diff --git a/tests/BamReaderTest.cpp b/tests/BamReaderTest.cpp index 2c3a10063..f16e9c1e1 100644 --- a/tests/BamReaderTest.cpp +++ b/tests/BamReaderTest.cpp @@ -84,15 +84,17 @@ TEST_CASE("HtsReaderTest: get_tag", TEST_GROUP) { dorado::HtsReader reader(sam.string(), std::nullopt); while (reader.read()) { - // All records in small.sam have this set to 0. - CHECK(reader.get_tag("rl") == 0); + // All records in small.sam have these set. + CHECK(reader.get_tag("XA") == 42); + CHECK(reader.get_tag("XB") == "test"); // Intentionally bad tag to test that missing tags don't return garbage. CHECK(reader.get_tag("##") == 0); CHECK(reader.get_tag("##") == 0); CHECK(reader.get_tag("##") == ""); // Type mismatch doesn't crash. - CHECK(reader.get_tag("rl") == 0); - CHECK(reader.get_tag("rl") == ""); + CHECK(reader.get_tag("XB") == 0); + CHECK(reader.get_tag("XB") == 0); + CHECK(reader.get_tag("XA") == ""); } } diff --git a/tests/data/bam_reader/small.sam b/tests/data/bam_reader/small.sam index 8a5ab5e96..2e79b5f4c 100644 --- a/tests/data/bam_reader/small.sam +++ b/tests/data/bam_reader/small.sam @@ -2,14 +2,14 @@ @SQ SN:NZ_CP062160.1 LN:5498557 @SQ SN:NZ_CP062161.1 LN:104844 @PG ID:minimap2 PN:minimap2 VN:2.24-r1155-dirty CL:minimap2 -k 19 -w 19 -H -a --MD -o test2.sam /Users/joyjit.daw/references/ecoli-GCF_014825845.1_ASM1482584v1_genomic.fn /Users/joyjit.daw/Downloads/temp.fasta -f25635d3-3b81-4ff2-8510-f28330590801 4 * 0 0 * * 0 0 TGCTCAGATGGGGGAATGAAAACAATACTCGACAGGAACTACAACGCCACAGCGGCGATTGTATCAGAAAGTTGACACTGGAAGATAAACTGGTGGAGAAACCTGTCACGGGGAAGAGCAGAGCTTGACGCGCTTCGCTTGTCCCGGCCTCACGACCCGCGAAAGAGTTTCGCGAACCGTTCACCGTTTTTCAATATGATTCTGTCTGCTTTGGTCATTAAAGCAGACGATAGTGTCCAACTTCCCCGTATATAACGGTACGTGCTCATCGGTAAGAGCTGGCGGTATTGTGTTTATCAGGGGAAGTTTTCAGATACTCACGAAAATGCCTGGCAGTACCGCCGTCTACAATGCCATCGATAATATGTAGGTGTTTTCACCTAATTTTGCCATGATGATAATCCTTATATTACGGTTTGTGAATAGGTCTGCTTGTCAGGGTTTGTGTAACCTTTTAACCTTAGCAATGCGTAACGCGTGTACTTTGCGTTCAATGGTTACGTATTGCTGGGTTAGAGAGGACAAAGGTTTCAACTGCCCCCAGCACCTCTGGTTAATTGGATAGCGACACTTCCTGTATCATTCGGTGGCGGAAAATCAGTGGAATCGCCGAAATGGCTGGCGCGATTAACCATTTTGCGCCTGGCACCTGCTCTATTTTACCGATTTATCAACTGGCCTCGCCTGCGGCGAATTGTTAGTGGAATGATAGCTGAAGAGCTGCAAAGTTCAGG * rl:i:0 pi:Z:aaaaaaaaaa -95e6aa45-efe0-4ed9-b7b9-2f35164f9836 0 NZ_CP062160.1 1012347 60 1S43M1D8M1D11M1D5M1I10M1D2M5D2M1I37M1I102M2D14M2D25M3D90M2D7M1I35M3D8M1D73M1I28M1D9M1D2M1D9M3D5M3D28M1D21M4D62M1D6M1D5M1D52M1D2M1D39M1D45M1I30M2D119M1D2M2D20M2I76M1D12M1D4M1I176M1D22M780S * 0 0 TGTAATCACGCCGTCTGCCAGTAGGATCACTTTGTTGGCGGTTGAGCGGGATAATGCCAATCGTTCTGCTCAATGCTGCCCGGCATCTCAGCAAAGGCCGCGACACGGGTGCTGAGCTGCCACGACATCCGAGGTGGAGTAGTCTGTTTCAATAGCGATATAAGGAATGTTGTGCTGCTGGCGCACATGACGTTTAATCGCCAGCGATTCCACCGCGTAGGTATCGCGCCTGCAAAATCATCAACTACGCCATCGACCTGATATTCAACCATCTGGCTGAGCATTTGCGGGCGCTGATCGTTCGGCGAAACACAGGAGCAGCCAATCGCCAGATATTTATCCGCCAGCGCGTCATACATCACCCCGTTTCCGCCACGCATTGCTCGGTGGCTTTCGCGGTGCAGTTTCATAACCGACAACCCAGCCGCCATTCTCTTCAATCGCGCGCACCACTTTCTCTGCTGCGCCGCCAATTGGAGCAGCCGGTGATTAAAATACGTGGGCGCGGTCCTGTCATGCCTTCTTCCTGCTGAACGCGGGCGGTCATTGCATCCAGTTCGTGATCAACGCCTCTTTATCGGGCAGGTTGCGCCGTAGACTACTTTCAGAATGTCGCTGCCGCTAAGCGCTGGAGGATTTAACGCACAAATGATAAAGTTGGCCAGTGCGCGACGTTCGCGGTTTTTCAGCGCAATGGCATCGCGCGATATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACTGTTTTTGCAAGCGCAGCATCTCGGCTTTCCATAATGCACGCGAGGCGCTCGTCCTTAACGCTGTTTGGCAACTGCATCATGAACGGGCTTAAATTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCACAGGTGGTTTCACCGACCACCAGATCAGAAAAACAGAAGTAGGGGCATTTATCGGTTTTGCCGAAGCGGCTGCTTTTAATCAGCGGGCAGAGAGGTTGCGCGGCAGATCTTTCTCGGCTTCTTCAATGGTTTCATCAGAGGTGGAACATAGCGAAACCACAACCACCCGGCTGCCATCGGATACTCTTGCGGCATAAAGGTGCAGTAGGTGCCAACCAGCGGAATGCCGCGCTCCTTGAGATCCATGACGGTGAGAAAGCCTTTCTGGCGAGCTTCAGAGAACTGATCGAAAATGGCGGGTAGCTCGGTAACAAGTGACATGATTTTCCTTCCCCGTACCACGGGAGATAATGAAAAGAGCCACATTATTACCATTCTTTTGTTGTACTTCGTTCGATTGCATTACTGGGTGGCAGCGGCGTTCGAACGGCACTGATATCAACTGAAACAGACCATGGCGATGAGCTGTTGGGCGAGCAGGAGGAGCTGGTGGGCAACAAGGTCGCGAAAAAGCTGACCACTGACGCTTCTGAATGGAAGTCTTGCTGGATGGCGAAAAGGTAAAGTGAAATGGTCGCTGGTGACGAGCATAATATGCGTAGCTGATGGCGATTGCGGCGGCTCGCCATGTTGGTGTAGCGGCGGATACTCACCAGGTTCGTTTTAACGCTCGTCGCCGTCTGGAGTTGCACCATCCGCCAGCACGGATCTGCTCCAGCTACCTGGCTGTGGTTCTGAATAATGGTGAGCATGTTTTCCCGGCGTTAACCGTAATGGTCATCGGCTCGCGCCATCTGTCGCGGTGACTGACTTGCGGAATATCGGCGTTAGCCATAAAAGCAGAGAACAGCGCAGCCGCATAACTGCAATACGACAGTTAATGGTCTTGACGAGACTATCCGTGTATGTTGTAACTAAACAGAGTTTATCGTATTTGCCCACGGGCGGGACGCAGTCGCTAAGTGGCAGAACAAATGCCACCAGCGCCGGGATAGATAAATAAACCAGACGGCGCGCTTCGCTGACGCTCGGTGCTTCCTGATAGCCAAATCCCTTCAGTGTGCCAAACAGCGAAATTGTGAGTTGAGCACCGCGCTCATATCGAAGGCGATTTCCTGAAGATGGTTCCACAATCCGGCTTCATGAAATGCGCGAATGGCA * NM:i:124 ms:i:1853 AS:i:1832 nn:i:0 tp:A:P cm:i:24 s1:i:396 s2:i:0 de:f:0.0802 MD:Z:17G4A4C5G7A1^A1C1A1A2^C11^A0A1A5C4A1^T2^TTACA8A0T18A11A56A17T25^GG1A12^CA25^TTC3C19T1A64^GT1G5G8T17C7^CCC8^T70C20G2C2A3^G5A3^G0C1^G9^CCA5^GAC3T12C2G8^A0T20^AACC2A13A2C29C8G3^T2C3^G5^A3A48^A2^G0C12T20C2C1^C6T26C11A5T16G6^CA16C35G26C5G0T32^C2^TA3A41C32G15G1^A12^G28A24A70A5G49^G22 rl:i:0 pi:Z:aaaaaaaaaa -13d1b2d7-b6a8-4c58-a709-49f0f341c26f 4 * 0 0 * * 0 0 CTACCCAGATTTTTGTGCAAAACCGTGACGGTACTGATCGGCATGGGGAAATTCTTCGCTATCCTGGTCACCGGTATCGACCTTTCGGTTAGCGCGATTCTGGCGCTTTCCGGTATGGTGACCGCTAAACTGATGTTGGCAGGTATTGATCCGTTTCTCGCGGCGCTAATTGGCGGTGTACTGGTTGGCGGCGCACTGGGGCGATCAACGGCTGCCTGGTCAACTGGACGGGACTACACCCGTTCATTATCACCTTAGCACCAACGCTATTTTCCGTGGGATCACGCTGGTGATCTCCGATGCCAACTCGGTAGCCGACTTCTCATTTGACCGTGAACTTCTTTTGCCGCCAGCGTAATTGGGATACCTGTCCCCGTTATCTTCTCGCTAATTGCTTCGCGCTCATCCTTTGGTTTCTGACAACGCGTATGCGCTCGGGCGCAACATCTACGCACTGGGCGGCAGCAAAAACTCGGCGTTATTCCGGGATTGACGTGAAATAGGTGCTGAAGCGTTGAGTATCCTCTTGGCGCCTTAGCAGTACGTAGCCTTGTGTTGCCGCGTTTCAATTTACGTATTTGCTAAAAGGTTAAACAGGCGACTACAAACAGAATCGACGCTTTACCCGCAAACAATGCCCGTTGAAATTTATCCGCCGTTCATAGCCTCACCTCCGCAAATAACGGATGGCGTAGTTTTACACTGAGAAATGAAAGGATTTGAAAAAACCGCAAAGCGGGCGAAACGATATATACAGAAAGAAAGGAAAGCACTCTATCCAACAAACACACCCACAGTTGATCGGAATAAAAAGCAGA * rl:i:0 -489f7224-7d18-41d4-9129-d28c3e6aa780 16 NZ_CP062160.1 1629814 60 2S9M1I95M1D3M1D53M1I17M1D75M1I46M1I6M1I23M1I22M168S * 0 0 CTTATCATGTCTTTTTGGGTGAGTATTCATCCATAATGCGTCCTCTTCTTAGCGGTTGAACTAACGGACACCTTTCGGGATGGAAAAAACTTACTGACCTGGACTTGCCTTCGTTTGTTAGCTTAACTATAAGCCACTCTTTGCAGGTTTTCATCGCATTATTAATGAAAAATTGCAATTAGAAGGAAGCGGGACAGGACTCACTTTTTCAGCCTAGCACCAACCCGCAGCAGGTAAAAGCAGTTTGCCCGAACTGTTTCATAACATTTCAGAATTATCGCCAGAAGAAATTGGTGACACTAAGTACTGGTGATTGCTCTGAATATGACGTAATAAATCGAGGAATGAATAAAGAATATGTAACGTCCGGCTTCATCCGGATTTTCTGAGGCTACCGTGTTCACCACAACCGTGGTGCTGTTACGTTTTGTTTTGAGCTGAATGTGCAGTTTCAGTCGGTTTCCTGCACCGTCTTTCAGCACGCCTGAAATCTGTACTGCCATATTCACTCCACAAATAAAAAAG * NM:i:22 ms:i:566 AS:i:566 nn:i:0 tp:A:P cm:i:6 s1:i:121 s2:i:0 de:f:0.0615 MD:Z:33C6C63^C3^C54C8A6^G17G12T0A35T22G12T20C0A26C19 rl:i:0 -d7500028-dfcc-4404-b636-13edae804c55 16 NZ_CP062160.1 3164467 1 174M2D20M329S * 0 0 CGCCGCCGGTGCGGCAATCCGGAACGATACCGATGCCGGATCGCCCCGCTGCCCCCACGCATTTACTGCCCGGACTGTCAGCGTGTACCGCCCCAGCGCCAGTTGCGTGAAGCGGTATGTGGTTTCCGTCGTCCGGGCCGTGCTGACCAGCCGCTCACTGCCGTCATCCGCTGCCGGTCAGGCGAAGCATAAAGGTGCTGTCGATTCCGTTTGTAGTCGTCTGTTTAACCTTAGCAATACGTAACTGAACGAAGTACAACACATTTTTTTTTTTTTTTTTTCAGTTACGTATTGCCAAGGTTAAGAGAGGTCAGCGTTTCAACGCTCAGCACCTATCGCTCCGGAAGTGGACGTTGACGACGAGCCAGAAGAAGAATAATTTCATCGCTTTCATGCCAGGGAAAAGGGAGCCATCTCCTCTTTGAATTGAAAAGTCCAGGCTGTAAAGTCTGGGCTTTTGTCGTATTAGGCGCGGTGTTTGGCTGTGCCTCGTAAAAAATGGCTGGCTATACACAAGGAATAG * NM:i:12 ms:i:321 AS:i:320 nn:i:0 tp:A:P cm:i:4 s1:i:70 s2:i:77 de:f:0.0564 SA:Z:NZ_CP062160.1,4112332,+,2S187M334S,19,20; MD:Z:3T29C12T19C15C4G0T0T4G76G2^CA20 rl:i:0 -d7500028-dfcc-4404-b636-13edae804c55 256 NZ_CP062160.1 2003415 0 334S14M2D175M * 0 0 * * NM:i:12 ms:i:311 AS:i:310 nn:i:0 tp:A:S cm:i:3 s1:i:51 de:f:0.0579 MD:Z:14^GT72G12A0A0C4G15G14A4A12G29A3 rl:i:0 -d7500028-dfcc-4404-b636-13edae804c55 256 NZ_CP062160.1 2912586 0 334S14M2D175M * 0 0 * * NM:i:14 ms:i:299 AS:i:298 nn:i:0 tp:A:S cm:i:4 s1:i:77 de:f:0.0684 MD:Z:14^GT40A7A31C4A0A0C4G1T13G14A4A42A3 rl:i:0 -d7500028-dfcc-4404-b636-13edae804c55 272 NZ_CP062160.1 3313878 0 174M2D15M334S * 0 0 * * NM:i:15 ms:i:293 AS:i:292 nn:i:0 tp:A:S cm:i:3 s1:i:58 de:f:0.0737 MD:Z:3T42T4T14C8A6C4G0T0T44T6A20A2G8^CA15 rl:i:0 -d7500028-dfcc-4404-b636-13edae804c55 2048 NZ_CP062160.1 4112332 19 2H31M1I13M3D6M1D52M2D16M4I9M3I2M2D50M334H * 0 0 ATTCCTTGTGTATAGCCAGCCATTTTTTACGAGGCACAGCCAAACACCGCGCCTAATACGACAAAAGCCCAGACTTTACAGCCTGGACTTTTCAATTCAAAGAGGAGATGGCTCCCTTTTCCCTGGCATGAAAGCGATGAAATTATTCTTCTTCTGGCTCGTCGTCAACGTCCACTTCCGGAGCGAT * NM:i:20 ms:i:283 AS:i:274 nn:i:0 tp:A:P cm:i:3 s1:i:64 s2:i:0 de:f:0.0591 SA:Z:NZ_CP062160.1,3164467,-,194M2D329S,1,12; MD:Z:32A11^TTT6^C26G23A1^AG27^AG1A48 rl:i:0 -60588a89-f191-414e-b444-ad0815b7d9c9 4 * 0 0 * * 0 0 CTGCATTTCATCGACCACCGGCTTGGTCTGCCAGGCGATAAGCTCCAGGCAAATTCAGCCAGTGAGTCGGTGGTACGGCATCACCTGCAATAATCGGATACAGTTCCTCTTCCAGGGGAAGCGGAGCATTTCACCGGGTGGAGGAGGGCGTTGGCAGTACCTTGCTGTATTTTTGAGTTTCGAACGTGTCCATAATGAGGTTGATAAAACAACGGTAAAGCGGGTATTTTCATCAGGTATTTACCCACAGGACCGTTGTCGTTATTTTTATTTATTGTCGTTGCCCAGGGCGGCGAGACTAATACTGGTAGCATTTCTGAGTTTGCAAAATCTTCATTGCGGCTATTCCAGTAATTGCTGGCATTGTTATAAGTCCGCGGCGTGTGGCGATAACCTCATGACTAATTTTTCGGCCAGCAGGGTTGCATTGGTAATGAAACCAGCAATGTATGTTTGCGTTTATCTCTTTTTACCCCAATGCTTCGGCTAATGCTAACGCTATTGTGAAGGAAAATTTTCAGCACTTTTTATTAGTCGTTCATAACAGCGTTTACAGTATTATCGGTGGCTTCTATTAGGGCTGAAACAGCGCATAGGGATGGTTGACCATGTAAGTACATCACCAACTGTCATGTTGAGCATAGGGAACCAGGCGGTAGTGCCGTTGCCTTGTTCATAATACTGTAGCTGACCAACTGGTACCATAGATTAAACATCAATGTGTTGATAGTTTTCAAGTATTTCAAGCGTGACAGGATCTGTCGCGCTACCAGTTTTAACATTTCCAGTTGTGGAATATCGGCGAGCTGGTGCAATCGTTGGTATCTCATGGAGCGCTTCAGCGTTGGCATTAAAATAGCAATTAACGGTTGGCGATAGACTGATATATCTGGTAACACAACGAGTAATTTTGCAATACAGTTATTCAGACTTCCTTTTCAGCCAGCGATAAATGTTAG * rl:i:0 -dbd32a76-43d2-40d6-9ccc-610af70a4051 16 NZ_CP062160.1 2846079 60 130S32M3I13M1D9M1I13M4I85M3I16M3I24M1I16M1D86M2I14M3D113M3I1M1I25M5I1M2I191M3I57M2I4M1D30M2I1M2I31M3D59M1D10M2D35M1D31M341S * 0 0 TAAATAAAGTTTGTTTAATGGCTTCGTTTATTCGCCAGGCTGATTAATCACATGCAGGCTATCTGACCGCCAGCACCAAGAATCAGTACATTTTTCATGAAACTTTCCCAGGATTACGCGGCAAGCACATGCCATATCACTATTACGGATTTGAATATGTTTCCCCATTACAGAGTTTCTCAAAGAATCAGAGCTAATACTTCTCGAAATTACTTCAGCCACATAGACTTTGCCATCATAAAGATCCATATGGTTTGCGCCTTCAACAATGTGATAGCGTTTATCCTCGCGCTTTGATGCTCGATCGTACAGCAGGCCGTCACTCATCCATTTGCTCCCCAGCCAGGCTGCTCACATAATCTGTATCGGCTGAGTCAGGTACACTTCCGCCATATGGTAAGCATCATAGGTAATAATCTGGTTAAGGCTGCGCAAAGTAGCGCGTAACCCGGTGCTGGATACTGCGCGCGAGGGGTGTGGTAATATTCCCAGGCCTGACGCAGTTCTTCGTTCGGCGCATCGGACTCCTTCATTGGTGCCAGTGGCATAGTGGCGCATTCTCCGCTGCGTTTCAATATCGCTGGTTCGGGCGTTTGAAATTTTCTGGGGCGTCAACGTATGGTAGGGCATCAACAGATTTCACATTGTTTTCCCAACCATTACGGAACATCGAACCAATATTGACCGCACTAACAGTACCGATGGCCTTGATGCGCGGATCCCGAATTGCAGCATTGGCTGTATATCCTGCACCGGCACAAATTCCCATCGCACCAATTCGGGTATTGTCGACATAACCTGAAAGCGTTGTCAGGTAATCAATCACGGCACTGACGTCTTCAGTACGAATGTATGGGGCGTTTTAACTGACGCGGCTCGCCGCCGCTTTCTTCGTCTTTGATAAGATGCGTCATAAGCAATAGTGACAACTTTTTCCGCCAGTTTTTCGGCATAGGTTCCGGCCGTTTGCTCTTTAACGCCCCCACCTGGTGAGATACCAATTGCCGGATACTGACGGGTTTCATCAAATTTTGAGGGAAATAGATCACTGCAGACAAAGAGATAGGTGCTGAAGCGTTGAAACCTTTGTCCTCTCTTAACCTTAGCAATACGTAACCAAACGTGAAGTGCCGAAAGATAAGCAGCAACAGACGTGACTACGGAATCGACAGCACCCATAGCGTACCGAGCGCCACCAGAAAGATTTTTGCGGATTCATCATCGCGGTACCACAAAAATCACCAATAGAAGCGGATGCCAGGATGCGGCACGTTGCGCAACATCTGAATTGAGGTATCCAGGCAGTCGCTTCACTCCCAGCGACAGCCCGCCAATCAGCCCTTACAGTAGAATTCAATCCCCAGCGATCTCGCCAATTGAAAAGCCAACGAACGCCCGCCAGGAG * NM:i:87 ms:i:1407 AS:i:1380 nn:i:0 tp:A:P cm:i:19 s1:i:360 s2:i:0 de:f:0.0652 MD:Z:14G30^C10G17G14G7G52G9C12T22T3T6C1^G0C2C6C0G88^TGT30C63A5T27T11C0C2T11C10T60G20G0C5T131T3^C21A5A0C33^ATC1C26C11T18^G10^CA13T21^G4A26 rl:i:0 +f25635d3-3b81-4ff2-8510-f28330590801 4 * 0 0 * * 0 0 TGCTCAGATGGGGGAATGAAAACAATACTCGACAGGAACTACAACGCCACAGCGGCGATTGTATCAGAAAGTTGACACTGGAAGATAAACTGGTGGAGAAACCTGTCACGGGGAAGAGCAGAGCTTGACGCGCTTCGCTTGTCCCGGCCTCACGACCCGCGAAAGAGTTTCGCGAACCGTTCACCGTTTTTCAATATGATTCTGTCTGCTTTGGTCATTAAAGCAGACGATAGTGTCCAACTTCCCCGTATATAACGGTACGTGCTCATCGGTAAGAGCTGGCGGTATTGTGTTTATCAGGGGAAGTTTTCAGATACTCACGAAAATGCCTGGCAGTACCGCCGTCTACAATGCCATCGATAATATGTAGGTGTTTTCACCTAATTTTGCCATGATGATAATCCTTATATTACGGTTTGTGAATAGGTCTGCTTGTCAGGGTTTGTGTAACCTTTTAACCTTAGCAATGCGTAACGCGTGTACTTTGCGTTCAATGGTTACGTATTGCTGGGTTAGAGAGGACAAAGGTTTCAACTGCCCCCAGCACCTCTGGTTAATTGGATAGCGACACTTCCTGTATCATTCGGTGGCGGAAAATCAGTGGAATCGCCGAAATGGCTGGCGCGATTAACCATTTTGCGCCTGGCACCTGCTCTATTTTACCGATTTATCAACTGGCCTCGCCTGCGGCGAATTGTTAGTGGAATGATAGCTGAAGAGCTGCAAAGTTCAGG * rl:i:0 pi:Z:aaaaaaaaaa XA:i:42 XB:Z:test +95e6aa45-efe0-4ed9-b7b9-2f35164f9836 0 NZ_CP062160.1 1012347 60 1S43M1D8M1D11M1D5M1I10M1D2M5D2M1I37M1I102M2D14M2D25M3D90M2D7M1I35M3D8M1D73M1I28M1D9M1D2M1D9M3D5M3D28M1D21M4D62M1D6M1D5M1D52M1D2M1D39M1D45M1I30M2D119M1D2M2D20M2I76M1D12M1D4M1I176M1D22M780S * 0 0 TGTAATCACGCCGTCTGCCAGTAGGATCACTTTGTTGGCGGTTGAGCGGGATAATGCCAATCGTTCTGCTCAATGCTGCCCGGCATCTCAGCAAAGGCCGCGACACGGGTGCTGAGCTGCCACGACATCCGAGGTGGAGTAGTCTGTTTCAATAGCGATATAAGGAATGTTGTGCTGCTGGCGCACATGACGTTTAATCGCCAGCGATTCCACCGCGTAGGTATCGCGCCTGCAAAATCATCAACTACGCCATCGACCTGATATTCAACCATCTGGCTGAGCATTTGCGGGCGCTGATCGTTCGGCGAAACACAGGAGCAGCCAATCGCCAGATATTTATCCGCCAGCGCGTCATACATCACCCCGTTTCCGCCACGCATTGCTCGGTGGCTTTCGCGGTGCAGTTTCATAACCGACAACCCAGCCGCCATTCTCTTCAATCGCGCGCACCACTTTCTCTGCTGCGCCGCCAATTGGAGCAGCCGGTGATTAAAATACGTGGGCGCGGTCCTGTCATGCCTTCTTCCTGCTGAACGCGGGCGGTCATTGCATCCAGTTCGTGATCAACGCCTCTTTATCGGGCAGGTTGCGCCGTAGACTACTTTCAGAATGTCGCTGCCGCTAAGCGCTGGAGGATTTAACGCACAAATGATAAAGTTGGCCAGTGCGCGACGTTCGCGGTTTTTCAGCGCAATGGCATCGCGCGATATCTTCGCTAATCTCGTGCCCAAAACGTTCTTCTACTGTTTTTGCAAGCGCAGCATCTCGGCTTTCCATAATGCACGCGAGGCGCTCGTCCTTAACGCTGTTTGGCAACTGCATCATGAACGGGCTTAAATTCCGCCATGTATTCATACATTTTCTTTTTGCCGTCACAGGTGGTTTCACCGACCACCAGATCAGAAAAACAGAAGTAGGGGCATTTATCGGTTTTGCCGAAGCGGCTGCTTTTAATCAGCGGGCAGAGAGGTTGCGCGGCAGATCTTTCTCGGCTTCTTCAATGGTTTCATCAGAGGTGGAACATAGCGAAACCACAACCACCCGGCTGCCATCGGATACTCTTGCGGCATAAAGGTGCAGTAGGTGCCAACCAGCGGAATGCCGCGCTCCTTGAGATCCATGACGGTGAGAAAGCCTTTCTGGCGAGCTTCAGAGAACTGATCGAAAATGGCGGGTAGCTCGGTAACAAGTGACATGATTTTCCTTCCCCGTACCACGGGAGATAATGAAAAGAGCCACATTATTACCATTCTTTTGTTGTACTTCGTTCGATTGCATTACTGGGTGGCAGCGGCGTTCGAACGGCACTGATATCAACTGAAACAGACCATGGCGATGAGCTGTTGGGCGAGCAGGAGGAGCTGGTGGGCAACAAGGTCGCGAAAAAGCTGACCACTGACGCTTCTGAATGGAAGTCTTGCTGGATGGCGAAAAGGTAAAGTGAAATGGTCGCTGGTGACGAGCATAATATGCGTAGCTGATGGCGATTGCGGCGGCTCGCCATGTTGGTGTAGCGGCGGATACTCACCAGGTTCGTTTTAACGCTCGTCGCCGTCTGGAGTTGCACCATCCGCCAGCACGGATCTGCTCCAGCTACCTGGCTGTGGTTCTGAATAATGGTGAGCATGTTTTCCCGGCGTTAACCGTAATGGTCATCGGCTCGCGCCATCTGTCGCGGTGACTGACTTGCGGAATATCGGCGTTAGCCATAAAAGCAGAGAACAGCGCAGCCGCATAACTGCAATACGACAGTTAATGGTCTTGACGAGACTATCCGTGTATGTTGTAACTAAACAGAGTTTATCGTATTTGCCCACGGGCGGGACGCAGTCGCTAAGTGGCAGAACAAATGCCACCAGCGCCGGGATAGATAAATAAACCAGACGGCGCGCTTCGCTGACGCTCGGTGCTTCCTGATAGCCAAATCCCTTCAGTGTGCCAAACAGCGAAATTGTGAGTTGAGCACCGCGCTCATATCGAAGGCGATTTCCTGAAGATGGTTCCACAATCCGGCTTCATGAAATGCGCGAATGGCA * NM:i:124 ms:i:1853 AS:i:1832 nn:i:0 tp:A:P cm:i:24 s1:i:396 s2:i:0 de:f:0.0802 MD:Z:17G4A4C5G7A1^A1C1A1A2^C11^A0A1A5C4A1^T2^TTACA8A0T18A11A56A17T25^GG1A12^CA25^TTC3C19T1A64^GT1G5G8T17C7^CCC8^T70C20G2C2A3^G5A3^G0C1^G9^CCA5^GAC3T12C2G8^A0T20^AACC2A13A2C29C8G3^T2C3^G5^A3A48^A2^G0C12T20C2C1^C6T26C11A5T16G6^CA16C35G26C5G0T32^C2^TA3A41C32G15G1^A12^G28A24A70A5G49^G22 rl:i:0 pi:Z:aaaaaaaaaa XA:i:42 XB:Z:test +13d1b2d7-b6a8-4c58-a709-49f0f341c26f 4 * 0 0 * * 0 0 CTACCCAGATTTTTGTGCAAAACCGTGACGGTACTGATCGGCATGGGGAAATTCTTCGCTATCCTGGTCACCGGTATCGACCTTTCGGTTAGCGCGATTCTGGCGCTTTCCGGTATGGTGACCGCTAAACTGATGTTGGCAGGTATTGATCCGTTTCTCGCGGCGCTAATTGGCGGTGTACTGGTTGGCGGCGCACTGGGGCGATCAACGGCTGCCTGGTCAACTGGACGGGACTACACCCGTTCATTATCACCTTAGCACCAACGCTATTTTCCGTGGGATCACGCTGGTGATCTCCGATGCCAACTCGGTAGCCGACTTCTCATTTGACCGTGAACTTCTTTTGCCGCCAGCGTAATTGGGATACCTGTCCCCGTTATCTTCTCGCTAATTGCTTCGCGCTCATCCTTTGGTTTCTGACAACGCGTATGCGCTCGGGCGCAACATCTACGCACTGGGCGGCAGCAAAAACTCGGCGTTATTCCGGGATTGACGTGAAATAGGTGCTGAAGCGTTGAGTATCCTCTTGGCGCCTTAGCAGTACGTAGCCTTGTGTTGCCGCGTTTCAATTTACGTATTTGCTAAAAGGTTAAACAGGCGACTACAAACAGAATCGACGCTTTACCCGCAAACAATGCCCGTTGAAATTTATCCGCCGTTCATAGCCTCACCTCCGCAAATAACGGATGGCGTAGTTTTACACTGAGAAATGAAAGGATTTGAAAAAACCGCAAAGCGGGCGAAACGATATATACAGAAAGAAAGGAAAGCACTCTATCCAACAAACACACCCACAGTTGATCGGAATAAAAAGCAGA * rl:i:0 XA:i:42 XB:Z:test +489f7224-7d18-41d4-9129-d28c3e6aa780 16 NZ_CP062160.1 1629814 60 2S9M1I95M1D3M1D53M1I17M1D75M1I46M1I6M1I23M1I22M168S * 0 0 CTTATCATGTCTTTTTGGGTGAGTATTCATCCATAATGCGTCCTCTTCTTAGCGGTTGAACTAACGGACACCTTTCGGGATGGAAAAAACTTACTGACCTGGACTTGCCTTCGTTTGTTAGCTTAACTATAAGCCACTCTTTGCAGGTTTTCATCGCATTATTAATGAAAAATTGCAATTAGAAGGAAGCGGGACAGGACTCACTTTTTCAGCCTAGCACCAACCCGCAGCAGGTAAAAGCAGTTTGCCCGAACTGTTTCATAACATTTCAGAATTATCGCCAGAAGAAATTGGTGACACTAAGTACTGGTGATTGCTCTGAATATGACGTAATAAATCGAGGAATGAATAAAGAATATGTAACGTCCGGCTTCATCCGGATTTTCTGAGGCTACCGTGTTCACCACAACCGTGGTGCTGTTACGTTTTGTTTTGAGCTGAATGTGCAGTTTCAGTCGGTTTCCTGCACCGTCTTTCAGCACGCCTGAAATCTGTACTGCCATATTCACTCCACAAATAAAAAAG * NM:i:22 ms:i:566 AS:i:566 nn:i:0 tp:A:P cm:i:6 s1:i:121 s2:i:0 de:f:0.0615 MD:Z:33C6C63^C3^C54C8A6^G17G12T0A35T22G12T20C0A26C19 rl:i:0 XA:i:42 XB:Z:test +d7500028-dfcc-4404-b636-13edae804c55 16 NZ_CP062160.1 3164467 1 174M2D20M329S * 0 0 CGCCGCCGGTGCGGCAATCCGGAACGATACCGATGCCGGATCGCCCCGCTGCCCCCACGCATTTACTGCCCGGACTGTCAGCGTGTACCGCCCCAGCGCCAGTTGCGTGAAGCGGTATGTGGTTTCCGTCGTCCGGGCCGTGCTGACCAGCCGCTCACTGCCGTCATCCGCTGCCGGTCAGGCGAAGCATAAAGGTGCTGTCGATTCCGTTTGTAGTCGTCTGTTTAACCTTAGCAATACGTAACTGAACGAAGTACAACACATTTTTTTTTTTTTTTTTTCAGTTACGTATTGCCAAGGTTAAGAGAGGTCAGCGTTTCAACGCTCAGCACCTATCGCTCCGGAAGTGGACGTTGACGACGAGCCAGAAGAAGAATAATTTCATCGCTTTCATGCCAGGGAAAAGGGAGCCATCTCCTCTTTGAATTGAAAAGTCCAGGCTGTAAAGTCTGGGCTTTTGTCGTATTAGGCGCGGTGTTTGGCTGTGCCTCGTAAAAAATGGCTGGCTATACACAAGGAATAG * NM:i:12 ms:i:321 AS:i:320 nn:i:0 tp:A:P cm:i:4 s1:i:70 s2:i:77 de:f:0.0564 SA:Z:NZ_CP062160.1,4112332,+,2S187M334S,19,20; MD:Z:3T29C12T19C15C4G0T0T4G76G2^CA20 rl:i:0 XA:i:42 XB:Z:test +d7500028-dfcc-4404-b636-13edae804c55 256 NZ_CP062160.1 2003415 0 334S14M2D175M * 0 0 * * NM:i:12 ms:i:311 AS:i:310 nn:i:0 tp:A:S cm:i:3 s1:i:51 de:f:0.0579 MD:Z:14^GT72G12A0A0C4G15G14A4A12G29A3 rl:i:0 XA:i:42 XB:Z:test +d7500028-dfcc-4404-b636-13edae804c55 256 NZ_CP062160.1 2912586 0 334S14M2D175M * 0 0 * * NM:i:14 ms:i:299 AS:i:298 nn:i:0 tp:A:S cm:i:4 s1:i:77 de:f:0.0684 MD:Z:14^GT40A7A31C4A0A0C4G1T13G14A4A42A3 rl:i:0 XA:i:42 XB:Z:test +d7500028-dfcc-4404-b636-13edae804c55 272 NZ_CP062160.1 3313878 0 174M2D15M334S * 0 0 * * NM:i:15 ms:i:293 AS:i:292 nn:i:0 tp:A:S cm:i:3 s1:i:58 de:f:0.0737 MD:Z:3T42T4T14C8A6C4G0T0T44T6A20A2G8^CA15 rl:i:0 XA:i:42 XB:Z:test +d7500028-dfcc-4404-b636-13edae804c55 2048 NZ_CP062160.1 4112332 19 2H31M1I13M3D6M1D52M2D16M4I9M3I2M2D50M334H * 0 0 ATTCCTTGTGTATAGCCAGCCATTTTTTACGAGGCACAGCCAAACACCGCGCCTAATACGACAAAAGCCCAGACTTTACAGCCTGGACTTTTCAATTCAAAGAGGAGATGGCTCCCTTTTCCCTGGCATGAAAGCGATGAAATTATTCTTCTTCTGGCTCGTCGTCAACGTCCACTTCCGGAGCGAT * NM:i:20 ms:i:283 AS:i:274 nn:i:0 tp:A:P cm:i:3 s1:i:64 s2:i:0 de:f:0.0591 SA:Z:NZ_CP062160.1,3164467,-,194M2D329S,1,12; MD:Z:32A11^TTT6^C26G23A1^AG27^AG1A48 rl:i:0 XA:i:42 XB:Z:test +60588a89-f191-414e-b444-ad0815b7d9c9 4 * 0 0 * * 0 0 CTGCATTTCATCGACCACCGGCTTGGTCTGCCAGGCGATAAGCTCCAGGCAAATTCAGCCAGTGAGTCGGTGGTACGGCATCACCTGCAATAATCGGATACAGTTCCTCTTCCAGGGGAAGCGGAGCATTTCACCGGGTGGAGGAGGGCGTTGGCAGTACCTTGCTGTATTTTTGAGTTTCGAACGTGTCCATAATGAGGTTGATAAAACAACGGTAAAGCGGGTATTTTCATCAGGTATTTACCCACAGGACCGTTGTCGTTATTTTTATTTATTGTCGTTGCCCAGGGCGGCGAGACTAATACTGGTAGCATTTCTGAGTTTGCAAAATCTTCATTGCGGCTATTCCAGTAATTGCTGGCATTGTTATAAGTCCGCGGCGTGTGGCGATAACCTCATGACTAATTTTTCGGCCAGCAGGGTTGCATTGGTAATGAAACCAGCAATGTATGTTTGCGTTTATCTCTTTTTACCCCAATGCTTCGGCTAATGCTAACGCTATTGTGAAGGAAAATTTTCAGCACTTTTTATTAGTCGTTCATAACAGCGTTTACAGTATTATCGGTGGCTTCTATTAGGGCTGAAACAGCGCATAGGGATGGTTGACCATGTAAGTACATCACCAACTGTCATGTTGAGCATAGGGAACCAGGCGGTAGTGCCGTTGCCTTGTTCATAATACTGTAGCTGACCAACTGGTACCATAGATTAAACATCAATGTGTTGATAGTTTTCAAGTATTTCAAGCGTGACAGGATCTGTCGCGCTACCAGTTTTAACATTTCCAGTTGTGGAATATCGGCGAGCTGGTGCAATCGTTGGTATCTCATGGAGCGCTTCAGCGTTGGCATTAAAATAGCAATTAACGGTTGGCGATAGACTGATATATCTGGTAACACAACGAGTAATTTTGCAATACAGTTATTCAGACTTCCTTTTCAGCCAGCGATAAATGTTAG * rl:i:0 XA:i:42 XB:Z:test +dbd32a76-43d2-40d6-9ccc-610af70a4051 16 NZ_CP062160.1 2846079 60 130S32M3I13M1D9M1I13M4I85M3I16M3I24M1I16M1D86M2I14M3D113M3I1M1I25M5I1M2I191M3I57M2I4M1D30M2I1M2I31M3D59M1D10M2D35M1D31M341S * 0 0 TAAATAAAGTTTGTTTAATGGCTTCGTTTATTCGCCAGGCTGATTAATCACATGCAGGCTATCTGACCGCCAGCACCAAGAATCAGTACATTTTTCATGAAACTTTCCCAGGATTACGCGGCAAGCACATGCCATATCACTATTACGGATTTGAATATGTTTCCCCATTACAGAGTTTCTCAAAGAATCAGAGCTAATACTTCTCGAAATTACTTCAGCCACATAGACTTTGCCATCATAAAGATCCATATGGTTTGCGCCTTCAACAATGTGATAGCGTTTATCCTCGCGCTTTGATGCTCGATCGTACAGCAGGCCGTCACTCATCCATTTGCTCCCCAGCCAGGCTGCTCACATAATCTGTATCGGCTGAGTCAGGTACACTTCCGCCATATGGTAAGCATCATAGGTAATAATCTGGTTAAGGCTGCGCAAAGTAGCGCGTAACCCGGTGCTGGATACTGCGCGCGAGGGGTGTGGTAATATTCCCAGGCCTGACGCAGTTCTTCGTTCGGCGCATCGGACTCCTTCATTGGTGCCAGTGGCATAGTGGCGCATTCTCCGCTGCGTTTCAATATCGCTGGTTCGGGCGTTTGAAATTTTCTGGGGCGTCAACGTATGGTAGGGCATCAACAGATTTCACATTGTTTTCCCAACCATTACGGAACATCGAACCAATATTGACCGCACTAACAGTACCGATGGCCTTGATGCGCGGATCCCGAATTGCAGCATTGGCTGTATATCCTGCACCGGCACAAATTCCCATCGCACCAATTCGGGTATTGTCGACATAACCTGAAAGCGTTGTCAGGTAATCAATCACGGCACTGACGTCTTCAGTACGAATGTATGGGGCGTTTTAACTGACGCGGCTCGCCGCCGCTTTCTTCGTCTTTGATAAGATGCGTCATAAGCAATAGTGACAACTTTTTCCGCCAGTTTTTCGGCATAGGTTCCGGCCGTTTGCTCTTTAACGCCCCCACCTGGTGAGATACCAATTGCCGGATACTGACGGGTTTCATCAAATTTTGAGGGAAATAGATCACTGCAGACAAAGAGATAGGTGCTGAAGCGTTGAAACCTTTGTCCTCTCTTAACCTTAGCAATACGTAACCAAACGTGAAGTGCCGAAAGATAAGCAGCAACAGACGTGACTACGGAATCGACAGCACCCATAGCGTACCGAGCGCCACCAGAAAGATTTTTGCGGATTCATCATCGCGGTACCACAAAAATCACCAATAGAAGCGGATGCCAGGATGCGGCACGTTGCGCAACATCTGAATTGAGGTATCCAGGCAGTCGCTTCACTCCCAGCGACAGCCCGCCAATCAGCCCTTACAGTAGAATTCAATCCCCAGCGATCTCGCCAATTGAAAAGCCAACGAACGCCCGCCAGGAG * NM:i:87 ms:i:1407 AS:i:1380 nn:i:0 tp:A:P cm:i:19 s1:i:360 s2:i:0 de:f:0.0652 MD:Z:14G30^C10G17G14G7G52G9C12T22T3T6C1^G0C2C6C0G88^TGT30C63A5T27T11C0C2T11C10T60G20G0C5T131T3^C21A5A0C33^ATC1C26C11T18^G10^CA13T21^G4A26 rl:i:0 XA:i:42 XB:Z:test