80/1_CA\tchrM\t15364\tNA\tCA\t1\tCA\t1\t456\n+chrM_15408_15863_2:1:0_3:0:0_1e6/1_AG\tchrM\t15407\tNA\tAG\t1\tAG\t1\t457\n+chrM_15439_15924_0:0:0_4:0:0_172/1_TG\tchrM\t15438\tNA\tTG\t1\tTG\t1\t458\n+chrM_14931_15457_2:0:0_4:1:0_1a1/1_AA\tchrM\t15457\tNA\tAA\t1\tAA\t1\t459\n+chrM_15547_16054_5:0:0_1:0:0_af/1_GA\tchrM\t15546\tNA\tGA\t1\tGA\t1\t460\n+chrM_15134_15560_3:0:0_4:0:0_1c4/1_GG\tchrM\t15560\tNA\tGG\t1\tGG\t1\t461\n+chrM_15575_16118_5:0:0_4:0:0_1aa/1_GC\tchrM\t15574\tNA\tGC\t1\tGC\t1\t462\n+chrM_15052_15629_7:0:0_9:0:0_15f/1_GA\tchrM\t15629\tNA\tGA\t1\tGA\t1\t463\n+chrM_15698_16224_5:0:0_6:0:0_138/1_AC\tchrM\t15697\tNA\tAC\t1\tAC\t1\t464\n+chrM_15247_15721_2:1:0_6:0:0_17/1_TC\tchrM\t15721\tNA\tTC\t1\tTC\t1\t465\n+chrM_15218_15763_2:0:0_2:0:0_171/1_AG\tchrM\t15763\tNA\tAG\t1\tAG\t1\t466\n+chrM_15860_16419_5:0:0_8:0:0_53/1_TA\tchrM\t15859\tNA\tTA\t1\tTA\t1\t467\n+chrM_15864_16329_3:0:0_3:0:0_18b/1_CG\tchrM\t15863\tNA\tCG\t1\tCG\t1\t468\n+chrM_15507_15962_3:0:0_0:0:0_5b/1_GT\tchrM\t15962\tNA\tGT\t1\tGT\t1\t469\n+chrM_15430_15985_5:0:0_3:0:0_2c/1_AT\tchrM\t15985\tNA\tAT\t1\tAT\t1\t470\n+chrM_15706_16238_6:0:0_7:0:0_7b/1_AG\tchrM\t16238\tNA\tAG\t1\tAG\t1\t471\n+chrM_16252_16701_2:1:0_5:0:0_147/1_TA\tchrM\t16251\tNA\tTA\t1\tTA\t1\t472\n+chrM_15753_16280_5:0:0_6:0:0_180/1_TG\tchrM\t16280\tNA\tTG\t1\tTG\t1\t473\n+chrM_15777_16347_2:0:0_6:0:0_16/1_AT\tchrM\t16347\tNA\tAT\t1\tAT\t1\t474\n+chrM_16366_16911_6:1:0_6:1:1_168/1_CC\tchrM\t16365\tNA\tCC\t1\tCC\t1\t475\n+chrM_16370_16833_6:1:0_6:0:1_1bb/1_AC\tchrM\t16369\tNA\tAC\t1\tAC\t1\t476\n+chrM_16402_16876_2:0:0_1:0:1_98/1_CA\tchrM\t16401\tNA\tCA\t1\tCA\t1\t477\n+chrM_16426_16953_3:0:0_2:2:0_60/1_AA\tchrM\t16425\tNA\tAA\t1\tAA\t1\t478\n+chrM_15986_16442_3:0:0_7:0:0_15d/1_TG\tchrM\t16442\tNA\tTG\t1\tTG\t1\t479\n+chrM_16030_16460_6:0:0_4:1:0_20/1_AT\tchrM\t16460\tNA\tAT\t1\tAT\t1\t480\n+chrM_15909_16463_3:0:0_7:1:0_106/1_GT\tchrM\t16463\tNA\tGT\t1\tGT\t1\t481\n+chrM_15984_16500_4:0:0_1:0:0_6b/1_GT\tchrM\t16500\tNA\tGT\t1\tGT\t1\t482\n+chrM_16070_16513_3:0:0_7:1:0_1e7/1_TA\tchrM\t16513\tNA\tTA\t1\tTA\t1\t483\n+chrM_16064_16572_4:0:0_6:1:0_f1/1_TG\tchrM\t16572\tNA\tTG\t1\tTG\t1\t484\n+chrM_16245_16740_4:1:0_2:0:1_127/1_TA\tchrM\t16742\tNA\tTA\t1\tTA\t1\t485\n+chrM_16315_16834_5:0:0_3:0:1_18/1_TT\tchrM\t16834\tNA\tTT\t1\tTT\t1\t486\n+chrM_16229_16843_2:1:0_2:0:1_c4/1_GC\tchrM\t16843\tNA\tGC\t1\tGC\t1\t487\n+chrM_16420_16905_5:0:0_2:0:1_159/1_GT\tchrM\t16905\tNA\tGT\t2\tGT\t2\t488\n+chrM_16420_16905_5:0:0_2:0:1_159/1_GT\tchrM\t16905\tNA\tGT\t2\tGT\t2\t488\n+chrM_16419_16923_3:0:0_3:0:1_183/1_CG\tchrM\t16923\tNA\tCG\t1\tCG\t1\t489\n+chrM_16585_16993_5:0:1_5:1:0_1b9/1_GA\tchrM\t16993\tNA\tGA\t1\tGA\t1\t490\n' |
| b |
| diff -r 000000000000 -r 860bc357b678 test-data/group_out4.bam |
| b |
| Binary file test-data/group_out4.bam has changed |
| b |
| diff -r 000000000000 -r 860bc357b678 test-data/group_out5.bam |
| b |
| Binary file test-data/group_out5.bam has changed |
| b |
| diff -r 000000000000 -r 860bc357b678 test-data/group_out6.bam |
| b |
| Binary file test-data/group_out6.bam has changed |
| b |
| diff -r 000000000000 -r 860bc357b678 test-data/out_R1.fastq.gz |
| b |
| Binary file test-data/out_R1.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 860bc357b678 test-data/out_R2.fastq.gz |
| b |
| Binary file test-data/out_R2.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 860bc357b678 test-data/out_SE.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_SE.fastq Tue Aug 29 17:37:21 2017 -0400 |
| b |
| b"@@ -0,0 +1,288 @@\n+@HISEQ:105:C2UE1ACXX:3:1101:11160:2245_TTA 1:N:0:CAGATC\n+AAAAGTAGTTAATATATTAGATTTGTTTGATAGTGGTAGTATATATTTTTTATTTTAGTATTTAGGAGGTAGAGGTAGATGAATTTTTGAGTTTAAAG\n++\n+BBBFFFFBFFFFFIIIIIIBIIIIBIFFBFIIBBFFFFFFFFIIIIIIIIIIIIIIIBFIIIIIB7BBBFBBFFFF77<F7BFFFFFF7B7BBFFFF7\n+@HISEQ:105:C2UE1ACXX:3:1101:19467:2281_TTT 1:N:0:CATATC\n+TTGGTTAGGGTGAGATGTATAGTTTGGATTTTAGTGATTTTTGTAAAGGGGGAAAAGAATGGAGTTTTGGGTGTAGTGAGAGGTTATAGGAGTAGGGA\n++\n+<B<<FFFBBFFFFFFFFFIFIBFFI<<BFFFIIBBBFFIIIIBFFIIBBF7BBFFFBFFF77BBFBFF777BBBBBB<<<B<7<7BBF77<7<70000\n+@HISEQ:105:C2UE1ACXX:3:1101:7009:2740_TAG 1:N:0:CAGATC\n+AAGTTTTGTTTTTTATTTGGAGGTTATGGAATGTTAAGTAAGGTTTTTTTGGGTTTTGTTATTTATTTGATAATTGTGATTGTAATGTTAATAAGGGA\n++\n+BBBFFFFFFFFFFIIIIIB<FFFFFFIBBFIIFFFIIFIIIFFIFFIIII<0<BBFFBFFFFFFFFFF<BBFFFF<BBBBF7BFFF<BBFFFFF<00<\n+@HISEQ:105:C2UE1ACXX:3:1101:19067:2707_TTT 1:N:0:CAGATC\n+GTTTTTTTATTTGATATTTTAAAGGTTTTTTTTTTTTTTTTAGAAAATTTTTTTTAGTAAGATAGATTTTAAAGGGTTTGTTTTTTTTTTTTTTTTTT\n++\n+BBBFFFFFFFFFBBFFFFIIIFIFFIFFIIIIIIIFFFFFB7'0<B0<BBFF'7<0'0<<''0<'0'0<BBB<<B'7'0'0'0<BFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:4999:3182_AGG 1:N:0:CAGATC\n+GTTTTATGAGGATTTTAGGGGAGTGATTGTTTAAAGTTTATAAGATTTATGATTTATATATAGTTAGAATAGTATGTGTTAAATAAATATAAAGGGAG\n++\n+<BBFFFFBFFFFFFIIFBBBFFFIIFFIBFFIFIIBFFIIIIIFFIIIIIBFFIIIIIIIIIBFFIBFIII<FFFBFBFFFFFFFFFFFFFFF<07<7\n+@HISEQ:105:C2UE1ACXX:3:1101:2300:3263_GTT 1:N:0:TAGATC\n+TTATTTTTAATAAAATTTTTATTATTTAATTTATTAGTTAATATTTAGGAGTTTTATGTTGTGGTAAAATTTTGTTAGAGAGATAGAGAAAGTATTTA\n++\n+BBBFFFFFFFFBFFIIIIIIBIBBFFI0<FFFBFF70B00<'0<FFFBBBBFF''0B0BB000'7BBFFFFII'<BF0<'<''07'70BBF'7BBBFB\n+@HISEQ:105:C2UE1ACXX:3:1101:5605:3427_AGA 1:N:0:CAGATC\n+AGATGAGAGGTATAGGATGTGGGGAGTTTTAGTAAGATTTATAGATAAGAAGTGGTTCGGTTATAGGATTTGTTTTAGATTTTTAGATTTTTTTGTGT\n++\n+BBBFBFFFFFFFFFFBFFFFIIIIIIIBFFFBFFIBFFIIIIIFFIIIFFIBF7BFBFBBFFIFF<<FFFFBBFFBF0<BFFFFF7<BFFFFFF0B7B\n+@HISEQ:105:C2UE1ACXX:3:1101:8129:3589_GAT 1:N:0:CAGATC\n+TTTTAGTTTTTAGTTAGGATTATACGTTTATTGTGATAAAAGAGTTTTTTGATTTATCGGGTTATGTTAGGGTTTATTGATATTAGGGAATTTGAAGA\n++\n+BBBFFBFFFFFFBFFFBBFIIFIIFBFFFFII<BBFFFIIIBFFIFIIIIBBFFIIII<7<FBFF<FBF<7<BBFFFF7<BFFFF700<BBFF0<B'<\n+@HISEQ:105:C2UE1ACXX:3:1101:14304:3866_TAA 1:N:0:CAGATC\n+GTGTTTATATAGGGGATTTTTGAGTTTGATAGGTTGTTTTTGTAGAGGGTAGAATTTTGTGGAAATGTTGGTATTGGTTAAGGGGTTTTAGTGAAGAA\n++\n+<BBFFFFFFFFFFFFFFFFII<BBFFFBFFIFBFFBFFFII7FFFFFFFIF<BFIIII<F<BBFIFBFB7<BFFFBBBBBF777<B7BBF7B<BB7BB\n+@HISEQ:105:C2UE1ACXX:3:1101:12720:4398_AGT 1:N:0:CAGATC\n+GTATGTGTGTGTGTGTGTGTATTTAATTGAAGTTGGGTTTGGTGATATATATGTTTAATTTTAGTATTTTAGTGGTAGAGGTAGGTTAATTTTTGTTG\n++\n+<BBFBFFFFFFFFIFIFIFFFFFIIFII0BFBFFB7BFFF<BFFFFIIIIIIBFIIIIFIIII<FIFIIIFBFBBFB7B<<BB7<B<BFFFFFF0<B0\n+@HISEQ:105:C2UE1ACXX:3:1101:14945:4439_ATT 1:N:0:CAGATC\n+AGTGTTGAGTGGAGTATTAGAGAAGAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTT\n++\n+BBBBFFBFFFFFFFFFFIIBIFFIFFBFFIIIIBFFIIIIIIBFFIIIBFFBFFFIIIFBFFBFBFFIIIIIFFFBBF77BBFFF7BBFF<BBF<<BF\n+@HISEQ:105:C2UE1ACXX:3:1101:8616:4508_AGG 1:N:0:CAGATC\n+AGAAATTTTGGGGGTGTAGGAGTGGTAGGATAGGAGTGTTGTTTTGTAATAGTTTTTTTTGAGGTTTAATAGGTAGGGTAGTTATTTTTAGTATTGTA\n++\n+BBBFFFFFFBBBFFFIIFFFIFFFIIFFIIFIFBFFFIIF<FBFI<FFIIIBFFFFFFFF077<B<BBBFF<<BBBBBB<7B<BFFFFFF0BBFF0<B\n+@HISEQ:105:C2UE1ACXX:3:1101:18975:4834_GAG 1:N:0:CAGATC\n+TATAAATGGTAATTTTGTAATTTAAAGATTTAAAAGTAATTATTGGTAATAGTTATTTGTGGGAGGTTGAGGTAGGGGGATTTTTGTAGAGATCGGAA\n++\n+BBBFFFFBBFFFFIIIBFIIIIIFIIFFFFIFIIIBFIIIIIIIB<FFIFIBFFFIIIBFFBFFFII<<BFBFFFFIFF<BBBFF0BB7<<<BF707B\n+@HISEQ:105:C2UE1ACXX:3:1101:4984:5374_TTG 1:N:0:CAGATC\n+TGTATCGAGGTTTGAATGAGAGTGGTATTTTTGTTATTTGTTAGTTAATGGTTTTGAGTATTAGTTTGGAAAATGATAATAAGTATTAGTTGAGGTGT\n++\n+B<BFFFBFFFFBF<FFFBFFFFFFFIFFFIII<BFFIIIBFFFFFFIIIBBFFFIBBBFFFIIBFFF<<BFFFFBBFFFFFF<BBFFF<BB7<7<BBB\n+@HISEQ:105:C2UE1ACXX:3:1101:12336:6058_TTT 1:N:0:CAGATC\n+ATTTAGATGATGGTTTTTTTATTTGATATTTTAAAGGTTTTTTTTTTTTTTTTTTAAAAAATTTTTTTTATAAAAATAAATTTTAAAGGGTTTTTTTT\n++\n+BBBFFBFFBFFBBFFFIIIIIIIIBFFIIIIIIIIBFFFFIIIIIFFFFFFFFF700<BF0BBFFF0<70''00'0'000'<<'<B<00'0'00007<\n+@HISEQ:105:C2UE1ACXX:3:1101:5999:6265_ATG 1:N:0:CAGATC\n+TATATTGTTATATATTTGTGTTTTTTTTGAA"..b"FFFIBBFFIIIIFIBFFIBBFFFIFIFIIFFIFFIBFIIIFBFFFIIIIIBFBBFFFBFFF<<FFFFI70<7BFF<BFFFFFFBBBF7\n+@HISEQ:105:C2UE1ACXX:3:1101:13060:22287_TGT 1:N:0:CAGATC\n+TAGTGAAGAATAAATTTTTATGTTGTATATTATTTTTTTTTAGTTCGTATATATCGGTATACGTGTTAGGATTTATAAAGATAGTTATTATTTTTTGT\n++\n+BBBFFFFFFFFFFIIIIIIIIBFIFFIIIIIIIIIIIIIIII<FFIBFFIIIIIIB<BFFFFBBBBBF<<BBFFFBFFF<BBF7<BFFFFFFFFFF7B\n+@HISEQ:105:C2UE1ACXX:3:1101:7272:22581_TTA 1:N:0:CAGATC\n+TTAATGATATTAAGAATTTTTTAAAGAATTTTATTTTTTTTAGGAATAGAAGGAGGAGGAGTATTTTGATCGATTTTTTAGGTTTTTTATAGGTGGAG\n++\n+BBBFFBFFFFFFF<BFIIIIIIFIIBFFFFIIFIIIIIIIII<<FFFIBFIBBFFBFFFFFFBBFFF<BBF<BBFFFFFF00<BBFFFFFF000<777\n+@HISEQ:105:C2UE1ACXX:3:1101:10060:23020_TTT 1:N:0:CAGATC\n+TTTTAGATTATTTAAGAAGGTATTAGGTTTTTAAGAGGAAAGGGTAGTCTTATAGTTTTGAGTATTTTTTTTAAAAGGAAGTAAGGATGGTGTTTTTA\n++\n+BBBFFBFFFFFFFIIBFIFFFFFIBBBFFFFIIIBFFFIFIBFFIFFFFIIFFFBFFII7B<FFFIIIIIFFFFBB77<B<BBF<7BB<<BBBBBFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:14440:23104_TTT 1:N:0:CAGATC\n+TTTAAATTTAAGTTAAGGTTTGGGGAGTTGATTTTTGTTTTGTGGGTTGTTTTTTTTGTAGGAGTTGGTTTTTAGAGGTTTTTAGGAATTTTTGGTGT\n++\n+BBBFFFFFFFFFFFIIBBIFIBBBFFFFFBFFIIIIBFFIIBFBFFFFFFIIIIFFF7BB<<BBFB<BBBBFFB7<00B<BBFF00<BBFFFF''77B\n+@HISEQ:105:C2UE1ACXX:3:1101:6941:23338_GTT 1:N:0:CAGATC\n+AGAAAGGTTTTAAGTTGGTTGGGAATATAGGGGTTTTTTAGAGTTTTTATTAGGAGTTATAGTGTGTTGAATTTGGTTTTGGGTGTTGATTATAGGTT\n++\n+BBBFFFFFFFFFFBFFBBFFBBBFFFFIIBFFFIFFIIIIBFFFFFIIIIIIB<FFFFFFFBFBFFFF<BBFFF<<BBBB700<BBB0BBFFFF00<B\n+@HISEQ:105:C2UE1ACXX:3:1101:10069:23622_TTT 1:N:0:CAGATC\n+TTTTGTTTTAGGGTTTTATTTTTGTGTTTTATTTTTATTTTCGTATTATTAGTTTTTTTTATACGTTATTTGTAGAAGGTTAGTTTTTTTAATTTAGG\n++\n+BBBFBFFFFFBBBFFFIFIIIIIBFBFFIIBFIIIIIIIIIIBFFFIIIIIFFIIIIIIFFFFF<BFFFFF<BF<<B77BBB7BBFFFFFFFFFFF00\n+@HISEQ:105:C2UE1ACXX:3:1101:14079:24078_AGT 1:N:0:CAGATC\n+TTTAAAGTTTTTAGTTTTGAGTGGAATTTTAAGAATATTAGTGCGTTTTAAGCTTAGGTAGTTTTGGTAGTTTGAAAGTAATAGGGTGTATTTTGTAA\n++\n+BBBFFFFFFFFFFBFFFI<BBFFFFFFIIIIIBFFFIIIIBFFFFFFIIIIBFFIIBBFFFFFFI<7BFBFFF<BBF<BBFFF<07BBBBBFFF<BFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12064:24631_TTT 1:N:0:CCGATC\n+TTATAGTGTATTTATATATATGAAATGAATTAATGAATTTTAAAAAAAAAGAAAGTAAGTTGTTTTTAGGATTGATATTTAGAGTTAATTTTTTGAGT\n++\n+BBBFFBFFFFFFFIIIIIIIIBFIFF0BFIIIIIBFFIIIIIIIIIIIIIBFIIFFFIBFFBFFFFFFB<BFF7BBFFFFF<B<BBBFFFFFFF'70<\n+@HISEQ:105:C2UE1ACXX:3:1101:11630:24964_GAT 1:N:0:TAGATC\n+TTAGTTTTTTTAGTGTTTTTTATTTATTTCGTTTTATTATTGGAGTTTGTTAAGAAAATTAGGGTTTGATTTGGATGTTAAGGATTGGTTTTTTTTTT\n++\n+BBBBFFFFFFFFBFFFFIIIIIIIIIIIIIBFFFIFIIIIIB7BFFFFBFFIIBFIIIIIFB<BFBFBFFFF<7BB<BBFF<7<BB77BBFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12594:24878_AAT 1:N:0:CCGATC\n+TTTAATAGGATATGATATTATTTAATTTATAGATTATGGAAATTTTTTATATTTAATGAAGAAAGTTGGAATGTTTTGGGAGGTGTTTAGAATAAATA\n++\n+BBBFFFFB0BFFF<FFIIIFIIFIIIFIFIF<BFFFF<<BFFFIIIIIIIIIIIIIIBFFBFFIBFB7'<FF<<BBF0''77<BFB<BB0<BBBBBFF\n+@HISEQ:105:C2UE1ACXX:3:1101:4483:25030_ATT 1:N:0:CAGATC\n+AGGATGGTGTTTTTATTTTTAGATTTATATTATTTTGTTATATTTGTATTTGAGTAAGTTTATGGGTTTTTTAAAGAGGTAGGAGGAAGTTTTTTGTT\n++\n+B<BFFFFFFFFFFIIIIIIIIBBFIIFIIIIFIIII<BFFIFFIIBFIIII<BBFFIFIFIIIB7<FFFIIIFBF<<77BB00<70<B7BBBFFF0BB\n+@HISEQ:105:C2UE1ACXX:3:1101:12198:25235_TTA 1:N:0:CAGATC\n+ATATATGTAGTTTGTATTATTTTTGTTATAGTATATAAAGGTTAAAGAGTAGTTGTTTTAATTTTAGAGGTGGAGATTGGGTTGTATAGTTTTGGTTT\n++\n+BBBFFFBFFFFFFBFFIIFIIIII0BF<FF0BFFFIFFIBBFBFII<FBFBBFF7FFFIIIIIIII<F7<B'<BB7<B''0<<0<BBB77<BB'0<<B\n+@HISEQ:105:C2UE1ACXX:3:1101:20477:25084_TGT 1:N:0:CATATC\n+AGAGTTTATTGAGAAGTAAAGTATTAATTTTATGGGAGAAATGGGATAGAGGTAGTAGAAGTTGTTATGGAATGGGATTAATTAGGAAGTTAATTAAG\n++\n+BBBFFFFFFF0BBFFBFFIIFFIIIIIIIIIFIBB7FFFFIIFFBFFIFIBFFFFIIFIIFFFBFFFF77BFF<<B<FFFFFFF70<B7BBFFFFFF7\n+@HISEQ:105:C2UE1ACXX:3:1101:5725:25359_TAG 1:N:0:CAGATC\n+GAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATTAAGAAGTATAGTATTATATA\n++\n+BBBFFFFFFBFFFIIIIIIIIIIIBIFBFFFFIIBBFFFFFFFIIIIIIFFFBFFBBFFFIIBFFIIBFIIFIFIFFFFF<BF<BBFF7<<FFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:5502:25591_AGA 1:N:0:CAGATC\n+ATATGATTTTATTTTTAGGGATAATATTTTTTAAGTGAATTTTGATTTTTTGGTTAGTTATTTTGATGATGTGTAGAGGGTGTATAGTTTTTGGATAT\n++\n+BBBFBFFFFFFFFIIIIBBBFFFIIIIIIIIIIIBFFFIIIIIBFFIIIII<7BFFBFFFIIII<FF<FFBFFFFFB<<<BFBBBF<<BFFF00<BFB\n" |
| b |
| diff -r 000000000000 -r 860bc357b678 test-data/out_paired.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_paired.log Tue Aug 29 17:37:21 2017 -0400 |
| b |
| @@ -0,0 +1,36 @@ +# output generated by extract --bc-pattern=NNNXXX --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --log=/tmp/tmpREDhtd/files/003/dataset_3773.dat +# job started at Tue Aug 29 14:20:44 2017 on gaius -- 5913ff4c-b1d1-4f65-abec-66ca6684bdbd +# pid: 21437, system: Linux 4.10.0-33-generic #37-Ubuntu SMP Fri Aug 11 10:55:28 UTC 2017 x86_64 +# blacklist : None +# compresslevel : 6 +# error_correct_cell : False +# extract_method : string +# filter_cell_barcode : None +# filter_cell_barcodes : False +# log2stderr : False +# loglevel : 1 +# pattern : NNNXXX +# pattern2 : None +# prime3 : None +# quality_encoding : None +# quality_filter_mask : None +# quality_filter_threshold : None +# random_seed : None +# read2_in : input_read2.gz +# read2_out : out2.gz +# read2_stdout : False +# reads_subset : None +# reconcile : False +# short_help : None +# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> +# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'> +# stdlog : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3773.dat' mode='a' encoding='UTF-8'> +# stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'> +# timeit_file : None +# timeit_header : None +# timeit_name : all +# whitelist : None +2017-08-29 14:20:44,451 INFO Starting barcode extraction +2017-08-29 14:20:44,461 INFO Input Reads: 100 +2017-08-29 14:20:44,461 INFO Reads output: 100 +# job finished in 0 seconds at Tue Aug 29 14:20:44 2017 -- 0.73 0.05 0.00 0.00 -- 5913ff4c-b1d1-4f65-abec-66ca6684bdbd |
| b |
| diff -r 000000000000 -r 860bc357b678 test-data/out_single.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_single.log Tue Aug 29 17:37:21 2017 -0400 |
| b |
| @@ -0,0 +1,37 @@ +# output generated by extract --bc-pattern=XXXNNN --stdin=/tmp/tmpREDhtd/files/003/dataset_3766.dat --stdout /tmp/tmpREDhtd/files/003/dataset_3767.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/tmp/tmpREDhtd/files/003/dataset_3768.dat +# job started at Tue Aug 29 14:20:26 2017 on gaius -- 1cfd46e7-5d74-4c25-8cdd-89cf8f41a393 +# pid: 21338, system: Linux 4.10.0-33-generic #37-Ubuntu SMP Fri Aug 11 10:55:28 UTC 2017 x86_64 +# blacklist : None +# compresslevel : 6 +# error_correct_cell : False +# extract_method : string +# filter_cell_barcode : None +# filter_cell_barcodes : False +# log2stderr : False +# loglevel : 1 +# pattern : XXXNNN +# pattern2 : None +# prime3 : True +# quality_encoding : phred33 +# quality_filter_mask : None +# quality_filter_threshold : 10 +# random_seed : None +# read2_in : None +# read2_out : False +# read2_stdout : False +# reads_subset : None +# reconcile : False +# short_help : None +# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> +# stdin : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3766.dat' mode='r' encoding='UTF-8'> +# stdlog : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3768.dat' mode='a' encoding='UTF-8'> +# stdout : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3767.dat' mode='w' encoding='UTF-8'> +# timeit_file : None +# timeit_header : None +# timeit_name : all +# whitelist : None +2017-08-29 14:20:26,493 INFO Starting barcode extraction +2017-08-29 14:20:26,495 INFO Input Reads: 100 +2017-08-29 14:20:26,495 INFO Reads output: 72 +2017-08-29 14:20:26,495 INFO filtered: umi quality: 28 +# job finished in 0 seconds at Tue Aug 29 14:20:26 2017 -- 0.75 0.02 0.00 0.00 -- 1cfd46e7-5d74-4c25-8cdd-89cf8f41a393 |
| b |
| diff -r 000000000000 -r 860bc357b678 test-data/t_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t_R1.fastq Tue Aug 29 17:37:21 2017 -0400 |
| b |
| b"@@ -0,0 +1,400 @@\n+@HISEQ:105:C2UE1ACXX:3:1101:11160:2245 1:N:0:CAGATC\n+AAAAGTAGTTAATATATTAGATTTGTTTGATAGTGGTAGTATATATTTTTTATTTTAGTATTTAGGAGGTAGAGGTAGATGAATTTTTGAGTTTAAAGTTA\n++\n+BBBFFFFBFFFFFIIIIIIBIIIIBIFFBFIIBBFFFFFFFFIIIIIIIIIIIIIIIBFIIIIIB7BBBFBBFFFF77<F7BFFFFFF7B7BBFFFF7<BF\n+@HISEQ:105:C2UE1ACXX:3:1101:19338:2197 1:N:0:CAGATC\n+TTTTTTTTTAGAGGGATTAGTTTTTTTTATTGAGGTTTTTGAAAGTTGTTGTATGTTAATTGTTTTTAGAATGTTGGGTATAAGTAGGATTTAGGTCTATT\n++\n+BBBFFFFFFB0<BF7BBBF7BFFIIIII7BF'0<0BBFFF'<BB'<B7<B07<B7<BFBBF0<BBBBB0<<B0BB<<000<BF00<<'0<BBB0'00BBF#\n+@HISEQ:105:C2UE1ACXX:3:1101:19467:2281 1:N:0:CATATC\n+TTGGTTAGGGTGAGATGTATAGTTTGGATTTTAGTGATTTTTGTAAAGGGGGAAAAGAATGGAGTTTTGGGTGTAGTGAGAGGTTATAGGAGTAGGGATTT\n++\n+<B<<FFFBBFFFFFFFFFIFIBFFI<<BFFFIIBBBFFIIIIBFFIIBBF7BBFFFBFFF77BBFBFF777BBBBBB<<<B<7<7BBF77<7<700007BB\n+@HISEQ:105:C2UE1ACXX:3:1101:7009:2740 1:N:0:CAGATC\n+AAGTTTTGTTTTTTATTTGGAGGTTATGGAATGTTAAGTAAGGTTTTTTTGGGTTTTGTTATTTATTTGATAATTGTGATTGTAATGTTAATAAGGGATAG\n++\n+BBBFFFFFFFFFFIIIIIB<FFFFFFIBBFIIFFFIIFIIIFFIFFIIII<0<BBFFBFFFFFFFFFF<BBFFFF<BBBBF7BFFF<BBFFFFF<00<BB0\n+@HISEQ:105:C2UE1ACXX:3:1101:13708:2613 1:N:0:CAGATC\n+ATATAATAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAAAGATAATTAATTTTTAAAATTTTTTTTTTTTTAATAAAA\n++\n+BBBFFFFFBFFFFIIIIIIIIIIIFFFFFB7B007BB0''''''0077BFF7'077BF0''0''''''00''00''''00'<BBBFBBFFFFF########\n+@HISEQ:105:C2UE1ACXX:3:1101:19067:2707 1:N:0:CAGATC\n+GTTTTTTTATTTGATATTTTAAAGGTTTTTTTTTTTTTTTTAGAAAATTTTTTTTAGTAAGATAGATTTTAAAGGGTTTGTTTTTTTTTTTTTTTTTTTTT\n++\n+BBBFFFFFFFFFBBFFFFIIIFIFFIFFIIIIIIIFFFFFB7'0<B0<BBFF'7<0'0<<''0<'0'0<BBB<<B'7'0'0'0<BFFFFFFFFFFFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:4999:3182 1:N:0:CAGATC\n+GTTTTATGAGGATTTTAGGGGAGTGATTGTTTAAAGTTTATAAGATTTATGATTTATATATAGTTAGAATAGTATGTGTTAAATAAATATAAAGGGAGAGG\n++\n+<BBFFFFBFFFFFFIIFBBBFFFIIFFIBFFIFIIBFFIIIIIFFIIIIIBFFIIIIIIIIIBFFIBFIII<FFFBFBFFFFFFFFFFFFFFF<07<7<<7\n+@HISEQ:105:C2UE1ACXX:3:1101:16790:3145 1:N:0:CAGATC\n+TATAGAGGTATTTTGTTATTTTGTTTTAGTTATTGCGGGTTAGAGTAGATGGTTATTTTTAGTAGAGTATTGTTTGTTGTTTTTTATATGTGGTATAGAGG\n++\n+BBBF<BBFFFFFFI<FFFIFIIBBFFIIBFFFFI<BBBFFFF<FFFF7FF70<BFFIFIIF7BFBB<FFBF'BBF'<<0<BFFBBBBBF'<70<<<B####\n+@HISEQ:105:C2UE1ACXX:3:1101:18065:3106 1:N:0:CAGATC\n+AAGTATTTGTTATATATATTTTAAAGTTTTTTTTTTTTTTAGGAATTTTTTTTTATAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTTT\n++\n+BBBFFFFFBFFFFIIIIFIIIIIIIFIFIIIIIIIIIIFF''00<<BB'<<'7''000<BFFF77<77BFF77BFBB07<7<BFFFFFFFF##########\n+@HISEQ:105:C2UE1ACXX:3:1101:2300:3263 1:N:0:TAGATC\n+TTATTTTTAATAAAATTTTTATTATTTAATTTATTAGTTAATATTTAGGAGTTTTATGTTGTGGTAAAATTTTGTTAGAGAGATAGAGAAAGTATTTAGTT\n++\n+BBBFFFFFFFFBFFIIIIIIBIBBFFI0<FFFBFF70B00<'0<FFFBBBBFF''0B0BB000'7BBFFFFII'<BF0<'<''07'70BBF'7BBBFB7<B\n+@HISEQ:105:C2UE1ACXX:3:1101:5605:3427 1:N:0:CAGATC\n+AGATGAGAGGTATAGGATGTGGGGAGTTTTAGTAAGATTTATAGATAAGAAGTGGTTCGGTTATAGGATTTGTTTTAGATTTTTAGATTTTTTTGTGTAGA\n++\n+BBBFBFFFFFFFFFFBFFFFIIIIIIIBFFFBFFIBFFIIIIIFFIIIFFIBF7BFBFBBFFIFF<<FFFFBBFFBF0<BFFFFF7<BFFFFFF0B7BF0<\n+@HISEQ:105:C2UE1ACXX:3:1101:8129:3589 1:N:0:CAGATC\n+TTTTAGTTTTTAGTTAGGATTATACGTTTATTGTGATAAAAGAGTTTTTTGATTTATCGGGTTATGTTAGGGTTTATTGATATTAGGGAATTTGAAGAGAT\n++\n+BBBFFBFFFFFFBFFFBBFIIFIIFBFFFFII<BBFFFIIIBFFIFIIIIBBFFIIII<7<FBFF<FBF<7<BBFFFF7<BFFFF700<BBFF0<B'<07B\n+@HISEQ:105:C2UE1ACXX:3:1101:14304:3866 1:N:0:CAGATC\n+GTGTTTATATAGGGGATTTTTGAGTTTGATAGGTTGTTTTTGTAGAGGGTAGAATTTTGTGGAAATGTTGGTATTGGTTAAGGGGTTTTAGTGAAGAATAA\n++\n+<BBFFFFFFFFFFFFFFFFII<BBFFFBFFIFBFFBFFFII7FFFFFFFIF<BFIIII<F<BBFIFBFB7<BFFFBBBBBF777<B7BBF7B<BB7BBFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12720:4398 1:N:0:CAGATC\n+GTATGTGTGTGTGTGTGTGTATTTAATTGAAGTTGGGTTTGGTGATATATATGTTTAATTTTAGTATTTTAGTGGTAGAGGTAGGTTAATTTTTGTTGAGT\n++\n+<BBFBFFFFFFFFIFIFIFFFFFIIFII0BFBFFB7BFFF<BFFFFIIIIIIBFIIIIFIIII<FIFIIIFBFBBFB7B<<BB7<B<BFFFFFF0<B0<7B\n+@HISEQ:105:C2UE1ACXX:3:1101:14945:4439 1:N:0:CAGATC\n+AGTGTTGAGTGGAGTATTAGAGAAGAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATT\n++\n+BBBBFFBFFFFFFFFFFIIBIFFIFFBFFIIIIBFFIIIIIIBFFIIIBFFBFFFIIIFBFFBFBFFIIIIIFFFBBF77BBFFF7BBFF<BBF<<BFFFB\n+@HISEQ:105:C2UE1ACXX:3:1101:8616:4508 1:N:0:CAGATC\n+AGA"..b"0<BFFBFFFBF7FBFIIFIF7BFFI7<7B<BBFB'<BF'7BBFF7BBBBBBB#######\n+@HISEQ:105:C2UE1ACXX:3:1101:7272:22581 1:N:0:CAGATC\n+TTAATGATATTAAGAATTTTTTAAAGAATTTTATTTTTTTTAGGAATAGAAGGAGGAGGAGTATTTTGATCGATTTTTTAGGTTTTTTATAGGTGGAGTTA\n++\n+BBBFFBFFFFFFF<BFIIIIIIFIIBFFFFIIFIIIIIIIII<<FFFIBFIBBFFBFFFFFFBBFFF<BBF<BBFFFFFF00<BBFFFFFF000<777B<B\n+@HISEQ:105:C2UE1ACXX:3:1101:10060:23020 1:N:0:CAGATC\n+TTTTAGATTATTTAAGAAGGTATTAGGTTTTTAAGAGGAAAGGGTAGTCTTATAGTTTTGAGTATTTTTTTTAAAAGGAAGTAAGGATGGTGTTTTTATTT\n++\n+BBBFFBFFFFFFFIIBFIFFFFFIBBBFFFFIIIBFFFIFIBFFIFFFFIIFFFBFFII7B<FFFIIIIIFFFFBB77<B<BBF<7BB<<BBBBBFFFFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:14440:23104 1:N:0:CAGATC\n+TTTAAATTTAAGTTAAGGTTTGGGGAGTTGATTTTTGTTTTGTGGGTTGTTTTTTTTGTAGGAGTTGGTTTTTAGAGGTTTTTAGGAATTTTTGGTGTTTT\n++\n+BBBFFFFFFFFFFFIIBBIFIBBBFFFFFBFFIIIIBFFIIBFBFFFFFFIIIIFFF7BB<<BBFB<BBBBFFB7<00B<BBFF00<BBFFFF''77BBBF\n+@HISEQ:105:C2UE1ACXX:3:1101:6941:23338 1:N:0:CAGATC\n+AGAAAGGTTTTAAGTTGGTTGGGAATATAGGGGTTTTTTAGAGTTTTTATTAGGAGTTATAGTGTGTTGAATTTGGTTTTGGGTGTTGATTATAGGTTGTT\n++\n+BBBFFFFFFFFFFBFFBBFFBBBFFFFIIBFFFIFFIIIIBFFFFFIIIIIIB<FFFFFFFBFBFFFF<BBFFF<<BBBB700<BBB0BBFFFF00<B7<B\n+@HISEQ:105:C2UE1ACXX:3:1101:10069:23622 1:N:0:CAGATC\n+TTTTGTTTTAGGGTTTTATTTTTGTGTTTTATTTTTATTTTCGTATTATTAGTTTTTTTTATACGTTATTTGTAGAAGGTTAGTTTTTTTAATTTAGGTTT\n++\n+BBBFBFFFFFBBBFFFIFIIIIIBFBFFIIBFIIIIIIIIIIBFFFIIIIIFFIIIIIIFFFFF<BFFFFF<BF<<B77BBB7BBFFFFFFFFFFF00<BB\n+@HISEQ:105:C2UE1ACXX:3:1101:14079:24078 1:N:0:CAGATC\n+TTTAAAGTTTTTAGTTTTGAGTGGAATTTTAAGAATATTAGTGCGTTTTAAGCTTAGGTAGTTTTGGTAGTTTGAAAGTAATAGGGTGTATTTTGTAAAGT\n++\n+BBBFFFFFFFFFFBFFFI<BBFFFFFFIIIIIBFFFIIIIBFFFFFFIIIIBFFIIBBFFFFFFI<7BFBFFF<BBF<BBFFF<07BBBBBFFF<BFFF<B\n+@HISEQ:105:C2UE1ACXX:3:1101:12064:24631 1:N:0:CCGATC\n+TTATAGTGTATTTATATATATGAAATGAATTAATGAATTTTAAAAAAAAAGAAAGTAAGTTGTTTTTAGGATTGATATTTAGAGTTAATTTTTTGAGTTTT\n++\n+BBBFFBFFFFFFFIIIIIIIIBFIFF0BFIIIIIBFFIIIIIIIIIIIIIBFIIFFFIBFFBFFFFFFB<BFF7BBFFFFF<B<BBBFFFFFFF'70<<BF\n+@HISEQ:105:C2UE1ACXX:3:1101:6662:24968 1:N:0:CAGATC\n+AGGTGTCGTTTAATTGTTTAGGTTTATGGTATTGTGTTTCGTTTTTTTGGTATTTGTGAGGGTAGAATTGTTTTTGGGTTTTAATTTTTTTAAGTATGGGA\n++\n+BBBFFFFFFFFFFIIBFFIFBBFFFFIB<FFFI<FBFFFFBFFIIIII77BFFIIBFBFBBBFBBFFFF<BBFFF'07BBBBFFFFFFFFFFB0<BF####\n+@HISEQ:105:C2UE1ACXX:3:1101:11630:24964 1:N:0:TAGATC\n+TTAGTTTTTTTAGTGTTTTTTATTTATTTCGTTTTATTATTGGAGTTTGTTAAGAAAATTAGGGTTTGATTTGGATGTTAAGGATTGGTTTTTTTTTTGAT\n++\n+BBBBFFFFFFFFBFFFFIIIIIIIIIIIIIBFFFIFIIIIIB7BFFFFBFFIIBFIIIIIFB<BFBFBFFFF<7BB<BBFF<7<BB77BBFFFFFFFF0<B\n+@HISEQ:105:C2UE1ACXX:3:1101:12594:24878 1:N:0:CCGATC\n+TTTAATAGGATATGATATTATTTAATTTATAGATTATGGAAATTTTTTATATTTAATGAAGAAAGTTGGAATGTTTTGGGAGGTGTTTAGAATAAATAAAT\n++\n+BBBFFFFB0BFFF<FFIIIFIIFIIIFIFIF<BFFFF<<BFFFIIIIIIIIIIIIIIBFFBFFIBFB7'<FF<<BBF0''77<BFB<BB0<BBBBBFFBBF\n+@HISEQ:105:C2UE1ACXX:3:1101:4483:25030 1:N:0:CAGATC\n+AGGATGGTGTTTTTATTTTTAGATTTATATTATTTTGTTATATTTGTATTTGAGTAAGTTTATGGGTTTTTTAAAGAGGTAGGAGGAAGTTTTTTGTTATT\n++\n+B<BFFFFFFFFFFIIIIIIIIBBFIIFIIIIFIIII<BFFIFFIIBFIIII<BBFFIFIFIIIB7<FFFIIIFBF<<77BB00<70<B7BBBFFF0BBFFF\n+@HISEQ:105:C2UE1ACXX:3:1101:12198:25235 1:N:0:CAGATC\n+ATATATGTAGTTTGTATTATTTTTGTTATAGTATATAAAGGTTAAAGAGTAGTTGTTTTAATTTTAGAGGTGGAGATTGGGTTGTATAGTTTTGGTTTTTA\n++\n+BBBFFFBFFFFFFBFFIIFIIIII0BF<FF0BFFFIFFIBBFBFII<FBFBBFF7FFFIIIIIIII<F7<B'<BB7<B''0<<0<BBB77<BB'0<<BBFB\n+@HISEQ:105:C2UE1ACXX:3:1101:20477:25084 1:N:0:CATATC\n+AGAGTTTATTGAGAAGTAAAGTATTAATTTTATGGGAGAAATGGGATAGAGGTAGTAGAAGTTGTTATGGAATGGGATTAATTAGGAAGTTAATTAAGTGT\n++\n+BBBFFFFFFF0BBFFBFFIIFFIIIIIIIIIFIBB7FFFFIIFFBFFIFIBFFFFIIFIIFFFBFFFF77BFF<<B<FFFFFFF70<B7BBFFFFFF7B<B\n+@HISEQ:105:C2UE1ACXX:3:1101:5725:25359 1:N:0:CAGATC\n+GAGAAATAAGATAATAAAGTAATAGTTGTGATTAGGAGGTTTTTTATAAGTTGATGGTTTATGTTAAGTAAGTTTATTAAGAAGTATAGTATTATATATAG\n++\n+BBBFFFFFFBFFFIIIIIIIIIIIBIFBFFFFIIBBFFFFFFFIIIIIIFFFBFFBBFFFIIBFFIIBFIIFIFIFFFFF<BF<BBFF7<<FFFFFFFFF0\n+@HISEQ:105:C2UE1ACXX:3:1101:5502:25591 1:N:0:CAGATC\n+ATATGATTTTATTTTTAGGGATAATATTTTTTAAGTGAATTTTGATTTTTTGGTTAGTTATTTTGATGATGTGTAGAGGGTGTATAGTTTTTGGATATAGA\n++\n+BBBFBFFFFFFFFIIIIBBBFFFIIIIIIIIIIIBFFFIIIIIBFFIIIII<7BFFBFFFIIII<FF<FFBFFFFFB<<<BFBBBF<<BFFF00<BFBF7<\n" |
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| b'@@ -0,0 +1,368 @@\n+<tool id="umi_tools_group" name="UMI-tools group" version="@VERSION@.0">\n+ <description>Extract UMI from fastq files</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ <requirement type="package" version="1.5">samtools</requirement>\n+ </expand>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $input.is_of_type("sam"):\n+ #set $input_file = $input\n+ #else:\n+ ln -sf \'${input}\' \'input.bam\' &&\n+ ln -sf \'$input.metadata.bam_index\' \'input.bam.bai\' &&\n+ #set $input_file = \'input.bam\'\n+ #end if\n+\n+ umi_tools group --extract-umi-method $extract_umi_method\n+ #if str($extract_umi_method) != \'read_id\':\n+ --umi-separator \'$umi_separator\' --umi-tag $umi_tag\n+ #end if\n+ --method $method --edit-distance-threshold $edit_distance_threshold\n+ $paired $spliced_is_unique --soft-clip-threshold $soft_clip_threshold\n+ $read_length $whole_contig --subset $subset $per_contig $per_gene\n+ #if $gene_transcript_map:\n+ --gene-transcript-map \'$gene_transcript_map\'\n+ #end if\n+ #if len(str($gene_tag)) > 0:\n+ --gene-tag \'$gene_tag\'\n+ #end if\n+ #if $group_output:\n+ --group-out \'$group_out\'\n+ #end if\n+ #if $input.is_of_type("sam"):\n+ --in-sam\n+ #end if\n+ --output-bam\n+ -I \'$input_file\' -S grouped.bam &&\n+ samtools sort grouped.bam -@ \\${GALAXY_SLOTS:-1} -o \'$output\' -O BAM\n+ ]]></command>\n+ <inputs>\n+ <param name="input" type="data" format="sam,bam" label="Reads to group in SAM or BAM format" />\n+ <param name="extract_umi_method" argument="--extract-umi-method" type="select">\n+ <option value="read_id" selected="True">Read ID</option>\n+ <option value="tag">Tag</option>\n+ </param>\n+ <param name="group_output" argument="--group-out" type="boolean" truevalue="--group-out" falsevalue="" label="Output a flatfile describing the read groups" />\n+ <param name="umi_separator" argument="--umi-separator" type="text" label="Separator between read id and UMI." help="Ignored unless extracting by tag" />\n+ <param name="umi_tag" argument="--umi-tag" type="text" label="Tag which contains UMI." />\n+ <param argument="--method" type="select" label="Method used to identify PCR duplicates within reads." help="All methods start by identifying the reads with the same mapping position">\n+ <option value="unique">Reads group share the exact same UMI</option>\n+ <option value="cluster">Identify clusters based on hamming distance</option>\n+ <option value="directional">Identify clusters based on distance and counts</option>\n+ </param>\n+ <param name="edit_distance_threshold" argument="--edit-distance-threshold" type="integer" value="1" label="Edit distance threshold" help="For the adjacency and cluster methods the threshold for the edit distance to connect two UMIs in the network can be increased. The default value of 1 works best unless the UMI is very long (>14bp)" />\n+ <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" label="BAM is paired end" help="This will also force the use of the template length to determine reads with the same mapping coordinates." />\n+ <param name="spliced_is_unique" argument="--spliced-is-unique" type="boolean" truevalue="--spliced-is-unique" falsevalue="" label="Spliced reads are unique" help="Causes two reads that start in the same position on the same strand and having the same UMI to be considered unique if one is spliced and the other is not. (Uses the \'N\' cigar operation to test for splicing)" />\n+ <param name="soft_clip_threshold" argument="--soft-clip-threshold" type="'..b'cted UMIs (based on edit distance\n+ threshold). Each network is a read group\n+\n+ - "directional"\n+ Identify clusters of connected UMIs (based on edit distance\n+ threshold) and umi A counts >= (2* umi B counts) - 1. Each\n+ network is a read group.\n+\n+--edit-distance-threshold (int)\n+ For the adjacency and cluster methods the threshold for the\n+ edit distance to connect two UMIs in the network can be\n+ increased. The default value of 1 works best unless the UMI is\n+ very long (>14bp)\n+\n+--paired\n+ BAM is paired end - output both read pairs. This will also\n+ force the use of the template length to determine reads with\n+ the same mapping coordinates.\n+\n+--spliced-is-unique\n+ Causes two reads that start in the same position on the same\n+ strand and having the same UMI to be considered unique if one is\n+ spliced and the other is not. (Uses the \'N\' cigar operation to test\n+ for splicing)\n+\n+--soft-clip-threshold (int)\n+ Mappers that soft clip, will sometimes do so rather than mapping a\n+ spliced read if there is only a small overhang over the exon\n+ junction. By setting this option, you can treat reads with at least\n+ this many bases soft-clipped at the 3\' end as spliced.\n+\n+--multimapping-detection-method (string, choice)\n+ If the sam/bam contains tags to identify multimapping reads, you can\n+ specify for use when selecting the best read at a given loci.\n+ Supported tags are "NH", "X0" and "XT". If not specified, the read\n+ with the highest mapping quality will be selected\n+\n+--read-length\n+ Use the read length as as a criteria when deduping, for e.g sRNA-Seq\n+\n+--whole-contig\n+ Consider all alignments to a single contig together. This is useful if\n+ you have aligned to a transcriptome multi-fasta\n+\n+--subset (float, [0-1])\n+ Only consider a fraction of the reads, chosen at random. This is useful\n+ for doing saturation analyses.\n+\n+--chrom\n+ Only consider a single chromosome. This is useful for debugging purposes\n+\n+--per-contig (string)\n+ Deduplicate per contig (field 3 in BAM; RNAME).\n+ All reads with the same contig will be\n+ considered to have the same alignment position. This is useful\n+ if your library prep generates PCR duplicates with non identical\n+ alignment positions such as CEL-Seq. In this case, you would\n+ align to a reference transcriptome with one transcript per gene\n+\n+--per-gene (string)\n+ Deduplicate per gene. As above except with this option you can\n+ align to a reference transcriptome with more than one transcript\n+ per gene. You need to also provide --gene-transcript-map option.\n+ This will also add a metacontig (\'MC\') tag to the reads if used\n+ in conjunction with --output-bam\n+\n+--gene-transcript-map (string)\n+ File mapping genes to transripts (tab separated), e.g:\n+\n+ gene1 transcript1\n+ gene1 transcript2\n+ gene2 transcript3\n+\n+--gene-tag (string)\n+ Deduplicate per gene. As per --per-gene except here the gene\n+ information is encoded in the bam read tag specified so you do\n+ not need to supply --gene-transcript-map\n+\n+--group-out (string, filename)\n+ Output a flatfile describing the read groups\n+\n+--output-bam (string, filename)\n+ Output a tagged bam file to stdout or -S <filename>\n+\n+-i, --in-sam/-o, --out-sam\n+ By default, inputs are assumed to be in BAM format and output are output\n+ in BAM format. Use these options to specify the use of SAM format for\n+ inputs or outputs.\n+\n+-I (string, filename) input file name\n+ The input file must be sorted and indexed.\n+\n+-S (string, filename) output file name\n+\n+-L (string, filename) log file name\n+\n+Usage\n+-----\n+ umi_tools group -I infile.bam --output-bam -S grouped.bam -L group.log --\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |