| Previous changeset 0:f8c1d2a93d43 (2024-04-04) Next changeset 2:ae537f4d4b93 (2024-04-05) |
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Commit message:
planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428 |
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added:
test-data/output_pairs_split.bam test-data/output_pairs_split.pairs |
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| diff -r f8c1d2a93d43 -r ccc7a8e707fb test-data/output_pairs_split.bam |
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| Binary file test-data/output_pairs_split.bam has changed |
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| diff -r f8c1d2a93d43 -r ccc7a8e707fb test-data/output_pairs_split.pairs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_pairs_split.pairs Fri Apr 05 10:29:49 2024 +0000 |
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| b'@@ -0,0 +1,842 @@\n+## pairs format v1.0.0\n+#sorted: chr1-chr2-pos1-pos2\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: chrI 230218\n+#chromsize: chrII 813184\n+#chromsize: chrIII 316620\n+#chromsize: chrIV 1531933\n+#chromsize: chrV 576874\n+#chromsize: chrVI 270161\n+#chromsize: chrVII 1090940\n+#chromsize: chrVIII 562643\n+#chromsize: chrIX 439888\n+#chromsize: chrX 745751\n+#chromsize: chrXI 666816\n+#chromsize: chrXII 1078177\n+#chromsize: chrXIII 924431\n+#chromsize: chrXIV 784333\n+#chromsize: chrXV 1091291\n+#chromsize: chrXVI 948066\n+#chromsize: chrM 85779\n+#samheader: @SQ\tSN:chrI\tLN:230218\n+#samheader: @SQ\tSN:chrII\tLN:813184\n+#samheader: @SQ\tSN:chrIII\tLN:316620\n+#samheader: @SQ\tSN:chrIV\tLN:1531933\n+#samheader: @SQ\tSN:chrIX\tLN:439888\n+#samheader: @SQ\tSN:chrM\tLN:85779\n+#samheader: @SQ\tSN:chrV\tLN:576874\n+#samheader: @SQ\tSN:chrVI\tLN:270161\n+#samheader: @SQ\tSN:chrVII\tLN:1090940\n+#samheader: @SQ\tSN:chrVIII\tLN:562643\n+#samheader: @SQ\tSN:chrX\tLN:745751\n+#samheader: @SQ\tSN:chrXI\tLN:666816\n+#samheader: @SQ\tSN:chrXII\tLN:1078177\n+#samheader: @SQ\tSN:chrXIII\tLN:924431\n+#samheader: @SQ\tSN:chrXIV\tLN:784333\n+#samheader: @SQ\tSN:chrXV\tLN:1091291\n+#samheader: @SQ\tSN:chrXVI\tLN:948066\n+#samheader: @PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz\n+#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam\tPP:bwa\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_sort-1.3\tPN:pairtools_sort\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs\tPP:pairtools_parse-1.2\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_dedup-1.4\tPN:pairtools_dedup\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-1.3\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_split-1.5\tPN:pairtools_split\tCL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-1.4\tVN:1.0.3\n+#samheader: @PG\tID:bwa-2CCE5976\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz\n+#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam\tPP:bwa-2CCE5976\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_sort-2.3\tPN:pairtools_sort\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs\tPP:pairtools_parse-2.2\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_dedup-2.4\tPN:pairtools_dedup\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-2.3\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_split-2.5\tPN:pairtools_split\tCL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-2.4\tVN:1.0.3\n+#samheader: @PG\tID:bwa-3CAFD9D9\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t '..b'hrXV\t878521\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:1856:3441\tchrXV\t911038\tchrXV\t912032\t+\t+\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1303:13504\tchrXV\t993225\tchrXV\t993464\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2162:12904\tchrXV\t993668\tchrXV\t993913\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:3013:3559\tchrXV\t995564\tchrXV\t1007197\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1944:12951\tchrXV\t998266\tchrXV\t1025065\t-\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1054:10660\tchrXV\t1006970\tchrXV\t1021642\t+\t+\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:19214:20422\tchrXV\t1012747\tchrXV\t1012994\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2421:3498\tchrXV\t1022592\tchrXV\t1022873\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1605:1769\tchrXV\t1032820\tchrXV\t1044962\t+\t+\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2344:18010\tchrXV\t1033494\tchrXV\t1041844\t+\t+\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2065:11779\tchrXV\t1043247\tchrXV\t1043503\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2162:14141\tchrXV\t407657\tchrXVI\t478758\t+\t+\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:15465:15952\tchrXV\t498518\tchrXVI\t364246\t+\t+\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2501:13913\tchrXV\t661271\tchrXVI\t491366\t-\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1811:9158\tchrXVI\t24355\tchrXVI\t24676\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2839:11156\tchrXVI\t51781\tchrXVI\t52065\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2110:21103\tchrXVI\t72287\tchrXVI\t72545\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2924:20591\tchrXVI\t108500\tchrXVI\t108737\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1844:11781\tchrXVI\t183393\tchrXVI\t183636\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1957:18550\tchrXVI\t183633\tchrXVI\t183921\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1966:13353\tchrXVI\t184850\tchrXVI\t185196\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:17669:27108\tchrXVI\t207984\tchrXVI\t222897\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:4004:12762\tchrXVI\t245084\tchrXVI\t245310\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:2801:3590\tchrXVI\t247841\tchrXVI\t248082\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:17157:9354\tchrXVI\t304602\tchrXVI\t309538\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2808:2937\tchrXVI\t308188\tchrXVI\t308416\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2263:12823\tchrXVI\t359050\tchrXVI\t359290\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:9894:27112\tchrXVI\t378353\tchrXVI\t378357\t+\t+\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1421:10190\tchrXVI\t394228\tchrXVI\t404268\t+\t+\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:15897:13614\tchrXVI\t416774\tchrXVI\t486947\t-\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2448:1677\tchrXVI\t453877\tchrXVI\t454144\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:10904:6070\tchrXVI\t464358\tchrXVI\t464618\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2898:6464\tchrXVI\t468451\tchrXVI\t607976\t-\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:20458:10815\tchrXVI\t469101\tchrXVI\t469361\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2737:7629\tchrXVI\t474805\tchrXVI\t475117\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2636:20802\tchrXVI\t475619\tchrXVI\t475870\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:19701:9203\tchrXVI\t506448\tchrXVI\t531470\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2789:3854\tchrXVI\t548088\tchrXVI\t548271\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:16977:3934\tchrXVI\t573767\tchrXVI\t616893\t-\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1105:17417\tchrXVI\t607678\tchrXVI\t672047\t+\t+\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2993:3814\tchrXVI\t610391\tchrXVI\t610663\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2709:14957\tchrXVI\t661889\tchrXVI\t664055\t-\t+\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1552:8158\tchrXVI\t663679\tchrXVI\t664015\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2340:18193\tchrXVI\t686023\tchrXVI\t697929\t+\t+\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2537:20994\tchrXVI\t709507\tchrXVI\t709753\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1508:20322\tchrXVI\t714432\tchrXVI\t721584\t-\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2251:19688\tchrXVI\t716030\tchrXVI\t716273\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:2051:4191\tchrXVI\t716323\tchrXVI\t751869\t-\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1430:3252\tchrXVI\t717154\tchrXVI\t718860\t-\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1270:7373\tchrXVI\t730548\tchrXVI\t730761\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:18943:15526\tchrXVI\t752962\tchrXVI\t753241\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:16774:5417\tchrXVI\t813494\tchrXVI\t813775\t+\t-\tUU\n+HWUSI-EAS1533_0033_FC:1:1:1716:21250\tchrXVI\t862498\tchrXVI\t873542\t+\t-\tUU\n+HWI-ST560:29:B0A7LABXX:2:1101:19165:17229\tchrXVI\t896753\tchrXVI\t897069\t+\t-\tUU\n' 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