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Fixes StringOutOfBoundException for cases of three indels/three delet…
…ions/ two deletions and insertion Added test case
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...resources/com/astrazeneca/vardict/integrationtests/N13532.TwoDels1InsStringBoundError.bam
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11,1278939,1281541,CGGTAAGACGCTGCAGAGCAGAGGTGCCCGGCATAGGGTGAGGGGGGACAGAGCCGGTGCCCACCAGGGGCCTGTGGGTTGGGCACAGGAGAGCAGAGGAGAGCCACTGTGTCCTGGCGTGACCGCGGCAGGACCACTCGGCAGAGATGGCCTCCAGGTGCTTCATTCTCCTCCTAACGATGAGGCTGGTGACCTCTGGCCTGCCCAGGAGTGGCCCAGGGACGTGGGAAGCAGCGGGGAGGTGGCCAAGCAAGGGGCCTGGAGGGAGCCCCCAGGGGCTGTGAAGCGGTCAGGTCCTCGGGGAAAAGCACGCCTGCGACTTACTCTGGGAACAAGTGGTCGGGAGGAGGAGTGAGCAGCGCCCAGACAGTGGCCTCCATCCTCCCGCAGTGTGCAACACAACCACCTGCCCCCAGAGCCTGCCTGTGTGCCCGCCAGGGCAGGAGTCCATCTGCACCCAGGAGGAGGGCGACTGCTGTCCCACCTTCCGCTGCAGTGAGCGGGGCTGGGGCCGGGCTCCTGGGTGGCCTCTTGCTGGGGGTGGGGGAGTGCAGGATGGTGGGGGCGCTGGAGCACATGCTCCCCACCACTTGTCGAGGGCTTAGCTCCCTTTCCTTCCAGGACCTCAGCTGTGTTCGTACAATGGCACCTTCTACGGGGTAAGGGCACAGCAGTGGGTGGGTGTGGCCCTGGGGCCTGAACATGTGTGTGGGATGCCCCGGGGCTCTCTGAGCCCCACTCCTTGTCTTGACATTCCTGCCCTGAGGGCCGATCCGCACAGGGGCCCTGGACACGTCAGAGCTGGGACATGCTTGGGACTCAGGGGCACCTTACGTCGACAGCCATGAGCTCCACAACTGCTGCCTCTGAGAGGTCCCTTCAGGGGCTCCCAGCAACAGCCTGGGGGCAGCACACACTGGCCTGGGGTCCCCGCCTGCCCGCCCAGATTCCTACCCGCCCGGATTCCTGCCTGCCAGATTCCTGCCCCCATGGGGTCTCTGCCCACCCAGATTCCTGCCCACATGGGGTCTCTGCCTGCCCAGATTCCCTGCCCACCTGTGGTCCCTGTGTGCATCAGCTCCCTGCCTGCCTGGGTCCATGCTCAGCCAGGGGTGCATCTATGCTCCATCTGAGGAAGGAACAACTCCCTGCAGGCCCCATTGGGTCATGGGGAGGGGTCCTGGCCCTGTTGCCCCACCAGTGCCCTCAGTGCCACCCTCCCACCCCTTGCAGGTTGGTGCAACCTTCCCAGGCGCCCTTCCCTGCCACATGTGTACCTGCCTCTCTGGGGACACCCAGGACCCAACGGTGCAATGTCAGGAGGATGCCTGCAACAATACTACCTGTCCCCAGGTGAGACCCGAGGCACCTGCCCCCAGGTGAGCCCCCGAGGCACCTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCTGAGTCACCCGCCCCCAGGTGAGCCCCCGAGGCACCTGCCCCCAGGTGAGTCCCTGAGGCACTTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCTGAGTCACCTGCCCCCAGGTGAGCCACCAAGGCACCTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGCCCACAGCTGCTGGGCAGACCCAGCCCTGAGTCACTTATCCTGGCTCCCTGGGGTTCTCTAGCTCAGCCATTGCTGGGGTCTTGTTTGTTTCCAAAGGGAGGGTATGAAGTAGGAGGATAACTGAGGGGGTCTGGGGGTGGGACAGGACCTGCAGGCTGCTGGGGACAGGGGCTGAGGTCAGGTTCCAGGAAGGCAGGGGTAGGCAGAGAGAAGGTGCTGGAAACTGGGGTGAGGCTGAGCCGGGATAACTGAGTGGGGGCAACTTCTTCGGGTATAGGCCCAGGCAGGGACAGGGCTAAGGGGTCCTGGACCACTGGGGTGTAGACAGGAGGGCAGGCTGGGCCGGGGCATGTGCTGGAGGAGAGGGTTAGGGCCTGACGCCCCTCATGTCCCCACAGGGCTTTGAGTACAAGAGAGTGGCCGGGCAGTGCTGTGGGGAGTGCGTCCAGACCGCCTGCCTCACGCCCGATGGCCAGCCAGTCCAGGTAACAGCAGAGGCATGTGGGGGCAGGTCTCAGCTCCCTCCCTGGAGACCCTCACCCCCAATGGGGCTCTGCACAAGAGGTAATCCCTACTCAGCTTCCACACTCACCCTTGCATTTCAGCTGAATGAAACCTGGGTCAACAGCCATGTGGACAACTGCACCGTGTACCTCTGTGAGGCTGAGGGTGGAGTCCATTTGCTGACCCCACAGCCTGCATCCTGCCCAGATGTGTCCAGCTGCAGGGTGTGTGCTGGAGGCCCTGCCCCTGCCTGGGAGTCCTTGTCCATCAGGGAGGCCCAACCCCTGTCTGGGATGCCCTGCACAGCAGGGAGGCCCCACCCCTGCTGGGGAGGCCCCACCCCTGCCTGGGAAGCCCCACCCCTGCCTGGGAGGCCCCGCCCCTGCCCGGGAGGCCATGCCCCTGCCCGGGTGGGCCCCTCCCCAGGAGGCCGCACCCACCAGGGAGGCC |
3 changes: 3 additions & 0 deletions
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...N13532.TwoDels1InsStringBoundError.bam;chr11;1280138-1280341;-f 0.0025 -F 0x700 -Q 10.txt
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Simple,GRCh37.fa,N13532.TwoDels1InsStringBoundError.bam,chr11,1280138,1280341,-f 0.0025 -F 0x700 -Q 10 | ||
N13532.TwoDels1InsStringBoundError testbed 11 1280291 1280344 GGTGAGACCCGAGGCACCTGCCCCCAGGTGAGCCCCCGAGGCACCTGCCCCCAA G 3733 39 1693 1990 0 39 G/-53 0.0104 2;1 48.6 1 34.3 1 48.5 78.000 0.0112 0 31 2.000 1 3.6 39 3488 AACAATACTACCTGTCCCCA GTGAGACCCGAGGCACCTGC 11:1280139-1280341 Deletion 0 0 | ||
N13532.TwoDels1InsStringBoundError testbed 11 1280301 1280301 G A 3708 33 1606 2012 11 22 G/A 0.0089 2;2 49.1 1 37.1 1 58.1 10.000 0.0088 0 0 1.000 1 1.8 30 3409 CCTGTCCCCAGGTGAGACCC AGGCACCTGCCCCCAGGTGA 11:1280139-1280341 SNV 0 0 |