| Next changeset 1:c0691d1977dd (2018-02-25) |
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Commit message:
planemo upload commit eea727c3bdfe36d9d16036d5ab79fb8b27c4e82e |
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added:
macros.xml test-data/dedup_out1.bam test-data/dedup_out2.bam test-data/dedup_out3.bam test-data/dedup_out4.bam test-data/dedup_out5.bam test-data/dedup_out6.bam 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_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_dedup.xml |
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| diff -r 000000000000 -r a6477bafd522 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jan 10 19:09:42 2018 -0500 |
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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@">0.5.3</token> +</macros> |
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| diff -r 000000000000 -r a6477bafd522 test-data/dedup_out1.bam |
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| Binary file test-data/dedup_out1.bam has changed |
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| Binary file test-data/dedup_out6.bam has changed |
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| diff -r 000000000000 -r a6477bafd522 test-data/group_in1.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group_in1.sam Wed Jan 10 19:09:42 2018 -0500 |
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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 a6477bafd522 test-data/group_out3.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group_out3.tab Wed Jan 10 19:09:42 2018 -0500 |
| 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 a6477bafd522 test-data/group_out4.bam |
| b |
| Binary file test-data/group_out4.bam has changed |
| b |
| diff -r 000000000000 -r a6477bafd522 test-data/group_out5.bam |
| b |
| Binary file test-data/group_out5.bam has changed |
| b |
| diff -r 000000000000 -r a6477bafd522 test-data/group_out6.bam |
| b |
| Binary file test-data/group_out6.bam has changed |
| b |
| diff -r 000000000000 -r a6477bafd522 test-data/out_R1.fastq.gz |
| b |
| Binary file test-data/out_R1.fastq.gz has changed |
| b |
| diff -r 000000000000 -r a6477bafd522 test-data/out_R2.fastq.gz |
| b |
| Binary file test-data/out_R2.fastq.gz has changed |
| b |
| diff -r 000000000000 -r a6477bafd522 test-data/out_SE.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_SE.fastq Wed Jan 10 19:09:42 2018 -0500 |
| 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 a6477bafd522 test-data/out_paired.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_paired.log Wed Jan 10 19:09:42 2018 -0500 |
| b |
| @@ -0,0 +1,37 @@ +# 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/tmpAvWtMd/files/000/dataset_20.dat +# job started at Wed Jan 3 17:06:39 2018 on tzk-ThinkPad-T450s -- 9eecaab6-9562-4b29-8a2e-ae6c1034a14c +# pid: 22903, system: Linux 4.10.0-42-generic #46~16.04.1-Ubuntu SMP Mon Dec 4 15:57:59 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 +# retain_umi : None +# 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/tmpAvWtMd/files/000/dataset_20.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 +2018-01-03 17:06:39,365 INFO Starting barcode extraction +2018-01-03 17:06:39,377 INFO Input Reads: 100 +2018-01-03 17:06:39,377 INFO Reads output: 100 +# job finished in 0 seconds at Wed Jan 3 17:06:39 2018 -- 0.60 0.05 0.00 0.00 -- 9eecaab6-9562-4b29-8a2e-ae6c1034a14c |
| b |
| diff -r 000000000000 -r a6477bafd522 test-data/out_single.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_single.log Wed Jan 10 19:09:42 2018 -0500 |
| b |
| @@ -0,0 +1,38 @@ +# output generated by extract --bc-pattern=XXXNNN --stdin=/tmp/tmpAvWtMd/files/000/dataset_13.dat --stdout /tmp/tmpAvWtMd/files/000/dataset_14.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/tmp/tmpAvWtMd/files/000/dataset_15.dat +# job started at Wed Jan 3 17:06:20 2018 on tzk-ThinkPad-T450s -- 8897b3b4-c6e2-4ee3-b6c0-71044a63b7e1 +# pid: 22794, system: Linux 4.10.0-42-generic #46~16.04.1-Ubuntu SMP Mon Dec 4 15:57:59 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 +# retain_umi : None +# short_help : None +# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> +# stdin : <_io.TextIOWrapper name='/tmp/tmpAvWtMd/files/000/dataset_13.dat' mode='r' encoding='UTF-8'> +# stdlog : <_io.TextIOWrapper name='/tmp/tmpAvWtMd/files/000/dataset_15.dat' mode='a' encoding='UTF-8'> +# stdout : <_io.TextIOWrapper name='/tmp/tmpAvWtMd/files/000/dataset_14.dat' mode='w' encoding='UTF-8'> +# timeit_file : None +# timeit_header : None +# timeit_name : all +# whitelist : None +2018-01-03 17:06:20,360 INFO Starting barcode extraction +2018-01-03 17:06:20,362 INFO Input Reads: 100 +2018-01-03 17:06:20,362 INFO Reads output: 72 +2018-01-03 17:06:20,362 INFO filtered: umi quality: 28 +# job finished in 0 seconds at Wed Jan 3 17:06:20 2018 -- 0.58 0.06 0.00 0.00 -- 8897b3b4-c6e2-4ee3-b6c0-71044a63b7e1 |
| b |
| diff -r 000000000000 -r a6477bafd522 test-data/t_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t_R1.fastq Wed Jan 10 19:09:42 2018 -0500 |
| 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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| diff -r 000000000000 -r a6477bafd522 umi-tools_dedup.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/umi-tools_dedup.xml Wed Jan 10 19:09:42 2018 -0500 |
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| b'@@ -0,0 +1,292 @@\n+<tool id="umi_tools_dedup" name="UMI-tools deduplicate" 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="1.6">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 dedup\n+ --random-seed 0\n+ --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 $input.is_of_type("sam"):\n+ --in-sam\n+ #end if\n+ -I \'$input_file\' -S deduped.bam &&\n+ samtools sort deduped.bam -@ \\${GALAXY_SLOTS:-1} -o \'$output\' -O BAM\n+ ]]></command>\n+ <inputs>\n+ <param name="input" type="data" format="sam,bam" label="Reads to deduplicate 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="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="percentile">Reads group share the exact same UMI. UMIs with counts less than 1% of the median counts for UMIs at the same position are ignored</option>\n+ <option value="cluster">Identify clusters based on hamming distance</option>\n+ <option value="adjacency">Identify clusters based on hamming distance and resolve networks by using the node counts</option>\n+ <option value="directional">Identify clusters based on distance and counts, restrict network expansion by threshold</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'..b' - "read_id" (default)\n+ UMIs contained at the end of the read separated as\n+ specified with --umi-separator option\n+\n+ - "tag"\n+ UMIs contained in a tag, see --umi-tag option\n+\n+--umi-separator (string)\n+ Separator between read id and UMI. See --extract-umi-method above\n+\n+--umi-tag (string)\n+ Tag which contains UMI. See --extract-umi-method above\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+--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 dedup -I infile.bam -S grouped.bam --\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |