| Previous changeset 8:914533f3507e (2025-06-27) Next changeset 10:41faa653d86c (2025-08-13) |
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Commit message:
planemo upload for repository https://github.com/open2c/pairtools commit 365c6f6387b2f90af22a62e673873b90e7f7394a |
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added:
test-data/output_parsed_pairs_sam_mapq.pairs |
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| diff -r 914533f3507e -r 608ea80cccba test-data/output_parsed_pairs_sam_mapq.pairs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_parsed_pairs_sam_mapq.pairs Fri Jul 25 13:54:54 2025 +0000 |
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| b'@@ -0,0 +1,600 @@\n+## pairs format v1.0.0\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: Test_seq 450060\n+#samheader: @SQ\tSN:Test_seq\tLN:450060\n+#samheader: @PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SP -T0 -t 8 test test_hic_reads_1.fq test_hic_reads_2.fq\n+#samheader: @PG\tID:pairtools_parse\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpu2wbua_3/files/c/8/8/dataset_c88eeb08-5a4e-41bc-84ac-fe34bb7e42f9.dat -c /tmp/tmpu2wbua_3/files/2/8/b/dataset_28bb6843-f06e-45f9-b608-6c75c7408162.dat -o /tmp/tmpu2wbua_3/job_working_directory/000/31/outputs/dataset_0a810c2e-9b60-4852-b164-7a4b14ffcdac.dat --min-mapq 1 --max-molecule-size 750 --add-columns mapq,seq --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-mem2\tVN:1.1.3\n+#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 mapq1 mapq2 seq1 seq2\n+A00126:224:H7HMWDSX3:3:1101:4779:3098\tTest_seq\t166211\tTest_seq\t214901\t-\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19113\x19Test_seq\x19166134\x1943\x1978M\x19=\x19214824\x1948691\x19GGGCACCAACTAGTTCTTCTGGTCTCAGGATAATGTAGGTCTCTGGTTCATGTGGCCCTTTCTGTCTCTTGGGTTCTT\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:78\x19MC:Z:78M\x19AS:i:78\x19XS:i:63\x19XA:Z:Test_seq,+214829,5S73M,2;\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19177\x19Test_seq\x19214824\x195\x1978M\x19=\x19166134\x19-48691\x19AAGAGCCCAAGAGACAGAAAGGGCCACATGAACCACAGACCTACATCATCCTGAGACCAGAAGAACTAGTTGGTGCCC\x19FFFF,FFFFFFFFFFFFF,FFFFFFFFFFFF:FF:,FFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF\x19NM:i:3\x19MD:Z:1T33G33A8\x19MC:Z:78M\x19AS:i:66\x19XS:i:63\x19XA:Z:Test_seq,+166134,78M,3;\x19Yt:Z:UU\t43\t5\tGGGCACCAACTAGTTCTTCTGGTCTCAGGATAATGTAGGTCTCTGGTTCATGTGGCCCTTTCTGTCTCTTGGGTTCTT\tAAGAGCCCAAGAGACAGAAAGGGCCACATGAACCACAGACCTACATCATCCTGAGACCAGAAGAACTAGTTGGTGCCC\n+A00126:224:H7HMWDSX3:3:1101:2908:3239\tTest_seq\t167331\tTest_seq\t167696\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x19161\x19Test_seq\x19167331\x1923\x19151M\x19=\x19167546\x19366\x19TGAGATGTCATAGCTGAATATTCTTTCCCAGTCTGTAGGTGGTCTTTTTACTCTTTTGGTGAAGTCTTTAGATGAGCATAGGTGTTTGATTTTTAGGAGCTCCCAGTTATCTGGTTTCTCTTCATCATTTTTGGTAATGTTTTGTATTCTG\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFF:FFFFF:FFFF:FFFFFFFFFFFFFFF:FF,,FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF:FFFFFFFF:FF,FF\x19NM:i:1\x19MD:Z:37A113\x19MC:Z:151M\x19AS:i:146\x19XS:i:135\x19XA:Z:Test_seq,-213553,151M,4;\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x1981\x19Test_seq\x19167546\x1944\x19151M\x19=\x19167331\x19-366\x19TAGTCTTTATGTTTAGGTCTTTGATCCACTTGGAGTTAGTTTTTGTGCATGGTGTGAGGTATGGGTCCTGTTTCATTCTTTTACAAATGGATATCCAGGTATGCCAGCACCATTTGTTAAAAAGACTATTATTTCCCCAATTGACTGACAC\x19FF,F,F:FFFFFFFFF,FFF:FFFFFF:FFFF:FFFFFFFFFFF:FF::F,FFFFFFFFF:,F,FFF:FFFFFFFFFFFFFFFFFFFFF:FF:FFF::FFFFFFFFFFFFF,FFFFFFF:FF:F,:FFFFFFFFFF,F,F:FFFFFFFFFF\x19NM:i:3\x19MD:Z:82G15T30C21\x19MC:Z:151M\x19AS:i:136\x19XS:i:114\x19XA:Z:Test_seq,+213342,118M2I23M2I6M,8;\x19Yt:Z:UU\t23\t44\tTGAGATGTCATAGCTGAATATTCTTTCCCAGTCTGTAGGTGGTCTTTTTACTCTTTTGGTGAAGTCTTTAGATGAGCATAGGTGTTTGATTTTTAGGAGCTCCCAGTTATCTGGTTTCTCTTCATCATTTTTGGTAATGTTTTGTATTCTG\tTAGTCTTTATGTTTAGGTCTTTGATCCACTTGGAGTTAGTTTTTGTGCATGGTGTGAGGTATGGGTCCTGTTTCATTCTTTTACAAATGGATATCCAGGTATGCCAGCACCATTTGTTAAAAAGACTATTATTTCCCCAATTGACTGACAC\n+A00126:224:H7HMWDSX3:3:1101:27208:4492\tTest_seq\t194620\tTest_seq\t194909\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x1997\x19Test_seq\x19194620\x1960\x19151M\x19=\x19194778\x19290\x19GCTGTGCAAACCACTGCTCCAGGCTATCTCAGCACTGAGCCAGAGACAAGGGCCAGTTCAGTCACCTGGAAAATCAGGCCAGCATCTCTGAAAAATAGGTGCCTCAGTGTTCACAGAAAAGGGCCATGTATTGAAGTAGGTCAGAGGAAGA\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:F,FF:::FFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:151\x19MC:Z:132M19S\x19AS:i:151\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x19145\x19Test_seq\x19194778\x1960\x19132M19S\x19=\x19194620\x19-290\x19CACTCACCAGATTCAGCCCAGGACCAGAGGCTGCCGAGGGCAGGTGTGGGACGAAGTCAAGATGAAGTCAGTTCATTGTGTGGTTTTCGGTACCAGGCTAGACCTAGATTTGAACCCCAAGTCTGCTACTTAGATCATTCATTCAATGTGT\x19FFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF'..b'296\x19145\x19Test_seq\x19169582\x1960\x19151M\x19=\x19169295\x19-438\x19GCTTTTGCTGTGTCCCAGAGGTTTTGATAGGAAGTATTTTCATTCTCGTTGCTTTCTATGAATTTCCTTATTCCCTCCTTGATGTCTTCTATAACCCAGTCTTTTTTCAGGAGGGTATTGTTCATTTTCCAAGTATTTGATTTCTTTTCCC\x19:FFF:FFFFFFFFF,:FFF,FFFFF:FFFFFFF:FFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:\x19NM:i:3\x19MD:Z:46T11A22G69\x19MC:Z:151M\x19AS:i:136\x19XS:i:22\x19Yt:Z:UU\t60\t60\tGTTTCCTTTCCTGTATTTCTTTAGTCAGTCTAGCCAATGGTTTATCAATTTTGTTAATTTTTTCAAAGAACCAGCTTTTGGCTTTGTTAATTCTTTCAATTGTTTTTCTGTTCTCTAATTCATTTAGTTCAGCTCTAATTTTTATTATTTG\tGCTTTTGCTGTGTCCCAGAGGTTTTGATAGGAAGTATTTTCATTCTCGTTGCTTTCTATGAATTTCCTTATTCCCTCCTTGATGTCTTCTATAACCCAGTCTTTTTTCAGGAGGGTATTGTTCATTTTCCAAGTATTTGATTTCTTTTCCC\n+A00126:224:H7HMWDSX3:3:1116:5186:8719\t!\t0\tTest_seq\t169344\t-\t+\tNR\tA00126:224:H7HMWDSX3:3:1116:5186:8719\x1981\x19Test_seq\x19169618\x1960\x19129M22S\x19=\x19169344\x19-403\x19TTTTCATTCTCGTTGCTTTCTATGAATTTCCTTATTCCCTCCTTGATGTCTTCTATAACCCAGTCTTTTTTCAGGAGGGTATTGTTCATTTTCCAAGTATTTGATTTCTTTTCCCTCGTTCTTCTGTTATTGATCGATCTGTCATACTCTG\x19F:FFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFF:FFF:FFFFFFFFFFF\x19NM:i:5\x19MD:Z:10T11A22G70A3T8\x19MC:Z:151M\x19AS:i:104\x19XS:i:0\x19Yt:Z:NR\tA00126:224:H7HMWDSX3:3:1116:5186:8719\x19161\x19Test_seq\x19169344\x1960\x19151M\x19=\x19169618\x19403\x19TTTGTTAATTTTTTCAAAGAACCAGCTTTTGGCTTTGTTAATTCTTTCAATTGTTTTTCTGTTCTCTAATTCATTTAGTTCAGCTCTAATTTTTATTATTTGTTTTCTTCTGGTGCCTGATGGATTCTTTTGTTGCTCACTTTCTATTTGT\x19FFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFF,FFFFF:FFFF:FFFF,FF:FFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFF,FFFFFFFF,FFF:FFFFFF,FFFFFFFFFFFFF:FFFFFFF,FFFF,F:FFFFF,FFFF,F:F,\x19NM:i:1\x19MD:Z:123G27\x19MC:Z:129M22S\x19AS:i:146\x19XS:i:101\x19Yt:Z:NR\t0\t60\t\tTTTGTTAATTTTTTCAAAGAACCAGCTTTTGGCTTTGTTAATTCTTTCAATTGTTTTTCTGTTCTCTAATTCATTTAGTTCAGCTCTAATTTTTATTATTTGTTTTCTTCTGGTGCCTGATGGATTCTTTTGTTGCTCACTTTCTATTTGT\n+A00126:224:H7HMWDSX3:3:1116:11080:9690\tTest_seq\t171531\tTest_seq\t171917\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:11080:9690\x1997\x19Test_seq\x19171531\x1960\x19151M\x19=\x19171767\x19387\x19TTCCCTGGTCCTCCAGAAGTCCTAGTCTACATTCTAATTGCTCGAGTCTGCTCCTCTGACTTTCTATTGTGTTGTCAAATTCTATAATTTTATTGTTAATCTTTTGGATTTCTACATGCTGTCTCTCTATGTATTCTTGCAACTTATTAAT\x19FFFFFFF:F,FFFFFFFFFF::FFFFFFFFFF:FFFFFFF:FF:F:F,FFFFFFFF:F:::,FFFF:FFFFFFFFFFF,FF:FFF:F,:FFFFFFF:,FFFFFFF::FFF:FF:F,:F,,F:::F,:FFFFF,FF,FFF,,F,:FFFFF:F\x19NM:i:6\x19MD:Z:22C29T16C6T6G47G19\x19MC:Z:151M\x19AS:i:121\x19XS:i:53\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:11080:9690\x19145\x19Test_seq\x19171767\x1960\x19151M\x19=\x19171531\x19-387\x19ATTTCATTTGTGATATCTTTAAGCATTCTGTAAATTAGTTTTTTATATTCTGTATCTGATAATTCCAGGATTGTATCTTCATTTGGGAAAGATTTTGATTCTTTTGTTTGGGGGGTTGGAGAAGCTGTCATGGTCTGTTTCTTTATGTGGT\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF,F:FFFFF::FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:151\x19MC:Z:151M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UU\t60\t60\tTTCCCTGGTCCTCCAGAAGTCCTAGTCTACATTCTAATTGCTCGAGTCTGCTCCTCTGACTTTCTATTGTGTTGTCAAATTCTATAATTTTATTGTTAATCTTTTGGATTTCTACATGCTGTCTCTCTATGTATTCTTGCAACTTATTAAT\tATTTCATTTGTGATATCTTTAAGCATTCTGTAAATTAGTTTTTTATATTCTGTATCTGATAATTCCAGGATTGTATCTTCATTTGGGAAAGATTTTGATTCTTTTGTTTGGGGGGTTGGAGAAGCTGTCATGGTCTGTTTCTTTATGTGGT\n+A00126:224:H7HMWDSX3:3:1116:31367:10222\tTest_seq\t168346\tTest_seq\t168601\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:31367:10222\x1997\x19Test_seq\x19168346\x1960\x19130M\x19=\x19168472\x19256\x19ATCATGTCATCTGCAAATAGTGATAGCTTTACTTTGTCCTTACCAATCTGGATACCCTTTATTTTTTTGTCTAGCCTAATTGCCCTGGCTAGGACTTCAAGTACGATGTTGAATAAGAGTGGTGATAAAG\x19*\x19NM:i:7\x19MD:Z:0G18A14C0C5G22C54C10\x19MC:Z:130M\x19AS:i:99\x19XS:i:40\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:31367:10222\x19145\x19Test_seq\x19168472\x1960\x19130M\x19=\x19168346\x19-256\x19AAAGGGCATCCTTGTCTGGTTCCTGTTCTCAAGGGAAATGCTTTCAGGTTCTCTCCATTTAGAGTGATATTGGCTGTTGGCTTTGCATAGATGCCCTTTATTATGTTGAGGAATTTTCCTTCAATTCCTA\x19*\x19NM:i:0\x19MD:Z:130\x19MC:Z:130M\x19AS:i:130\x19XS:i:75\x19Yt:Z:UU\t60\t60\tATCATGTCATCTGCAAATAGTGATAGCTTTACTTTGTCCTTACCAATCTGGATACCCTTTATTTTTTTGTCTAGCCTAATTGCCCTGGCTAGGACTTCAAGTACGATGTTGAATAAGAGTGGTGATAAAG\tAAAGGGCATCCTTGTCTGGTTCCTGTTCTCAAGGGAAATGCTTTCAGGTTCTCTCCATTTAGAGTGATATTGGCTGTTGGCTTTGCATAGATGCCCTTTATTATGTTGAGGAATTTTCCTTCAATTCCTA\n' 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