1 /** 2 This package contains test data for the other packages in `dentist.common.binio`. 3 4 Copyright: © 2018 Arne Ludwig <arne.ludwig@posteo.de> 5 License: Subject to the terms of the MIT license, as written in the 6 included LICENSE file. 7 Authors: Arne Ludwig <arne.ludwig@posteo.de> 8 */ 9 module dentist.common.binio._testdata; 10 11 version (unittest) 12 { 13 import dentist.common : ReferencePoint; 14 import dentist.common.binio : CompressedSequence; 15 import dentist.common.alignments : 16 AlignmentChain, 17 AlignmentLocationSeed, 18 PileUp, 19 ReadAlignment, 20 SeededAlignment; 21 import dentist.common.insertions : 22 Insertion, 23 InsertionInfo, 24 SpliceSite; 25 import dentist.common.scaffold : 26 ContigNode, 27 ContigPart; 28 29 30 enum numInsertions = 12; 31 enum numCompressedBaseQuads = 6247; 32 enum numSpliceSites = 14; 33 34 Insertion[] getInsertionsTestData() 35 { 36 with (AlignmentChain) with (Flag) with (ContigPart) 37 return [ 38 Insertion( 39 ContigNode(1, begin), 40 ContigNode(1, end), 41 InsertionInfo( 42 CompressedSequence.from(""), 43 0, 44 [ 45 SpliceSite( 46 ReferencePoint(1, 200), 47 AlignmentLocationSeed.front, 48 emptyFlags, 49 ), 50 ] 51 ), 52 ), 53 Insertion( 54 ContigNode(1, begin), 55 ContigNode(1, end), 56 InsertionInfo( 57 CompressedSequence.from(""), 58 0, 59 [ 60 SpliceSite( 61 ReferencePoint(1, 700), 62 AlignmentLocationSeed.back, 63 emptyFlags, 64 ), 65 ] 66 ), 67 ), 68 Insertion( 69 ContigNode(1, begin), 70 ContigNode(206, end), 71 InsertionInfo( 72 CompressedSequence.from("gtttcgggattaaactgacagatcctcggttaccaagctaggttgcacccagaaactgtagaagttttatacacggccgtaatgaggtcagaacagtggcacctagctggcctactccaaattggttagctcactccagatacttcggctggtactacttaagagattcggcgcattccatatgcacgttagacaagtagcgtcagagcgcgcctccctgacgagttccttgtgaccgcgtaagcaagtggtgtctgctaactttcccccacattggacgcgccaacccagaccgcttgcgtgaggactagcccctaacaaccggagaagcatgcgttagcgttatttagactccgtcctgtgcgattctactcaacgggatctcggctccgcaattttccgcataaaatgcaagcttccaacctgtgtcgtgtgggtcgagcagtaagggtttaaagtaactagccttcaacgatagaccattctgaggtccggtcaatcccgccaccgcgtgcatgagagcgggccctgctagcctaagagcctgataaggaaataagttcgacgaaacttgaggactgcatccaaacgccggcataccattaatggggtaattatatccggggtagttggtcctccgaactctacagatcgtggccccaggtaccgctcgacacttaccggtcctttaggttggtcagtccccggctccacacagaacgtaatgacatggcatattgcaagtcctcttttcaacaagacagtaccagctccgggataatgtagagaggttttggtcgctaattaaccttgagagttagatcgtaaagcgtcatttctgtaaaaccggctggtatgacctgtgtttctagggtcgaccgagattcgagtatcgcccagccagctaatgacgcgcccatagaacgtatcgtggtccgcggtccctctgcagttggtgccgactataaaggaccagatccccttcacgtcgcgctttctcggcatactgattctggtcttagaagcgaacatgggctttccacccctcgagtttgaaccgacgctgataagattgatcagaaccgattttttaaagttatagcgcctgcgaattatccataggctgtcgtgggcctgtgctacccccccccctttcagaacatccagtatcctcgcgctatagtatttacgagtcgtcaagggtgttttagctagtgcgaccaatgttaggcacctactcctttgattgttttgcgagtgtgagacttcatagggtccatagtgctaacgaaaaagcaatgcgccgtcgtccgtcatcacgacacctatcatggcaatagggttgccacgttataaatatgcttagtgagatcgttcgaccggtgagtgtaactataactgctcacaaagctgtaaggattggcatcacatcgaggcctgaatttaattcataaccctaccgtatctagtcttggttgttcggtgaatcccccggcagaccacgggtcgttctgggctctctattcccaccttccctcttggaatcttcattagacaacgactcatagcgttttcggattgctggcctcttcttgcctctatagatgcagagggaccttacgatcgcagcttcgaggattaccgaggggcacccctacaatcctcgacgcagccgctccagagccaacacagagtagcacttcaggtacagcctgtgctttatatcgtaccccacgccgtgaagatcatatggtctcataataagtgtccgggacgacaatacattgattgatgcggagggacctaatccgtctacttccgatctgggagagtaagtagacacccactcagacacctcctctgggaggctcgagattccttagcggcgagggctttgtccaggcctaatttttgataagtatcgagcactcacatggggccacaatacgcaataattgttacgtctttgtctccgcactctgaaaacacgaaactactgtagatctcgccctacaggttgcctgaagagaattccccgaatccctacatgaatcggtatattcttaagatatacggctcttcgtgactatagccaactggcaatgtttttctgccaaaaggttgcgggggtcggttagacttaaacccactgacttaggatcatattgctcagttcggcttaactcctgcagtccggataatttagcagtgaatcggtcattcagagccgaattaaaatgaagtccgaccggcaacctgttaaacaagattgtgactttacgaaccacatccgctccgctaaagtgtttagctcgtctcttgccacgactgggtttgaagtatcgcatgcataacctccgtgtgaatgcacatgcgactcctagtcttatataaggtaggccacgttttctgcggcggaacagagaggcgacacctacatcagtaaaatc"), 73 0, 74 [ 75 SpliceSite( 76 ReferencePoint(1, 200), 77 AlignmentLocationSeed.front, 78 Flags(complement), 79 ), 80 SpliceSite( 81 ReferencePoint(206, 3900), 82 AlignmentLocationSeed.back, 83 Flags(complement), 84 ), 85 ] 86 ), 87 ), 88 Insertion( 89 ContigNode(1, end), 90 ContigNode(110, begin), 91 InsertionInfo( 92 CompressedSequence.from("gaccacccacgcacagacaagtgtattcgaagcttagtggccctgtaggtggtcctcgtgcaatgttaggaccaagtgcaatttatctgtattaagtgactttcaggtaagtgccaatcgcggcacacggagtggctaccatatcagttcatcgttacacgaccgacgtttgctacgggcggaaggtggtaatcagcatatagacagctagatagaatgttacacacacaaacactgggcataatgtatgctttcgaagggagcgacggtccgttaatttttgcgctagggagtattagacgttgaacactgttacaggcgcatcacgcctaagccaggcacttccctcttctgataagggcccttgtcgcataagtggcgctcaaaaacgcgaaatgacgatcgcctacgcgcacttgaccaaaaagaattatgacttgacggtatctgtaatgtcctgaccacctgtttaacaggtggtcgcaccgagaggaaggtgcgaggaggctctcttggggaatccaacagatcacacgtgggttctggatacatagacttcgggagttctttcctacctaccgcaccgacctgtggcggacacacccgccgcaatcgctgtgacacccacgcagttcgacaatcttagaacagccgctataacactttgggtaagatgttggagtcaggacaagtacgtatgcgtaaaacaatgtggcccgagtattgctagttcgaccgtgtatggttggatcagagactgtcgtgtgaacctcacgccagttcccaaactgcccgtcggagtttgctgagtaatgttggtgatcgatggttatcatgtgtcttcgtacggagaagatctccttatcgaaatcggtcagactaattaagtagcatagtgtgctaaattggaactaggcgacgggggctgctgtgcgcggttcttttcgactcctccgtcagtatgtctacacacgatgtcttctgatactcctcatacatagagacttttcgaggtcgcaactcgcgggtgcagtggacacctctaaaggcgtccacagtcatgtgccgaggagtggaaattcactcgcacactgcagcat"), 93 0, 94 [ 95 SpliceSite( 96 ReferencePoint(1, 700), 97 AlignmentLocationSeed.back, 98 emptyFlags, 99 ), 100 SpliceSite( 101 ReferencePoint(110, 200), 102 AlignmentLocationSeed.front, 103 emptyFlags, 104 ), 105 ] 106 ), 107 ), 108 Insertion( 109 ContigNode(4, begin), 110 ContigNode(4, end), 111 InsertionInfo( 112 CompressedSequence.from(""), 113 0, 114 [ 115 SpliceSite( 116 ReferencePoint(4, 3300), 117 AlignmentLocationSeed.front, 118 emptyFlags, 119 ), 120 ] 121 ), 122 ), 123 Insertion( 124 ContigNode(4, begin), 125 ContigNode(4, end), 126 InsertionInfo( 127 CompressedSequence.from(""), 128 0, 129 [ 130 SpliceSite( 131 ReferencePoint(4, 3400), 132 AlignmentLocationSeed.back, 133 emptyFlags, 134 ), 135 ] 136 ), 137 ), 138 Insertion( 139 ContigNode(4, end), 140 ContigNode(4, post), 141 InsertionInfo( 142 CompressedSequence.from("gtattcattatgggtacatgtcaacagcttaagatttaataccggagggcgaattcaatcccagcgctgtaaagagtaactggcgtgacatttatggacaattagactagcagcggatcttcatgatcacccccaagttgggacacacgcggggcgacgaagagttataattgaagcgtggcgatacacggtgtatctcgggtgtctttcgtagaccagcctgttaacttcacgagagtttgtccggcatcgcttgcggatcgggacgttcgttagttcgattaacgcgtgaactgccggttaaaggactatagatcggcgagagctttcttgtacgggtaacagtcgtttttactactcttggctcgactgttcttctgacactttagttgcaatgctacaagccaggatacgcatgtgggtaaacgtacatgattcggttcgagatattaatatgcatcccgatacgttttctgggactcgaatcggagactagtgttccgagaggaatcaaactaagatggagggggatacgagtaacggaccgtcctcggaatgtcgtctttaagatacttgcaaagacaagggacaaattcgccagttgttccttgcgaaggcgcatgtgaggcgtatacagggtcggcagtcagcaacacggctgaccctgggtcatcgactccacctcggttttaagagcacgttaacccccaggcacattttttggagtgtttcaagcggtgtgttggcccccaggcggggcggcactgcaggatcggggttaatagtgaccgagtgtcaggttctggggattgcaggataaaccgcgtctcatctgaacctgtctgttcaggttccaacccgtaaaactaggttactctaccgttgaaaggtggtactgccgagtgagacgcatactagcttgcaagtgatcggatccgggattacaacaaagccgcggggagtaaccacggcgagtgtagggacccagcgatacaccgcaaagccgaagtaactatttacggcaatcccctatgacttcgtagttagggggtccatgacgacaaagtatgcgagaggacccgggttttccttgttggccttcaaattcctccagtaatacatggagaatacgcgcactgaggagaccgcatcattgaccacgacggctggatttgtacccgtccgttccgaatatcctgcggtcccctcgacataattaaaccgccgttctcgttacagtagttctggaatagacccttctggcggtaggaaggctgtgaactaggcgaatatgccgcatgcatacacacgatgggtgttctagttgtccctgcattttagcatgctgtccccaactattgtctccgctcaattgtgtatcatgcaaacgaattctctacattaatgtagaaaatggagtattcacagttacagcgcatgcgatgccaggtctcaacgcgatccagcttttataactaagatctcgtttccgatcataatttcttaggtgtggggtgttccctcagcctgtccctagattcgcgagtgctttcggcgcctcccctggctaataaccgtctagataaagaactattagggggagacctaaatggtgcattcccaaaagtggtgcgcattgtacacaccatcggccagcatgctagaagcatgcctatcacttcccgcatcggtcctagagcacaaacatttagggcaactgatcgagatctccataacagcatcaacctacccccccatagccggagaactcgcaactagtaagttagtctaacctcaatctgtgcgagagtattcaagaagagtccgtgatttttacatgcttttctggacggtgtggcttaaacgctgggcatgttactctatcttgcctcatccaccggcgtggttccaaaaaccagggaagaatccgattgtaggagccaacggcaccgccggtacccctttatgaaaagggtgattcagcaccgctcgatccctacggtcagtttttcgtcgtgactgttggattctgtttgaacgtatagagccagtgtccacacgccggatcgttcacattatcggttgcgaaattatagacagggccacctgacttacctcagatgctcctcgattcaacaacgggtagcattcgtctggtggcctctcgccaggcaacagcttgtcgagcaggaaagggacgctagaacgattgaccgcggtccgttgcaatttaatgcgccatcagcgcgagggcctaattttatgcagaggacttagcgagatccattaagggaagttctgccgcacggatgaaaagggacagaactcaaattcctatacggtcgcaaaagcatagtgccttcggccgggctccatcatcaaaacgtacatttagcaacacatcaactacacatcggctcttctttactcaacggcgaattatatttcgcgcggcgctctgccagattagtggctgcagtcaggtggttagaggagtgaataatacagtggtatgaatgcttaacccattcattagatcgcgaactgggatatattggccccaccgcttgtacagatcaggcgcttaggattgttttttatacggctacatccctggaaccgtaaggttctacggcagtcagttttagcccggctggtacagtgcctcgctttaatagatctactgcctgtgcgaacgtagggttgcagagacattgctcttagattaaaatggacgtggctttgcgagtctagggcgccaaaatatacagggctttatgcttaccaggcaccctacaagtaagtctagtgcgaaataccgaccgggttcattctaatcatgaactgcacgtccacgaagaatgcacaggcgtgtgccaggtacattggctcggtcgggtaaaccaagaaattgagttaatattatgtccgtctggaagcggatgatcccgcgacaggcttcgactcgcgtggacttcatttcgcacccttattgtgcgctggcgagttgcctctctcgaataaccgttcaagacaccgtaatataactgtgttggcatgtccagaccaacagtggtaatctaggcgatctgcatattagctggctgaagtgcgctgtcgactgacctggcaggctgtcgcctgcatcagtgcagtagacataagttaacttaactttgcggcgtagcggtgttagtcggcccgaagacccctctaacaattagagtttgttatcgcatcggttttaaatgaactgctcgagtagagagtttacgccataggtcgattttgtgttgcagcgtatttccgctcatagcgagtcaaggcaaaaaaatacgcgctatgatcatgatgccaacctactacggatgtattacgtaggccggtcctatcattgacaaaaggggacaacaacacgactccaaagtcccaaatctacatcgtgcgtaggtgtattacatctcacgatagtcttcgcccttaaccacaagctttccgctaagtcgcctgcggcctattaactttaaacgatcgctaagggactcttgactcttacataccaagcgcggccccagatccccttagccctcttgtatgttttgcctctgaccaagtgaaacgaacagttccgagtacccttctcttttgatcaaatatctgccttaggatccgccacatgggtcgacaaccaagtaaggttgagagcctttactcggctctagtaagatctctccagtctttcagcgagggttgatgagccgacgacagccctgttcgtatcgcgaggccagtggtcagagttgcccgctcgctagacgtcgtgcatgataatcgtgtttcatcctcaattctccgtgcagggagaaccttcaaggcgaaggaacaagaagtaggctatcgtgcgccgttcacagtacccactacaccctacgtatgtactagtagcgatagtaaatggcttcgtccaggcttcgcattcagttatctagcggaggctggtagtcctcttcgtagatagacagccgggtgttggtttgtgggggaacacgcgacctagggggtgccctcctctcgtgtcatttgcgggtagaagctagtccccgatggtaa"), 143 0, 144 [ 145 SpliceSite( 146 ReferencePoint(4, 3400), 147 AlignmentLocationSeed.back, 148 Flags(complement), 149 ), 150 ] 151 ), 152 ), 153 Insertion( 154 ContigNode(4, pre), 155 ContigNode(4, begin), 156 InsertionInfo( 157 CompressedSequence.from("agaagtgtgcagcacgttcttacaatcagcgatcacgccggtatatctccttcaccacgtactctagagaccgttctaaaacatcttatcgtttaatataccaggggatatcaaacctcctgtcccgtttctcctgcaggttgccgccagatattcaggtcaagcgtgctgcagccccactaccagggcatccgaggacagagaaacgccgatttacaaaagtgtcgtaccctggttctgggggctcctgaatcagattctacgtttcatcacgattctttcaacgtcggaggatacggttgaccccggatttacaacaagcctttagtacacccccaacgaaggggttcaacctaacgtcgattgatgccttgtaagagaatatatgtttatacgttcgatgaacgaccggacgctcagactggattttgcgacacagcggccacgttacgttccgggtctatatcacggtcggacttaaatctgcaaatagctgtatactctacgaagttgtcttcggctcgcctcaacgacgtcctctggtaccatatgatgatacacttcgcaacgaaagagcgatttccggtgcacgcggcaactagacagcgcttcgaattcgaatatgatttcaggcgaatcgttctcggggggacacgagggtcagtgccaggcttgttccgtcccgcgctctggccgagcccgttccccaattaccatcggcaatgcggcgctctcctcctcaataacgacagcattttcgaacactttctattccaatgcgctgactcagtgtaggagcttcgcgtcggccgaccagatagagattaattgggactgtaacctactatctgatggacaaacataagaggcgacttcctctccctaaattgagcggtacggcgagatgcttgatcgttagtatgtgagtctgttctgctcctcagtgtattgtatgacttctggattatacaccatttaccacggcgtggttgtttataacgagggggggatacgggggttcttaacaagaaggcaatcagggtgctctatctgaggtccggggtctgtgtttcgtaaatgctcgattggtaaggatccgtcgcctgtcgagggatgttgaatgttaaagtcgtatattatttaccaattggccaaagtttcctacaactgcgatccattgatctggcagccgttacgttagcactccgaaaaatgtgtaatcggaccgagccggcacatgcgatataaggcatctccgaggttttgcgggtatcggggaactccatgacggtctattgagtcagccgatccagaacccatctcccgtgttgtgaagggaacacatcctatctagtgcaaccatgttctaaccgctccatccgtgtacttcccacagggtcgtgggccgtagacaagttctgaatgcggggatgcggccctcatttagtcctgctatgggcattatttcactctggatcgatgagctccaccgcgacagcgatatcggagcttgcttgaacggtcactcttcggcaaaagagtcgtgcaagttacggcgagtgcacccgcgagccatcctgaagaaccaaacactggctgacataatactaccttgcagagatgggctacgcaccgactaagatggagctagagcctattctacaacctcgttgctcggcgttgcctcacgctcaacagcaaagatataacgcgaaaagaacaacacgtagtttttaatacatgtaacatcaattcgttgccggtaagctcctcacctaccaaccgcaagacagggtagaggcggtttctacgtacattcgtaagtgtcaaggtacccgacgctccctatagcgagtccccctgcatttctctgcttgtcgaatatttacatccaccttacgctctaaaatccatcgttgagtccgggcgagaccaagcggccctcaatccaatagaacgaagcttggaaaatttgaactcattagacgcactccacattgctatcctggagggtactgcccgcagcccatggcatatttttctcagatcctctgtaggaggtggcccctcaggagacggaaattcctctggtaatagttaaattatagttactgcaaggcttctgcccagagtccctgccagacaacgctggtgccgtgttgcagttcgggagtggatcctgcaccccgcgtgatagccattttggacggactgtgagtgtcgttctcgactttttgcgtacctagttgatggcagggcatcaaataagtctcttctgttacaaaacctccttagcttggggcgtctctgcgcatactacgaagccccatgacaatagatttttttcccttgtttaagcggccgaaagaggtacgctggcgttatattagtctttgtaatagtgccactgactgatcacgatgtgtttggaaccatcactttgaggatgcacggacgacaggcgggattatcactctccaaatcgggaagcaaacgcactcgtacggccgtaagatgtaagtactgaagtgcatctcacctgcaggattttctccaatatggcgattatgggttcccccttaattaagggaggtgcctaccaaatgcctaagtgtcttaagttcagcgctatctcgacccaatcgtttgggagtgtttcccgtttgggctggatattatactccaactgtttgtggtagtggactccgcctctcagatcctcgtgaatacacctgtatcaacaagtagattatgatgacgctgcggacgaacctgcctgttgaagtatgtttacacgccagaacacatacatttgctgccaatccctggttgggttagcccccagattacggcgaatgaatagaatctgtctgcatctcaaaatttcgacgtgtcaccacctttgctctatgaacttgcgatctcgaaagcaataaagagtggtccggtgagggaatctcttgcaaactacggcgtcggcagtaggctagattccccagcattgcacgctctaaactcggctaacgtttggtcagtaacatcaatcaacgtcgtagagaccgcatggcttcaaaagggagcggacgtcaatagttcgacgacgttttatctacccacataccatgagttcggcggaatataagtattcgtaattcggagtcagttcatgctgacaaaatccgcaagcgaaatatcctacgtagctgtagggtaagccgagtgaacaggctacaggctcagttgaacgctgggtagcaacgacatagctctagccgtgcgcaacctgacccgctctggtcagtccgggggtgcgtcttgcgcggatacatgtgtgcggggtagtacagtcatcaatgtaggctccctcgatattaaaatgacaatgtgggatgaataagtggtgcgcctgtgagccacgtggcggagggagtacgacgtgctcaggagggtagccgcaatttaaatcgaactataggttgtgatacagctgatccgtcgatccctggagctgataatagtaccctgctaaagatcaccctcccgcttattgcggctttcccaaagagttcagacgccaatagaagcaatttccgaactatcctgctacattcaccgggcttgtgagtgttcgcatgcattcagtttttcgaaacgacatgtcatcctaccgtttttattgtcggcgatgtgataccaacacatgacgcctactccacgtcgcgggcggcgggcggtggcatttaatctgtaaacgtttacatcaagcgccccgttaagccatcgctcttctgtcaatgatccgaacatcgtgaagtcctgtattccggctatgaatccgcggaatgtagtgcggggcttgaataacgaagactagtcaggtcttacgtcacgactagctagagtaagacgactcatctctttgtcatacaagcataagtgcaatcctattagatccatctacaagaaaaactggcggtccatgatacgactgtggcggtagggcatgactgagggcgagactccgaacaggatattcccacgcctagcctggctcgtggctgttgttaccgcaagagaggatctcatcgatggttcgtgtagttgtacgtgacggggtatagcaaccagccacggggcggacacgggtttttaccgcaaagggtaattgatactagcgaggattagagctgccaactggcttagtgcgcgtgggggacgccttcaggggttggtgataggcagaggtcttggtgtaaactgttctaatgtgtatcggcaaacaactactgcgatcggggatgagattagtgcgccggatcggtttccggcactacgattccaaacacgacgacaaccaatagtatctggttgatgacaaatcttatgttggggtctacgtgcgaggggtcgaggtgcattatagattgctttatattacaacaaaatttcactcacgctatgaaccctgaagcaccgctagtgtttccgggattggtttatatcccctgaatcgaataacgaggaccaagcaagtgaggggtacctggctatatcagctaatatcaagggtaggataggtcccagagtaaaggactactagtacttcgccccgttccggcgagcataccgatgagggggcgtatgagtgatcctcacgcagttttatgatacactatggtacgctaccgggagttttactgtcaccgtgcgtcacccttatctcgtacccttgcccaggctggctgacagaaaattttaggagcaagagagatatgcggttttcacttagtatggtataggagacttacaataggaggtcagattatatgacgacgaaacagggaggtgtgcgaccatcaaaactttaccgaattcctaatacaaggtgtcggtgaccgtgagccactccttcgctcgcatggcgctgcagaacgtggattacattaccacgagagcgacatcccttctcatgatggtgccttgccttgaatgcctgtgggtagccgcgcactctcctacggagcgtatataggcgagacgttgtggcgaccgcatggatgaggaacgccgctagagcagagctagcccgtcgatcaacagcacgctctcgacgagttagcaatcagagctacacagattcaggcgcgcatagtattacatcccaactccgaaaccaaaataggtcccgattcattcgagagactaaacactcaatgaattcttaactatgtcaggactagcgctcataatgacgatctgattggttgaatcccttcttaaaattaactagctgtttctgcgacaccggatctacgattcctgcctcggacccttgagtggtacaattacacccgagggaggggtccgcttacgtcatacgagactccccctgggcactgctcgtcctcaccacggcatgagattgtccttgtaccatgaattcgttaatcgtaaacatcactgttttccactcaattgccgcgctgtaggagacgcggagtcttatgaggagaaaagaatatgtaagtaagacatttatcacctaggatgcagcgggtttaactacgcctcagtccagcgcgacgacatggaaacattctgttgtaaggggtacacttcggaagtctaagtcggtcgaactgcggtctaaatcccctgggctaaatccgggatgactggtgccccagtgaagcctcggaactactcaatcttgcatctgctactcgtctgacacatcagaagacgctctcttcttaggacctcactatcagtaagcagatattaaaatgaccggcctaacgccgaaaatatctgtaaagaccccaggccgccgggccttttaggcgtgtcatggcaaggtctagcagcagtttgcgagtacagaggaagactccgacgctggtagtccacctacgccgttgctcgtagccgcagccgaaagctgtgccgcccttctctaccgatttgaacgctgggcaatagctgccaccgttgttatatacggtcacgacgctacagtgcgactgtcgttttgtcgagtacaacttgctggtagaactactgctcacgccgctgcggacaagaaacctgaaattcggagtacagtcatgcaggtgaccgcttccttaacgtaagcaatatttccttaaacggttccctggcaggaaaatggggaaagaaacctatcacgtgcctagcgaccgaatcaccttgtgcctccttgcgcggtgtgagcgatggacgcatccgatccggcgtgatgctccaatatgagccgttccgtctgggaaacctcggcagaaccacggccaagattggcttagttgtacccataatcactcagtgcggccagtcccgataagaccctttgggctttcagtcattcgaatagcccgttcgtgcacgaatgagtcttgattaccatatagttatgaataaaagtaggactagtctctttcacagtataggggagacggcgccgaaccacccggttccggactacatagtccatgacataaatcgacctcgctagcaccgaggacaagttagcgagtcacctgcttggttgtagatgggaattataaactaacccgttggggggccaagccacgctctgaggtacgaacaggtttcagatatgaaaaggactccgttcctcgtcagcggctttgtaagagacacattagtcctgctgctccagaccataactccaccattgttgtgacgacgtgcgagggtttgatgtagaatacgacgtatcgtttctgagtggtatacggctgcaaccgggaaaaccttggatgaattcctgccgctatatcgatattaaactccgcgaccattacttccccgacgacgggcagccggttctgtttcataatgaggtcttaccactggtctttcggggctacagggccctacgcaatatgttatctctagcagcttgtggcgccgttctctcgataatcgttcgcgcggtcatagacaaaacgtacaatgcccggctgtgtttaacaatttaccccctggttttgcggctcagtacttgctacacactagttattgggatggaccacggagtgtcaacgtaattgatgaagtataggatccacatccgccgacggctacaattcgtgtaattacttttagggcttttctctggcgatttcgggacacatcacagcgcatacgcgtgccaggcgaaagagaatcatgaaagagcctacttttcaactcaggtaacataataagaggcgttaaagcgtacagtacggtagataagacggataatgtcgcctcatataattagcgtcttcgtaaccttcaacgaacgtcctactggcgcttcactcgagacgcttgactaagcacacggcgtggggacccatcgtcgaggaccgtggccaacggagttcgcgcaacatgtccgcaaagacctgtgcaattgtctcagaaggaccggagctggatccttgcgatcatccctgacaatctcaaaacttttaaaccttatgttgaagtctgctctgatagttagtatccagaggttttgaggtgagctcaacgcgaatcttcttcgtttgcgaggactcgccgtaccaatatggggacgctccacacggagtattccgcaatgcagttgggactttaaaaaaattgatcgtgcgctcgccattcagatcgcgcacaaaatagaaaggggtcctcgttgggcggaacggctcgagtcagtcaaaacgattactgctgaacgccccgcgtagcgcaaaccagtaggagccctaggcctgatttaggaagctcgttggaagaatgcacagtgccatcctttgatccatcgatgacccgagcgtatgtaaggaatcgcgcacaagctaagagagctgtcgtccgtgaggaaaatagggcgatgcgcgggcttatctagctggtggatagccactcccagcaaaagtcaaaactgacagcgtccaaagggttaatgcaaagttaaaggagcatctggtccgttcagatccgcgggctctattatgcatatacatggccagtgggatcagtcataggaggccgttatattgtcaaacagtcaatcttttgtcttccgactactcaaaactcgtaattttttcaacaggctcgctgggctgtctccgtccgtctaccttgcccgagcacgagccgtgaccgcctgactgtgcagtatgcccaggactcgtgttacgcttcgtcctaaatcaatcagcctctgttgctcgcagtccaaggggcctggaggtccgtaataataactacagccgctgtgtatccgccgttgcatacgctgaacagggccacgtaaccatgtgttgtaatgtgcaac"), 158 0, 159 [ 160 SpliceSite( 161 ReferencePoint(4, 3300), 162 AlignmentLocationSeed.front, 163 emptyFlags, 164 ), 165 ] 166 ), 167 ), 168 Insertion( 169 ContigNode(5, begin), 170 ContigNode(5, end), 171 InsertionInfo( 172 CompressedSequence.from(""), 173 0, 174 [ 175 SpliceSite( 176 ReferencePoint(5, 2600), 177 AlignmentLocationSeed.front, 178 emptyFlags, 179 ), 180 ] 181 ), 182 ), 183 Insertion( 184 ContigNode(5, begin), 185 ContigNode(5, end), 186 InsertionInfo( 187 CompressedSequence.from(""), 188 0, 189 [ 190 SpliceSite( 191 ReferencePoint(5, 2700), 192 AlignmentLocationSeed.back, 193 emptyFlags, 194 ), 195 ] 196 ), 197 ), 198 Insertion( 199 ContigNode(5, end), 200 ContigNode(5, post), 201 InsertionInfo( 202 CompressedSequence.from("ccacccaagctggatgtctcctccgcggctggcgttatgagtgtagtctagtaatgtccggtgactatgagcggttttgtatgtgggagcgtgatccaagttagaaaatcctagaatctattaatagcgaagaacaaagttttggcctaacacctagatgcctcaggtaacctcggatagggggatggataaccgcaactgacacgtggaggcagctctgcacgcaacccactgtcccgattaccggctctatattcttcactctgagtccttattatttggccgaatgttctgcaacgaatttgtcactgcagtgatagggagttggacccacactatgcatctgggaaggtaaaagtacatcgtccttttattcgatggccccggttgaaagcactagccatctgccggaaatagtgggcacatcagcgctgatcttatagatcctttcacacgacgtctctcgttctggttatcgttcccatttctgcgtacaagtagtttacgtcctctaattgaatgagttaccatctacaagagagttttacgctagtcacagcaaacgaacgacggaggacatttttcacagagtctcaccacgaaacccctaaaacaaccgaggtaccgttgtacgcttcaattcgttacaagtcactgatataaggagtgtgcttatctcgggctttgtcgctatgacaccaagatggttttcatcgtgatataaatcgaccttccgccctatgggggttttgccattagacaaaggacacaccagcagatagcgcattttaataaagaagatggaacccgaaacatgcggcaggaattggcgttttgacccctatcctcacttcgtccggagcccagattgaccgcgcgtgatgcagcgtcagtactggcggctaccgcctgaaggcctgtggacatctactatagaagatactccaacatgtctcgactggaatcaaggtcgcggctttaatacgctccgcttaaattaatcaagcccagagattgccgcagtgagtatctgagtaataacggattgagactaccaataccacgcaactctcagcgacagtgagacattgattcctgagaccgagaggacaacggcgaccgtgctataccgcccatcattaataaaccttttaccgcctattcctaaaccgactatgattctactatggaaagagaatatctccttggacacgaccttgatgagtccaccgcggacccgcttgcgaagggcatttggataggacatcataggcgacattcctggcacatgtcggctgttggactagcagtaaggttcacgcgctttggctgtggccattaaataggtacccgttacagtgcctcggactagccagttaaaattgctctcattagcgatgtcatggatttacgagaaacagccttcgtcactgtcgaaaggcaagagtgcttcacggcaacttgctctatgttattactttggattcgaaggtctgatagtgttgctagccgaggaggtagataattcggaatgcgaaattgttagaacctgctggaatgccagcatactggtaagaggctgatctgggggttccccattccccttccaacgatagctgttcgaactctgccgtgccaaaacacgctagccgagcctgttcagagattttcgggcttcaatgtaaagcctcgttatagccaggcacttggaatatggttttctaattatgaagttgccataaggcccgcgaacaaccattgctagctcgtgcctttgtcaactgtactcaatccctggagttagtatccggtgtcggcccagcaacaaaccttccgttctcggcgtcgcaagccctattcacatgttcgcctagggatgggggtgtaggctctactagaagggttctaacgactcctgagaacatgtccagaatcgtttagagggttcggggtggtaataacttgatccgcatcgccgcgtatatagtgcacgcgctcaattaagtaaggcacctgtccgatcctaaagggcttactcaaggtttcccggcggacaggtcttcgtcttgcagtgcgctagcacgccacgtgagcagatgtgcgtatttgaaagaactcaaaggccgcacacgctccggacactggtaacacgcggtctcactacgtagctactattccattctgtcataccttctggttggactttatcatgacgatgttcagttctttgtagtcctaaggctgctgcgatcagcattaatgattacgtgggcgattactctgtctgttgactgtaagggatcagaggcctccgcgagataagatcatcgggaccatttcggagcgagcaaccacctcgtgcgggccgacacaccggcgggcaacccactcttgtattgtttcagtaattttgtacgctgaccttgttatcccgataggtggaagcggtcagtacccagccccgagtcgtgtgtgggtccgtacgccgcacgttgcaccaggaaaagattcatatccttccagacgaagctcccatttatggatgtgggaggggatggtctacttattaaagggcgtggcataagagcctaccccaacgcgcgcttccctatggcaaagtcaatgcctcacgtagctggagttgcgagcctcggacgactgcgcactctcggcgcgaacgtaatcctccactgccttcgtctctcttatacaacgatgctatcccagatttaatctgttacggtatcttaatatgtcagatcacgatcggcagcttaagaagtatggtcaaccgaggtattagtgactagccgattctcgactaacgggaccgacggcaagtgtagcggtgtccagactgtttgtgcttgatggaaaatattatacccacagagtgcactatgtactctaccagtttgcggaccatggacgcacttggagctgcgggatggatgcgacccacccggcggccctacatgcctgcgaccgtgggagcatgatcatcaagagctattaacggggttctgtaaacacaaaagggtaggtgat"), 203 0, 204 [ 205 SpliceSite( 206 ReferencePoint(5, 2700), 207 AlignmentLocationSeed.back, 208 Flags(complement), 209 ), 210 ] 211 ), 212 ), 213 Insertion( 214 ContigNode(5, pre), 215 ContigNode(5, begin), 216 InsertionInfo( 217 CompressedSequence.from("gcccaggctaaacttgactgccgtagaaccttatcgggtatccagggatgtagtccgtataaaaaacaatcctaaagcgctatgatctgtacaagccggtggggcacatatatcccgttccgcgagtctaatgaatgggttaagcattcactaccactgtagttatttcacgtcctcctaacctacctgactgcagccactaatctggcagagacgcccggcgaaatataattgccgttgagtaaaggaacgagaccgcattgtgttagttgattgttagttgctaaatgtagttttgatgatgcggcccggccgaaggacactattgctttatgcgacccagtatatgagaatttgagttctgtccctgttcaatccgtccggcagaacgttcccttaatgggatctcccgctaagtcctctgacataaactttaggcgctgcgcgctgatgcggcattaaattgaacggaccgcggtcaatatcgttacctgcgtccctttcctgctcgacaagctgttgcctggctgaggaggccaccagacgaatgctacccgttgttgaatcgaggatgcatctgaggtaagtccaggtggctcctgcttattaatttccgcaaccgattaatgtgacacgatccgtgcgtgtggacactggctctatacgttcaaacagaatccaacagtcagcgacgaaaactgaccgtagggatcgagcgcgtgctgaatcacccttttcataaagggggtaccagggcggtgccgttggctcctacaatcggattctttccctggtttttggaaccacgccggtggatgaggcaatgattagattaaacatgcccagacgtttaagccacaccgtccagaaagagcatgtaaaaatcacggatctcttcttgtaaatacttcgcacagatgtgaggttagactaacttactagttgcgagttctcggctatgggggggtaggttatgctgttatggtagatctcgatcagttgccctaaatgtttgtgcttctaaggaccgatgcgggaagtgataggcatgcttctagcatgctggccgtggtgtgtaccaatgcgcaccacttttgcggaatgcactttaggttctccccctaatagttctttatctagacggttattagccaggggaggcgccgaaagcactcgcggatctagggacaggctgagggaacgaccccccacctaagaaattatgatcggaacacgagatcttagtatataaaaggctggatcgcgttgtagacctggcatccatgcgctgtaactgtgaatactccatttttctacattaatgtaagagaattcgtttgcagttgatacacaattgagcggagacaaatagttgggacagatggctttaaaatgcagggacaactagaacacccatcgtgtgtatgcatgcggcatattcgcctagttcacagccttcctaccgccagaagggtctattccagaactactgtaacgagaacggcggtttaattatgtcgaggggaccgcaggattattcggaacggagggtacaaatccagccgtcgtggtcaatgattggcggtctctcctcagtgcgcgtattctccatgtattactggaggaatttgaaggccaacaagggaaaacccgggtcctctcgcatacatttgtcgtcatggaccccctaactacgaagtcataggggattgccgtaaatagttacttcggctttgcggtgtatcgctgggtccctacactcgacgtggttactccccgcggctttgttgtaatcccggatctcgatcacttgcaagctagtatgcgtctcactcggcagtaccacctttcaacggtagagtaacctagttttacgggttggaacctgaacagacaggttcagatgagacgcggtttatcctgcaatccccaggaacctgacactcggtcactattaaccccgatcctgcagtccgccccgcctgggggccaacacaccgcttgaaacactccaaaaaatgtgcctgggggtgttaacgtgctcttaaaaccgaggtggagtcgatgacccagggtcagccgtgttgctgactgccgaccctgtatacgcctcacatgcgccttcgcaaggaacaactggcgaatttgtcccttgtctttgcaaaggtatcttaaagacgacattccgaggacggtccgttactcgtatccccctccatcttagtttgattcctctcggaacactagtctcccgattcgagtccccagaaaacgtatcgggatgcatataaatatctcgaaaccgtaatcatgttcgtttacccacatgcgtatcctggcttgtagcattgcaactaaaggtgtcagaagaaccagtcgagccaagagtagtaaaaacgactgttacccgtacaagaaagctctcgcccgatctatagtcctttaaccggcagttcacgcgttaatcgaactaacgaacgtcccgatccgcaagcgatgccggacaaactctccgtgaagttaacaggctggtctaccgaaagacacccgagactacaccgtgtatcgccacgcttcaattataactcttcgtcgccccgcgtgtgtcccaacttgggggtgatcatgaagatccgctgctagtctaattgtctataaatgtcacgccagttactctttacagcgctgggattgaattcgccctccggtattaaatcttaagctgttgacaatgtacccataatgaatacataaggcctagaaggccaattagtatcataatgatctgcacgactcttgattgcctatcttcattgcgatagcgacgaagacgacccctaggtcattccatcctcatgactatgctgttccctggcggaatacacagcctcttgccaggggaatcttcatcaagctgcttcatggttgaccttcaatatcaaactcagaatatcttagcaccaaacacaccgatgatctggaaccccccgcaaacatcgcacgcccggtttattctcccaatgagcgacgcctgcctatctctcggacaggcttagtagaagcgctgataccttaacaatgatgagtgcaaaccatgtgtggtccccgactggccttgtaggatatgcgaagtacctgacgccagcagcttcgcgccgaactaccctgcagaactgacgtcaaggtcctacggttgatagctgtttctgagggtgcttgggtcccaccgatgcgcttgtggacttgacaccggcgagggaaaccttccaagaaagcctaaaatgcttcacacacagcgacattaatacctcagcaacgttacgctgcaaaattgtatggcctacccatgattacatatttacgctaggtggtgacaccggtcctccagtcattagagtactcgtgattagtcgagatggagccccctgatcgctccgcggagagcagtggatatgtgcacgcccgtaagcatgggggagttccggcagttgggtgctcccgatcacccaactcatatttacggagaacgccggtgcaggataaggacagcaggttgaaggagtccctgcatggatagtataacagctctcgcttgcttccccatagtgggctgtctgagagggttagtctgccgcgagcgtagtgcaataatgagtcagtcgaaggcgagagtccatgggtcttcaaacgccttcgcgagcattgaagaacatgatttaataattgtcatttcatacaatgagtgggtcaccacccaaggcatatgatgtaacaatttcactcttggggccccctttgtttcaacagaaccgctccactcggacgttagtaccgcagacagttggtttcgaattggatatcgagggctaccttgacgttcatcttttaccaatgataccattgtaggaacgcacttgtagggttaggacaatcgaacccgtgccgaccgtgcccaccctaactgaccgcctaagatagctaagagagtatgcaggccagagacgaggccgaatatgactgttatatatatcatccggccccgaccagattacaatgaccccttttgtgaataatagatagaacggaacagagttgaaacctaagtttaagtacaattaatgcggtaacgctgattctagtcttgatgatcccaggccgtagcctgctgtgaccgtctactctgccttcgtcgagcccgactctggccgttttggcctcctcaggagtccgttcacaccatatggcctacttttagtatttgtcaaggctccctgcgtcgcggatctgaatcgtatgtgacagtccgggaaaatttcatcgggcgcgggtatactacatgcaactcggaaaagggatataagccccattcgtgtctctcgcgaaccgcccagggccattagcaacgggaacagcgccaaccgtatttacttatcgcgtaatcagaaagcgtccttactgtcccgtcaccgttctttagactgccggatacggagatgagagtgcattgagtagacacattcgtcgtagaaccggcggagtcatcattgggcaaatttcgacgacttagtccttggcgctggttgtgagtctacgtttggatcactctccttcgcaaggttgctattgtgccgggggtggcatcccaaagagtccctgcaaaccgcaggggctgggattaccgaagacctccatcgacagtgacagcccgccgttcaatagacagcacgatagcgcgagtggaagactgatcacttcggtggttctgtaatgttgtcggtttgtggcaagtctttttgcgcctaacagctcgctcacttcctaccgagctgcttcatccggtccgcatccgctagtgctgcgcttggtgatacctaataaaaattccgcgctgtcggacatcattgttgcttcgtagggatacagcgaagaaggccccaggctcggttgcaacttgcgcgcccttttgaccacgtgaatcggtgacaatgcaaggagcgaatgctcccgatttacgttaggagcgttaagacaatccttcgtcgtaacttgcctcccgtacgtctcctgatgctaggtcagttcgcggaccccacggcatgttaccaccctgagggaagtggatgtggtgcgcagatgactgtgctctctctttccgtcatttcaaatggggtccgaccccactgccatcggttgtccttaacggaggggagcttgggcttcggatcaggtcgtacgacactttgccttgaggggatagagtgaacaactgttggagtatactttgaggtctgtcgtgcatttctgacacagtcgaaatcccatagctaactgggcgttacaaccccatggcggggaaacaagccatttgataagggccgcgctggctgggcgttacccgtgtgcataggccggtgccaacggcgcgctgagagttctatgccctatcagtatggcgatgattcgaatcgaataaggaacgaatagctagttcaaaatccccgtcctggcagtgccacattcgcgattttagcatttacccggagagaaaccccgagctcaggtcagtcatgttccacggctaaatgtattgagagctcatgattgagtcatcgtgacgtgcgacgcgacgctagtcagcaccatttttggctactattttgatttgacagttcatctctcataaaagggagttccgttcggtttgtcttctaaaccccttacacttagtcagaagcgctagcttcagggatgtgtcgttgcacgacgtattctgtttgagcatctaccgtcgatctcccggtaaagaagaaggaagcgtttcctgtccttaggcaactttagggacacaagtactttctgggatataatagatgatcccttggtagagaccttcacagctctacacagacggagt"), 218 0, 219 [ 220 SpliceSite( 221 ReferencePoint(5, 2600), 222 AlignmentLocationSeed.front, 223 emptyFlags, 224 ), 225 ] 226 ), 227 ), 228 ]; 229 } 230 231 enum numPileUps = 2; 232 enum numReadAlignments = 5; 233 enum numSeededAlignments = 7; 234 enum numLocalAlignments = 8; 235 enum numTracePoints = 393; 236 237 PileUp[] getPileUpsTestData() 238 { 239 with (AlignmentChain) with (LocalAlignment) with (Flag) 240 return [ 241 [ 242 ReadAlignment( 243 SeededAlignment( 244 AlignmentChain( 245 9, 246 Contig(1, 8300), 247 Contig(1539, 6414), 248 Flags(complement), 249 [ 250 LocalAlignment( 251 Locus(0, 6227), 252 Locus(7, 6414), 253 309, 254 [ 255 TracePoint(10, 98), 256 TracePoint(7, 107), 257 TracePoint(7, 105), 258 TracePoint(8, 108), 259 TracePoint(4, 99), 260 TracePoint(4, 102), 261 TracePoint(5, 103), 262 TracePoint(5, 105), 263 TracePoint(1, 101), 264 TracePoint(8, 107), 265 TracePoint(6, 102), 266 TracePoint(8, 103), 267 TracePoint(7, 105), 268 TracePoint(6, 105), 269 TracePoint(2, 102), 270 TracePoint(4, 104), 271 TracePoint(5, 101), 272 TracePoint(5, 99), 273 TracePoint(0, 100), 274 TracePoint(0, 100), 275 TracePoint(10, 107), 276 TracePoint(7, 103), 277 TracePoint(5, 102), 278 TracePoint(4, 101), 279 TracePoint(2, 100), 280 TracePoint(7, 106), 281 TracePoint(1, 101), 282 TracePoint(5, 101), 283 TracePoint(7, 107), 284 TracePoint(6, 106), 285 TracePoint(3, 103), 286 TracePoint(3, 103), 287 TracePoint(7, 105), 288 TracePoint(4, 103), 289 TracePoint(5, 102), 290 TracePoint(7, 103), 291 TracePoint(7, 104), 292 TracePoint(5, 105), 293 TracePoint(5, 101), 294 TracePoint(8, 106), 295 TracePoint(4, 102), 296 TracePoint(9, 104), 297 TracePoint(2, 100), 298 TracePoint(6, 102), 299 TracePoint(8, 104), 300 TracePoint(8, 106), 301 TracePoint(6, 102), 302 TracePoint(4, 102), 303 TracePoint(2, 101), 304 TracePoint(4, 102), 305 TracePoint(4, 103), 306 TracePoint(3, 103), 307 TracePoint(4, 101), 308 TracePoint(8, 108), 309 TracePoint(2, 102), 310 TracePoint(2, 101), 311 TracePoint(3, 103), 312 TracePoint(2, 100), 313 TracePoint(3, 103), 314 TracePoint(5, 102), 315 TracePoint(6, 105), 316 TracePoint(3, 98), 317 TracePoint(1, 28), 318 ], 319 ), 320 ], 321 ), 322 AlignmentLocationSeed.front, 323 ), 324 ), 325 ReadAlignment( 326 SeededAlignment( 327 AlignmentChain( 328 17, 329 Contig(1, 8300), 330 Contig(3197, 8564), 331 Flags(complement), 332 [ 333 LocalAlignment( 334 Locus(0, 71), 335 Locus(12, 86), 336 3, 337 [ 338 TracePoint(3, 74), 339 ], 340 ), 341 LocalAlignment( 342 Locus(0, 8300), 343 Locus(0, 8530), 344 407, 345 [ 346 TracePoint(6, 105), 347 TracePoint(9, 108), 348 TracePoint(7, 105), 349 TracePoint(3, 103), 350 TracePoint(2, 100), 351 TracePoint(5, 100), 352 TracePoint(6, 104), 353 TracePoint(7, 104), 354 TracePoint(5, 99), 355 TracePoint(4, 104), 356 TracePoint(2, 101), 357 TracePoint(3, 103), 358 TracePoint(6, 102), 359 TracePoint(7, 102), 360 TracePoint(8, 102), 361 TracePoint(4, 104), 362 TracePoint(4, 104), 363 TracePoint(6, 99), 364 TracePoint(7, 104), 365 TracePoint(6, 105), 366 TracePoint(3, 99), 367 TracePoint(5, 102), 368 TracePoint(3, 103), 369 TracePoint(5, 103), 370 TracePoint(4, 104), 371 TracePoint(7, 104), 372 TracePoint(6, 106), 373 TracePoint(6, 105), 374 TracePoint(7, 105), 375 TracePoint(2, 100), 376 TracePoint(2, 101), 377 TracePoint(9, 101), 378 TracePoint(6, 104), 379 TracePoint(4, 102), 380 TracePoint(6, 101), 381 TracePoint(7, 104), 382 TracePoint(8, 103), 383 TracePoint(7, 107), 384 TracePoint(3, 103), 385 TracePoint(5, 103), 386 TracePoint(3, 103), 387 TracePoint(3, 101), 388 TracePoint(7, 104), 389 TracePoint(1, 101), 390 TracePoint(8, 103), 391 TracePoint(3, 103), 392 TracePoint(1, 101), 393 TracePoint(4, 103), 394 TracePoint(4, 103), 395 TracePoint(5, 104), 396 TracePoint(4, 99), 397 TracePoint(3, 103), 398 TracePoint(5, 103), 399 TracePoint(4, 102), 400 TracePoint(3, 99), 401 TracePoint(4, 98), 402 TracePoint(8, 108), 403 TracePoint(4, 104), 404 TracePoint(6, 106), 405 TracePoint(7, 106), 406 TracePoint(7, 105), 407 TracePoint(3, 103), 408 TracePoint(4, 101), 409 TracePoint(1, 101), 410 TracePoint(6, 102), 411 TracePoint(7, 104), 412 TracePoint(1, 101), 413 TracePoint(5, 98), 414 TracePoint(8, 104), 415 TracePoint(5, 104), 416 TracePoint(4, 104), 417 TracePoint(5, 102), 418 TracePoint(4, 103), 419 TracePoint(4, 100), 420 TracePoint(3, 103), 421 TracePoint(6, 104), 422 TracePoint(7, 103), 423 TracePoint(4, 104), 424 TracePoint(5, 103), 425 TracePoint(5, 102), 426 TracePoint(2, 100), 427 TracePoint(7, 102), 428 TracePoint(5, 105), 429 ], 430 ), 431 ], 432 ), 433 AlignmentLocationSeed.front, 434 ), 435 ), 436 ], 437 [ 438 ReadAlignment( 439 SeededAlignment( 440 AlignmentChain( 441 42, 442 Contig(1, 8300), 443 Contig(2325, 16069), 444 emptyFlags, 445 [ 446 LocalAlignment( 447 Locus(3562, 8300), 448 Locus(0, 4860), 449 229, 450 [ 451 TracePoint(3, 41), 452 TracePoint(7, 102), 453 TracePoint(2, 102), 454 TracePoint(3, 103), 455 TracePoint(4, 102), 456 TracePoint(8, 108), 457 TracePoint(2, 100), 458 TracePoint(6, 102), 459 TracePoint(6, 104), 460 TracePoint(2, 102), 461 TracePoint(4, 102), 462 TracePoint(7, 102), 463 TracePoint(3, 99), 464 TracePoint(2, 102), 465 TracePoint(3, 100), 466 TracePoint(6, 100), 467 TracePoint(3, 102), 468 TracePoint(5, 104), 469 TracePoint(5, 104), 470 TracePoint(4, 101), 471 TracePoint(5, 103), 472 TracePoint(2, 102), 473 TracePoint(7, 106), 474 TracePoint(7, 103), 475 TracePoint(3, 101), 476 TracePoint(8, 106), 477 TracePoint(6, 103), 478 TracePoint(6, 103), 479 TracePoint(4, 103), 480 TracePoint(3, 102), 481 TracePoint(2, 101), 482 TracePoint(7, 106), 483 TracePoint(4, 104), 484 TracePoint(3, 101), 485 TracePoint(8, 103), 486 TracePoint(10, 102), 487 TracePoint(8, 104), 488 TracePoint(7, 102), 489 TracePoint(3, 103), 490 TracePoint(5, 105), 491 TracePoint(6, 100), 492 TracePoint(7, 105), 493 TracePoint(3, 99), 494 TracePoint(3, 100), 495 TracePoint(5, 104), 496 TracePoint(4, 104), 497 TracePoint(3, 100), 498 TracePoint(5, 103), 499 ], 500 ), 501 ], 502 ), 503 AlignmentLocationSeed.back, 504 ), 505 SeededAlignment( 506 AlignmentChain( 507 76, 508 Contig(2, 8350), 509 Contig(2325, 16069), 510 emptyFlags, 511 [ 512 LocalAlignment( 513 Locus(0, 6798), 514 Locus(9086, 16069), 515 308, 516 [ 517 TracePoint(5, 103), 518 TracePoint(4, 101), 519 TracePoint(8, 106), 520 TracePoint(9, 104), 521 TracePoint(9, 104), 522 TracePoint(6, 106), 523 TracePoint(3, 101), 524 TracePoint(8, 104), 525 TracePoint(4, 104), 526 TracePoint(7, 101), 527 TracePoint(4, 102), 528 TracePoint(3, 100), 529 TracePoint(7, 105), 530 TracePoint(6, 99), 531 TracePoint(3, 103), 532 TracePoint(2, 102), 533 TracePoint(6, 102), 534 TracePoint(3, 103), 535 TracePoint(4, 102), 536 TracePoint(12, 110), 537 TracePoint(7, 103), 538 TracePoint(4, 104), 539 TracePoint(4, 102), 540 TracePoint(4, 100), 541 TracePoint(5, 105), 542 TracePoint(5, 100), 543 TracePoint(6, 102), 544 TracePoint(5, 105), 545 TracePoint(3, 102), 546 TracePoint(2, 102), 547 TracePoint(6, 103), 548 TracePoint(2, 100), 549 TracePoint(4, 104), 550 TracePoint(5, 103), 551 TracePoint(6, 104), 552 TracePoint(4, 104), 553 TracePoint(3, 101), 554 TracePoint(4, 104), 555 TracePoint(6, 104), 556 TracePoint(4, 104), 557 TracePoint(1, 101), 558 TracePoint(3, 103), 559 TracePoint(8, 105), 560 TracePoint(2, 102), 561 TracePoint(4, 104), 562 TracePoint(1, 99), 563 TracePoint(6, 102), 564 TracePoint(3, 101), 565 TracePoint(3, 101), 566 TracePoint(5, 105), 567 TracePoint(1, 101), 568 TracePoint(1, 100), 569 TracePoint(4, 102), 570 TracePoint(4, 101), 571 TracePoint(3, 103), 572 TracePoint(2, 101), 573 TracePoint(5, 101), 574 TracePoint(6, 103), 575 TracePoint(6, 105), 576 TracePoint(7, 106), 577 TracePoint(8, 107), 578 TracePoint(5, 103), 579 TracePoint(5, 105), 580 TracePoint(2, 102), 581 TracePoint(2, 100), 582 TracePoint(1, 100), 583 TracePoint(5, 103), 584 TracePoint(3, 99), 585 ], 586 ), 587 ], 588 ), 589 AlignmentLocationSeed.front, 590 ), 591 ), 592 ReadAlignment( 593 SeededAlignment( 594 AlignmentChain( 595 47, 596 Contig(1, 8300), 597 Contig(3332, 12946), 598 Flags(complement), 599 [ 600 LocalAlignment( 601 Locus(4899, 8300), 602 Locus(0, 3507), 603 154, 604 [ 605 TracePoint(0, 1), 606 TracePoint(7, 105), 607 TracePoint(6, 105), 608 TracePoint(6, 106), 609 TracePoint(7, 107), 610 TracePoint(3, 102), 611 TracePoint(7, 105), 612 TracePoint(3, 103), 613 TracePoint(2, 102), 614 TracePoint(4, 100), 615 TracePoint(3, 101), 616 TracePoint(5, 105), 617 TracePoint(3, 103), 618 TracePoint(7, 101), 619 TracePoint(3, 101), 620 TracePoint(5, 102), 621 TracePoint(7, 105), 622 TracePoint(4, 104), 623 TracePoint(3, 103), 624 TracePoint(4, 104), 625 TracePoint(3, 103), 626 TracePoint(6, 102), 627 TracePoint(4, 101), 628 TracePoint(6, 104), 629 TracePoint(2, 102), 630 TracePoint(8, 104), 631 TracePoint(4, 104), 632 TracePoint(4, 103), 633 TracePoint(1, 99), 634 TracePoint(0, 100), 635 TracePoint(9, 108), 636 TracePoint(5, 104), 637 TracePoint(5, 102), 638 TracePoint(5, 103), 639 TracePoint(3, 103), 640 ], 641 ), 642 ], 643 ), 644 AlignmentLocationSeed.back, 645 ), 646 SeededAlignment( 647 AlignmentChain( 648 89, 649 Contig(2, 8350), 650 Contig(3332, 12946), 651 Flags(complement), 652 [ 653 LocalAlignment( 654 Locus(0, 5082), 655 Locus(7726, 12946), 656 244, 657 [ 658 TracePoint(5, 104), 659 TracePoint(2, 99), 660 TracePoint(3, 103), 661 TracePoint(7, 103), 662 TracePoint(2, 98), 663 TracePoint(2, 102), 664 TracePoint(11, 107), 665 TracePoint(4, 104), 666 TracePoint(4, 102), 667 TracePoint(8, 106), 668 TracePoint(5, 105), 669 TracePoint(11, 109), 670 TracePoint(8, 101), 671 TracePoint(5, 103), 672 TracePoint(4, 104), 673 TracePoint(2, 102), 674 TracePoint(7, 105), 675 TracePoint(3, 103), 676 TracePoint(5, 101), 677 TracePoint(3, 101), 678 TracePoint(5, 102), 679 TracePoint(4, 102), 680 TracePoint(6, 103), 681 TracePoint(5, 105), 682 TracePoint(3, 99), 683 TracePoint(5, 103), 684 TracePoint(2, 100), 685 TracePoint(7, 105), 686 TracePoint(3, 101), 687 TracePoint(5, 105), 688 TracePoint(5, 103), 689 TracePoint(5, 105), 690 TracePoint(5, 105), 691 TracePoint(7, 105), 692 TracePoint(5, 102), 693 TracePoint(3, 100), 694 TracePoint(3, 102), 695 TracePoint(4, 102), 696 TracePoint(5, 103), 697 TracePoint(5, 105), 698 TracePoint(8, 100), 699 TracePoint(6, 103), 700 TracePoint(5, 102), 701 TracePoint(6, 105), 702 TracePoint(2, 98), 703 TracePoint(2, 100), 704 TracePoint(7, 104), 705 TracePoint(5, 104), 706 TracePoint(3, 103), 707 TracePoint(2, 100), 708 TracePoint(5, 82), 709 ], 710 ), 711 ], 712 ), 713 AlignmentLocationSeed.front, 714 ) 715 ), 716 ReadAlignment( 717 SeededAlignment( 718 AlignmentChain( 719 43, 720 Contig(1, 8300), 721 Contig(3593, 6783), 722 emptyFlags, 723 [ 724 LocalAlignment( 725 Locus(3943, 8300), 726 Locus(0, 4471), 727 213, 728 [ 729 TracePoint(3, 56), 730 TracePoint(7, 102), 731 TracePoint(2, 102), 732 TracePoint(7, 101), 733 TracePoint(7, 103), 734 TracePoint(9, 107), 735 TracePoint(4, 104), 736 TracePoint(4, 104), 737 TracePoint(5, 100), 738 TracePoint(4, 104), 739 TracePoint(3, 101), 740 TracePoint(5, 102), 741 TracePoint(5, 101), 742 TracePoint(2, 102), 743 TracePoint(2, 98), 744 TracePoint(6, 102), 745 TracePoint(10, 109), 746 TracePoint(1, 99), 747 TracePoint(6, 102), 748 TracePoint(1, 101), 749 TracePoint(3, 101), 750 TracePoint(5, 104), 751 TracePoint(7, 101), 752 TracePoint(7, 105), 753 TracePoint(5, 102), 754 TracePoint(0, 100), 755 TracePoint(4, 104), 756 TracePoint(10, 105), 757 TracePoint(7, 103), 758 TracePoint(11, 111), 759 TracePoint(8, 105), 760 TracePoint(4, 101), 761 TracePoint(4, 103), 762 TracePoint(3, 100), 763 TracePoint(5, 104), 764 TracePoint(4, 102), 765 TracePoint(7, 105), 766 TracePoint(5, 105), 767 TracePoint(6, 104), 768 TracePoint(5, 102), 769 TracePoint(3, 103), 770 TracePoint(3, 101), 771 TracePoint(2, 100), 772 TracePoint(2, 100), 773 ], 774 ), 775 ], 776 ), 777 AlignmentLocationSeed.back, 778 ) 779 ), 780 ], 781 ]; 782 } 783 }