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Commit 26fc1d8

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PolinaBevadPolinaBevad
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Added test case for duplicate reads (#131 test).
1 parent 2123a72 commit 26fc1d8

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‎src/test/resources/com/astrazeneca/vardict/integrationtests/NA21144.chrom11.Duplicates.bam‎

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‎src/test/resources/com/astrazeneca/vardict/integrationtests/NA21144.chrom11.Duplicates.bam.bai‎

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‎testdata/fastas/hs37d5.fa.csv‎

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11,401000,413000,CGCTCACCCCGGACCCCGCTCACACCCGCCCCGCTCACACCCGGCCCCGCTCACCCCCGCCCCGCTCACCCCCGGCCCGCTCACACCCGGCCCCGCTCACACCCGGCCCCGCTCACACCCGCCCCGCTCACCCCCGGCCCCGCTCACACCTGCCCCGCTCACACCCGGCCCCGCTCACACCCGGCCCCGCTCACACCCGGCCCGCTCACACCCGCCCCGCTCACCCCCGGCCCCGCTCACACCCGGCCCCGTTCACACCCGCCCCGCTCACACCCGCCCCGCTCACCCCCGGCCCGCTCACACCCGCCCCGCTCACCCCCGGCCCGCTCACACCCGGCCCCGCTCACACCCGGCCCCGCTCACACCCGCCCCGCTCACCCCCGGCCCCGCTCACACCCGCCCCGCTCACACCCGGCCCCGCTCACACCCGGCCCGCTCACACCCGCCCCGCTCACACCCGCCCCGCTCACACCCGCCCCGCTCACCCCCGGCCCCGCTCACCCCCGGCCCCGTTCACACCCGCCCCGCTCACACCCGCCCCGCTCACCCCCGGCCCGCTCACCCCCGGCCCCGCTCACACCCGGCCCCGCTCACACCCGCCCCGCTCACACCCGGCCCCGCTCACACCCGGCCCCGCTCACACCCGGCCCCGCTCACACCCGCCCCGCTCACCCCCGCCCCGCTCACCCCCGGCCCCGCTCACCCCCGGCCCCGCTCACCCCCGACCCCGCTCACCCCCGACCCCGCTCACCCCCGCCCCGCTCACCCCCGCCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGGCTCCACTGACCCCGGCCCCGCTCACCCCGGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGGCTCCACTGACCCCGGCCCCGCTCACCCCGGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGGCTCCACTGACCCCGGCCCCGCTCACCCCGGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGGCTCCACTGACCCCGGCCCCGCTCACCCCGGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGGCTCCACTGACCCCGGCCCCGCTCACCCCGACCCCGCTCACCCCAGACCCCCGGCCCCGCTCACCCCCGGCTCCACTGACCCCGGCCCCGCTCACCCCGGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGGCTCCACTGACCCCGGCCCCGCTCACCCCGGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGGCTCCACTGACCCCGGCCCCGCTCACCCCGGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGGCTCCACTGACCCCGGCCCCGCTCACCCCGGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGGCTCCACTGACCCCGGCCCCGCTCACCCCGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGGCCCCGCTCACCCCGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGACCCGCTCACCCCGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGACCCGCTCACCCCGACCCCGCTCACCCCCGCCCCGCTCACCCCTGCCCCGCTCACCCCGGGCCCCGCTCACCCCCGGCCCCGCTCACCCCGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGGCCCCGCTCACCCCCGCCCCGCTCACCCCCGCCCCGCTCACCCCGGGACCCGCTCACCCCGACCCCGCTCACCCCGGACCCCGCTCACCCCCGCCCCGCTCACCCCGGACCCCGCTCACCCCCGACCCCCGGCCCCGCTCACCCCCGCCCCGCTCACCCCGGACCCCGCTCACCCCCGCCCCACTCACACCCGACCCGCTCACCCCGACCCGCTCACCCCGACCCGCTCACCCCGACCCCGCCGACTCCTCCCCGCCCTGCGCAGCTGCCCCTCGCCGCCGATGCGCTCACCTTCGCGGAGGTGTCCAAGGACCCCAAGGGCCTCGAGTGGCTGTGGAGCCCCCAGATCGTGGGGCTGTACAACCGGCTGCTGCAGCGCTGCGAGCTCAACCGGCACACGACGGAGGCGGCCGCCGGGGCGCTGCAGAACATCACGGCAGGCGACCGCAGGGTGGGGCACCCAACCCAGACCCGAGGGGGTCCCAGGGGTTCATGCGGTTGAGGGGGGGACAGAGGAGGGAGAGGGAGGGGAGGAGGAAGGGGACGCCCAGGGTCCGCGGAGCCTCGGAGGTCAGCGTCCCGGTGGCGCAGGCCTTGGGCCTTGGGAGGATGGAAGTCCTGCCCTGGGTTTGAAGGGAGGCACCTGATCCGGGCTGCGGCTGATTCCCCCCGGCTGGGGGGCAAAGGCAGAAGCAGAGGCCCCCCTGAGGGTGGCGAGAGGATGCAGCGACCCCATTGTGGCAGGACCCCCTCAGGTGAGGGTCTGAGGCCTCCGGGTCACGGCTCACACCCTCCCTCCCCACAGTGGGCGGGGGTGCTGAGCCGCCTGGCCCTGGAGCAGGAGCGTATTCTGAACCCCCTGCTAGACCGTGTCAGGACCGCCGACCACCACCAGCTGCGCTCACTGACTGGCCTCATCCGAAACCTGTCTCGGAACGCTAGGAACAAGGACGAGATGTGTGAGTCGGGCAGCCCCTCGTCCCTGCCCTGCTGGACCCACATGTCAATTTTGTCTTTAAGTGTGGGCTTCAGACCACTGGGGCCAGTCCAGCTCCCTGGGGGAGGCAGGGGACCCCAGGTGCCCAGGTGGCCAGGAGTAGGGGTGCAGACTGACCCCCGGCCTCCCACAGCCACGAAGGTGGTGAGCCACCTGATCGAGAAGCTGCCGGGCAGCGTGGGTGAGAAGTCGCCCCCAGCCGAGGTGCTGGTCAACATCATAGCTGTGCTCAACAACCTGGTGGTGGCCAGCCCCATCGCTGCCCGAGACCTGCTGTATTTTGACGGACTCCGAAAGCTCATCTTCATCAAGAAGAAGCGGGACAGGTAGGGGCCGACCCAGCCGTGCAGCAGCCTGGTCAGGGGTCCTCCCAGTCCACCCTGCTTTCTGGCTGTGTGTCCCCTCCTGACTGCCCTCCACCCTCAGCCCCGACAGTGAGAAGTCCTCCCGGGCAGCATCCAGCCTCCTGGCCAACCTGTGGCAGTACAACAAGCTCCACCGTGACTTCCGGGCGGTACGTTTCCCGAGCCCAGGGCAAGCAGGGACCCGGGTGCAGGGCATGGGACGCCGGGGGAGGGTCAGTGAAGAGGCCCATGGGAGGATGGAGACCAGGGACCCAGAGAGGAAGGGTCCGGGCCACACCCAGCACACTGCAGGAGGGACAGCGGGCAGAGGGCCACATGGGCAGACATGCACCCTGACCTTGGGCCTCTCTCCACTGTAGAAGGGCTATCGGAAGGAGGACTTCCTGGGCCCATAGGTGAAGCCTTCTGGAGGAGAAGGTGACGTGGCCCAGCGTCCAAGGGACAGACTCAGCTCCAGGCTGCTTGGCAGCCCAGCCTGGAGGAGAAGGCTAATGACGGAGGGGCCCCTCGCTGGGGCCCCTGTGTGCATCTTTGAGGGTCCTGGGCCACCAGGAGGGGCAGGGTCTTATAGCTGGGGACTTGGCTTCCGCAGGGCAGGGGGTGGGGCAGGGCTCAAGGCTGCTCTGGTGTATGGGGTGGTGACCCAGTCACATTGGCAGAGGTGGGGGTTGGCTGTGGCCTGGCAGTATCTTGGGATAGCCAGCACTGGGAATAAAGATGGCCATGAACAGTCACTGCCCTGTGTCCTTCCATGGCTGGCCCGACCCTGTGGCTGGCAGCATGATCCTGGGACTCAAGGTGTCCCCAGGCACCCCCTGCCCCTGAGGACACCCACCCCCTGGGCTCACACACAAGCCTCCCAAGATCAGAGGACATAGGACATGGAGAGCCCAGCAGAGGGACAGCTGGCACCTCAGGGCCGAGAGGGGACAGGGTGGACAGCGGGTGCACCACAGGCACAGACGGAGCAGAGCTGGGGGCCTCGAGAGTAGAGGGGTGACTGGAGTAGGAACAGGGTGGCTGCCTCGTGGGCTACACTCATGCGGCAAATGAACCCAACTCCTCCGCCGCCCACCCTGGGCCTGGAGTTGCCTGGACCAGGGGCTCTCACACTGGCTGCCTGAGGTTTGGGGTCCAGTGGGCTCTCGGACACCCCCATCCATCTCACCCAGAGCCAGGCCATTTAGTTGTGAAGTTACTGTGGATATTCTTAAAACAGAAAGTTTCTGTGAAGCTCAGAACTTGAGGTCTCTAAGGAGCCTGCCCCCATCCAGGATCTGCCTGCATGGGAAGGGTCTAGGAAGAGTCACGTCCCCAACCAGGGACCAGGCAAGGAGGCCCAAGGAGGCTACTGTAAGCACGGGACACGCCTGAGCTGGCTTAGGAAGGGGGATGGAGAGAGGGCAGATTTGGTGATTTGGCGGGTGGGGATGAGAGAGGGAGGGGTGGGGATGAGAGAGGAGGGGTGGAAGGCTGAGAGAGCCGCAGAGGGAAGCCGAATCCGAAACCTTCCGCCGCAAGGGAGGAGACCGAGGCCCCAGCAGAATCCAAAAGGACTTTATTTTCTGGCACTGGGAGGCGCCCTGAGGCCACAGCCTTTTCCCAGGGCTGCTGGCAGGGTCCCAGGGCTGCTGGCAGGGGTTGTGGTCCTGTTGAGCAGAGGAGCGACGCCGCTGCCCTGGCCCCCGCTGTCCCTATGATCCTGCACTCTGGGGTGGGAGCTACATATCATCCTTGGACACCAGGCAGTAGAAGTCTGTGCGGGCACTGTAGTTTCGCGAGCCGAGATCCGAGACGTCCACTTCGCTGCTCCGGCTCTCTCCCAGCGAGACCCCACTGGTGTGCGGTGGAGCTGATGGCTCTCCAAAGACAGGCCCCCGGACACCTGGGGTGGGGAGACCGAGACGCCTGAGGTGGCCACCCACAGCCTTGGCCCAGACCCACTGCCAGGGGCTGCCCCTGCTCACCCCCTGCTGTGATGGCCTGTGAGGCCCAGGAAGTTCCCAGGCAGACCGAGGGCCGAGCACCTCCAGGGCAGAGGCCGTGCAGGGGCTCCCGGTGCCGGGAAGAGTCCTCAACACCTGGAGCCCCTCCAGGCCCTGTGCCCTGTGCCTGCCCCCACTCCGCCCTGTGCTGAGCTTCTCCAGTTGGGGAGTGGGGCTGGGCGGGCATACCCAGGTCGCCCTCAGGGTCCGGGTCCACCTCTGAGTCCAGGGCCCGGCCCTCAGGGACTCGGCCTCGAAGAATCAGCATGGGGTCCTTGTCGTCCTGCAGCTGCGTCTGGGGGTCTCCTTCCACAGGCCTGTACTGCACCTTCCGCGGCAGCGCCAGCTGCACTTCTTTCCAAAAATCGGAGGAAGGAGTCTGGGGGCCAGGTCGGGGCGGTTTGCAGGTGTGAACACCTCGGAAGCCCCTGGCGTCCTGGCCCCCAAGAGCACACCTGCGGCTGCCCACGGGTTCCACGCCCTGCGACAGCTATTCCGTGGCTCCGGGGGCCTCAAGGGCGGCTCCCCGCATCGGGGCCCCAGGCAGCGGAACCTCCCCCCAGGGCCCATTCACAAAGCGTGGTGCCGCAGAGCTCCCCACGGAGGGGTCCCAGCCTGGAGCCCGGGCACCGCCCATCTCTAACCCGCCGCTAGCCCCGGACCCTCCCGCGCCTGCTCCGCACCACGGAGCCGGGCCTCCAGAGCAGCAAGGTCACCAGGTGGCGGTGCTGGCGCAGCAGGCGGAGCGCCGGGTGCGCGGGGTCGCGCCTCTGGCCCTCGAAGGTGATGAAGATGGGTCTGCGGGTGAGCTCCAGCAGCCGGCACAGGCCCTCCCTGCGGGGCGGGACCGTCAGGGGGGTGGGTGCTACGCTGGGGCCCACCCAACCCCGCGCGGGACCCACCGGAAGCTGTGGCTGCACCAGGCCCGGCTCAGGAAGGCGTCCGAAAGCACCACGATGAGGCGTCGGCAGCGGCTCAGGTTCACCAAGAGGTCGGCGGAGGGCTCTGCGGGAGGGCGGGCGTCGGCGGCGCAGGGGCGGGGGCGGGGGAGGGCGGGGCCGGAGGCTCAGGGGCGGTGCCGGACGCAGAGCTCTAAGGGAGGGGCGGGGCCTGCGGGGTGGGCGGGTTTTTGAGGCGGGGCCTCGGGTGGGCGGGGATGGGGGCGGAGCTCGATGGTGGGGGTGGGGCCCCGGGTGGGACGGAGCATGGGGCGGGGCGGGGCGGGCCCTCCGGGTGGGCGGGGCACGGGGTGGGGCCCGGGATACCAGCGCGCGGCAGGAGGTCGCGGTCGTCCAGGAAGAGCTTGTAGCCCCGACGCCGCTCCAGCTGCGGCTTTAGGATGAAGTTCACGAACTTGCGGTCCTCGGGGCAGTCGCTGTAGGAGACGTAGGCGTCGTAGAGCTTCCCGTCTGCGGACGGCGGCCAGTCACCCCGATGGCTCCCGAGGCCTCACACCAGCCCTCGGGGTCCCCAACACCCCTAACCATCTCCCACGTGCACAGGGGCAGACCCGCCCCGGACTTTAACCCCAGCCGGGCCGCACAGAGCACCCGGGGGCTAACCCCTCCCCGCCGCACGCCTCCAAAGCCGAGCTCAGCAGCGCACTCTCAGGGAGGCCGTGGCGACCCCTCCTCGCGCCCACGCGGGCCCCACGCACCGTTTATCTCCACCTCCCCATACGCGTCCTGGTACCAGAGCAGCACGTTGAGACGGCACTTGACATAGAGCAGGGCGGCCAGCAGCAGGGCCAGCAGGACCAGGAGGGAGGCCAGCACCGCAGCCACGTGGCTTGTAGGGCCTGCGGATGGGTTGCCTGAGCCGCTGCCCCTCCAGCAGCCCCCAAGCCTCAAGATCCCTGGGCCTCACTAGGTCTAGGTCCCCTTCTACCCTCCACCTTGGGGAACCCCCATCACCAGCTCTCTGAAGAGTGAAGGAGGAGAAGCTGATGTTCTGGATGGAGCAGGTGAAGGCCCCATAGACTTCAGTGCTGGTCACGTTGACCCCCAGGACACTGGACACAAGCACCTCTGACAGGTTGGCCTTGACCCTGGGGATACCAAGCCAGGGTCAGGGTCGACTGGGGATACCAGTGGACACCCCCGAACCCCACCTGTCTGGGTTCACCCAGGGAGGCTGCAGAATTGGGCCTCCTGGGTGGTTCTTGGGCCTTAAGCCAAGAGAAGTGACCTGAACCTGGAGGGGATGCAGATTTGTTTCAGAACAGCCGTCCCAGTCCTGGGTCTGGGGCCTGGAGGTCCTTTGATCACAGACTTGGCCAGCTGGTCGGTGTTCATTCAGACCCTAGACTTTGCTGACACCCGTAGCCCTGGGCAGTTACGAGGTGTGTGCCTACAGGGGCCATGCAGACCCAAGGGTCTGTCCCTGACATTACTGACCCTCCGTCTGGGTCCACAGAGGCACTCTGCTCGTGACATGTCTGGCCAGGTGGTTACAGACCCAGGCATAGGTCAGGGAGACCACTGCCCTTGGCATGTCTGAGAGGTCACTCTGACCCTGGATACCCGGGTCTCTTACCAGGAGTACTCGTGGAGGCTGTAGTGGCCCCCAATTCCCAATGGAAGCCCGTCTTTCAGCCACTGGACTGAAGGCAGGGAGCAGTGGGGCCCAGAGACTACCCAAGCCGTGCAGTTCAGAGCCACTGAGCTGCCCAAGGCAGGCCTCAGCACCTGGTCTTCAGACGGGGAGAGGAAGTCAGGGGCCCTATCACAGACACCTGAAGAGAGAGGACACAGTGGGTCAGCTGTGCCAGGGTGCCTGGCCCCACCACCTCCACAGTGGTCCGTGGTGCAGGAAGAAATAAGGCCTCTGTGTGGCTTGGCAGTCACACCATGTCTGTCCACGAGTCCCATGGGGACAGGCTTAGCACTTGGCACGTCTTTCCCCAGTAGTGGCCAGGCTTTGGGTGTTCCGCCCACCCTGTGCTGAGGGGACAGAGAGCAGTGGCCACAGTTGAGCTGCCCCAGGCCCACGCTCAAGCCCCATCTGGCTGCTTGTCCACCCAGGATGTGAGTCCAGCCCCCCATTTCCCAGATGCACCTGTTGCCCACCCCTGGTGACACCATGATGCCTGTCTCATAGGAGGGGCCGGGCACTGCACCCCTCAGCCTGGCCTGCCTCTGCTGGGGAATCTGCAGAGAGTGTGGGCACCAGTGGGTTTGGGGACCCAGATGCCCAGTGTGCCAGCACCTTCCACCTGGATGGGCACAGCTGGGAGCCTGGAGCAGTTGGCCTCATTCCTGCCTTGGGGGTCTTGGGGCCCTCTGCTCCTGGCCACAGGCAAGCCCTCCCCACCACCTGAGGCCTGAACTTGTTCATCTTTACATCAGGGTGATGAGCCCTAGCGGGAGGTCAAACCACCATCTTCTCAGTAGGGTATGGTCTCCTGCCAGCTCACATCGGCCACACCCTGCTGTGGGCCCCAGCAGTGCCCACTCCTAGCATTCCTGGGCTTTACTGACCCTCATGAGCCTGGTCTGGGGCAGGAGAGGGTGCAGGGCTCATCCTCACCACTCGCCCTGGTTTCAGGGCCAAGGGCCCAGTGGGAGGGGTGAGCAGGGGCCTTTGTACCCCCGGCATGTGGCCAGGCAGAGTGCCTGGGATAAGAGCAGGATGCACAATGTGGAGCCAGCCTGAGGGGCAGGAGGTGGGAGTGGGGAATTCAAGCCCATCCCTCTCTGACCTGCCTACCTGGCATGGCTCTGAGCCGGGGCCTCCTCGGGGCAGGCTGGGCTCCAGGGTCACCCCTGGCTCCACCGGGCTCCTCGGCCAGCAGACTGATCCAAGAGCTGGGCAGGACTCCTCTCTGTCCTTGCAGTCAGCTGGACAGGGCACCTGGACAGGTCAGAGGCTGCCGCCATCCCCAGGGAACAAGTTAAACAGGAACAGGATGAGTTAACCAGTAACTGCCGGCCACAGACAGCACTGGCCCTGACCAGATGCGACCCTGAGCAGCCGCATGGATGCTGGCAGAGTTCTCGGAGGCCAGCAGGGTGTCTCTTTGAGCCCCTCACACGTGGCCAGAATGGGCACCACTTCACGCAGCCCAGGACCACGGGGAGGGGCCATCAAGTCCAGGATCACCTCCACCGGCCCTGGGGCCACCATGACGGCCCCAGGGTGCAGTGGACGAACACTAGGTGGGACCCTGTCTCCCGACATGGCAGTTGGCCTCACTCCTGGCTGTCCCCTTCAACAGAGCTGCCACTGCAGGGGGTGCTGCAGTGCCAGAGACACAGCCTGGCCTTGGGGCAGGGGTGTGAGTGATGTAACCTACACCATGGGAGATGCCCAGCTCTGACCATGTCTGGATACAGTCGGTGGGGGGTGCTCAGCTCTGACCATGTCTGGATGCAGTTGGGGTGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGCGGGGGGCTTTGCTTAGCTCTGACCATGTCTGGATGCAGTCGGGGGGGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGCCGGGGGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCAGGGAGGGGGTTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGGGGGGTGCCCAGCTCTGAACATGTCTGGATGCAGTCGGGGAGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGCGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGAGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGCGGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGAGGGGGGTGCCCAGCTCTGACCATGTCTGAATGCAGTCGGGGAGGGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGCGGGGGGGGTGCTCAGCTCTGACCATGTCTGGATGCAGTCGGGGAGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGGGGGGGGTGCCCAGCTCTGAACATGTCTGGATACAGTCGGGGAGGGGTGCTCAGCTCTGACCATGTCTGGATACAGTCGGGGGGGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGAGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGCGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGAGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGAGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGAGGGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGAGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGCGGGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGTGGGGGTTGCCCAGCTCTGACCATGTCTGGATACAGTCGGTGGGGGGGGGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGAGGGGTGCTCAGCTCTGACCATGTCTGGATGCAGTCGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGCGGGGGGGGGGCTCAGCTCTGACCATGTCTGGATACAGTCGGGGAGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGGGGGGGGGTGCTCAGCTCTGACCATGTCTGGATGCAGTCGGGGAGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTGGGGGGGGGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGGAGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGGGAGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGAGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGGGGGGGTGCCCAACTCTGACCATGTCTGGATGCAGTCGGCGGGGGTGCCCAGCTCTGACCATGTCTGAATGCAGTCGGGGAGGGGGGTGCCCAGCTCTGACCATGTCTGGATGCAGTCGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGCGGGGGGGGGTGCTCAGCTCTGACCATGTCTGGATGCAGTCGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGGGGGGTGCCCAGCTCTGACCATGTCTGGATACAGTCGGGGGGGGGTGCCCAGCTCTGAACATGTCTGGATACAGTCGGGGGGGGGTGCCCAGCTCTGAACATGTCTGGATACAGTCGGGGAGGGGTGCTCAGCTCTGACCATGTCTGGATACAGTCGGGGGGGGGGGGTGCCCAGCTCTAACCATGTCTGGATGCAGTCGAGGGGGGGTGCCCAGCTCTGGCCCACGTCTGGTTACAGTCAGGAGTGCACGTGAGCACAGACACCTCGAAACACCTCGGGAAACACCTCGGGAACCCTCAGCTTAGCCTCGCCCTGCGGTTGTGAGGCCGGAGGGTGAACAGCGCCCGGTGGGGATGGAGGTCTCGGGTCCCATGTCCTTTCCCAGCCCGTAGCAGCAGCCACACACACCTCAAGTCTCCCAAAGCTCCTCAGTGAGGTGGCTGCAGGGAGAAGCCCAGAGCCTCTTCCTTGGC

‎testdata/integrationtestcases/Simple;hs37d5.fa;NA21144.chrom11.Duplicates.bam;11;402283-410793;-F 0;.txt‎

Lines changed: 18 additions & 0 deletions
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1+
Simple,hs37d5.fa,NA21144.chrom11.Duplicates.bam,chr11,402283,410793, -F 0
2+
NA21144.chrom11.Duplicates testbed 11 403484 403484 G C 6 4 1 1 4 0 G/C 0.6667 2;0 15.0 1 36.8 1 60.0 8.000 0.6667 0 0 2.000 1 1.2 4 6 GGCTGCGGCTGATTCCCCCC GCTGGGGGGCAAAGGCAGAA 11:402284-410793 SNV 0 0
3+
NA21144.chrom11.Duplicates testbed 11 406043 406043 G A 7 7 0 0 5 2 A/A 1.0000 0;2 30.4 1 34.6 1 60.0 6.000 1.0000 0 0 1.000 1 1.3 6 6 GGAGCTGATGGCTCTCCAAA ACAGGCCCCCGGACACCTGG 11:402284-410793 SNV 0 0
4+
NA21144.chrom11.Duplicates testbed 11 406615 406615 C T 6 4 0 2 2 2 C/T 0.6667 0;2 21.0 1 39.0 1 60.0 8.000 0.8000 0 0 1.000 1 1.0 4 5 CCTGGCCCCCAAGAGCACAC TGCGGCTGCCCACGGGTTCC 11:402284-410793 SNV 0 0
5+
NA21144.chrom11.Duplicates testbed 11 403545 403545 C T 7 3 4 0 2 1 C/T 0.4286 0;2 12.0 1 36.0 1 60.0 6.000 0.5000 0 0 4.000 1 1.7 3 6 GGCGAGAGGATGCAGCGACC CATTGTGGCAGGACCCCCTC 11:402284-410793 SNV 0 0
6+
NA21144.chrom11.Duplicates testbed 11 409720 409720 T G 9 9 0 0 4 5 G/G 1.0000 0;2 23.6 1 34.1 1 56.6 18.000 1.0000 0 0 3.000 1 1.1 9 9 TTTCAGGGCCAAGGGCCCAG GGGAGGGGTGAGCAGGGGCC 11:402284-410793 SNV 0 0
7+
NA21144.chrom11.Duplicates testbed 11 407708 407708 A C 6 6 0 0 6 0 C/C 1.0000 0;0 21.7 1 33.5 1 60.0 5.000 1.0000 0 0 3.000 1 1.0 5 5 CCAGCCGGGCCGCACAGAGC CCCGGGGGCTAACCCCTCCC 11:402284-410793 SNV 0 0
8+
NA21144.chrom11.Duplicates testbed 11 409815 409815 G A 15 6 6 3 3 3 G/A 0.4000 2;2 35.5 1 37.5 1 60.0 12.000 0.4286 0 6 4.000 1 -3.3 6 14 CAATGTGGAGCCAGCCTGAG GGCAGGAGGTGGGAGTGGGG 11:402284-410793 SNV 0 0
9+
NA21144.chrom11.Duplicates testbed 11 408352 408352 C A 6 5 1 0 1 4 C/A 0.8333 0;2 17.8 1 38.4 1 60.0 10.000 0.8333 0 3 2.000 1 1.0 5 6 GCCAAGAGAAGTGACCTGAA CTGGAGGGGATGCAGATTTG 11:402284-410793 SNV 0 0
10+
NA21144.chrom11.Duplicates testbed 11 409385 409385 C G 10 9 0 0 4 5 G/G 0.9000 0;2 17.2 1 37.9 1 60.0 18.000 1.0000 0 1 2.000 2 1.0 9 9 ACCTTCCACCTGGATGGGCA AGCTGGGAGCCTGGAGCAGT 11:402284-410793 SNV 0 0
11+
NA21144.chrom11.Duplicates testbed 11 410462 410462 A G 7 7 0 0 2 5 G/G 1.0000 0;2 21.0 1 36.7 1 53.4 14.000 1.0000 0 0 1.000 1 1.1 7 7 GATGTAACCTACACCATGGG GATGCCCAGCTCTGACCATG 11:402284-410793 SNV 0 0
12+
NA21144.chrom11.Duplicates testbed 11 404317 404317 C T 7 4 1 2 2 2 C/T 0.5714 2;2 24.5 1 33.2 1 60.0 3.000 0.5000 0 1 2.000 1 1.5 3 6 AACAAGCTCCACCGTGACTT CGGGCGGTACGTTTCCCGAG 11:402284-410793 SNV 0 0
13+
NA21144.chrom11.Duplicates testbed 11 403880 403880 G C 8 3 2 3 2 1 G/C 0.3750 2;2 24.3 1 29.7 1 60.0 2.000 0.2857 0 0 4.000 1 2.0 2 7 CCAGCTCCCTGGGGGAGGCA GGGACCCCAGGTGCCCAGGT 11:402284-410793 SNV 0 0
14+
NA21144.chrom11.Duplicates testbed 11 406473 406473 A C 10 10 0 0 6 4 C/C 1.0000 0;2 24.3 1 32.5 1 56.9 9.000 1.0000 0 0 2.000 1 2.8 9 9 GTCTGGGGGTCTCCTTCCAC GGCCTGTACTGCACCTTCCG 11:402284-410793 SNV 0 0
15+
NA21144.chrom11.Duplicates testbed 11 406483 406483 T C 10 10 0 0 6 4 C/C 1.0000 0;2 26.1 1 33.4 1 57.7 20.000 1.0000 0 0 1.000 1 2.5 10 10 CTCCTTCCACAGGCCTGTAC GCACCTTCCGCGGCAGCGCC 11:402284-410793 SNV 0 0
16+
NA21144.chrom11.Duplicates testbed 11 403939 403939 A G 8 8 0 0 4 4 G/G 1.0000 0;2 21.9 1 28.8 1 56.1 7.000 1.0000 0 0 1.000 1 2.1 7 7 AGACTGACCCCCGGCCTCCC CAGCCACGAAGGTGGTGAGC 11:402284-410793 SNV 0 0
17+
NA21144.chrom11.Duplicates testbed 11 404468 404468 G A 5 4 1 0 2 2 G/A 0.8000 0;2 39.0 1 37.8 1 60.0 8.000 0.8000 0 1 3.000 1 1.2 4 5 ACACCCAGCACACTGCAGGA GGACAGCGGGCAGAGGGCCA 11:402284-410793 SNV 0 0
18+
NA21144.chrom11.Duplicates testbed 11 409592 409592 G A 12 2 4 6 1 1 G/A 0.1667 2;2 29.5 1 36.0 1 60.0 4.000 0.1667 0 0 1.000 1 1.0 2 12 CACATCGGCCACACCCTGCT TGGGCCCCAGCAGTGCCCAC 11:402284-410793 SNV 0 0

‎testdata/integrationtestcases/Simple;hs37d5.fa;NA21144.chrom11.Duplicates.bam;11;402283-410793;.txt‎

Lines changed: 18 additions & 0 deletions
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@@ -0,0 +1,18 @@
1+
Simple,hs37d5.fa,NA21144.chrom11.Duplicates.bam,chr11,402283,410793
2+
NA21144.chrom11.Duplicates testbed 11 403484 403484 G C 6 4 1 1 4 0 G/C 0.6667 2;0 15.0 1 36.8 1 60.0 8.000 0.6667 0 0 2.000 1 1.2 4 6 GGCTGCGGCTGATTCCCCCC GCTGGGGGGCAAAGGCAGAA 11:402284-410793 SNV 0 0
3+
NA21144.chrom11.Duplicates testbed 11 406043 406043 G A 7 7 0 0 5 2 A/A 1.0000 0;2 30.4 1 34.6 1 60.0 6.000 1.0000 0 0 1.000 1 1.3 6 6 GGAGCTGATGGCTCTCCAAA ACAGGCCCCCGGACACCTGG 11:402284-410793 SNV 0 0
4+
NA21144.chrom11.Duplicates testbed 11 406615 406615 C T 6 4 0 2 2 2 C/T 0.6667 0;2 21.0 1 39.0 1 60.0 8.000 0.8000 0 0 1.000 1 1.0 4 5 CCTGGCCCCCAAGAGCACAC TGCGGCTGCCCACGGGTTCC 11:402284-410793 SNV 0 0
5+
NA21144.chrom11.Duplicates testbed 11 403545 403545 C T 7 3 4 0 2 1 C/T 0.4286 0;2 12.0 1 36.0 1 60.0 6.000 0.5000 0 0 4.000 1 1.7 3 6 GGCGAGAGGATGCAGCGACC CATTGTGGCAGGACCCCCTC 11:402284-410793 SNV 0 0
6+
NA21144.chrom11.Duplicates testbed 11 409720 409720 T G 9 9 0 0 4 5 G/G 1.0000 0;2 23.6 1 34.1 1 56.6 18.000 1.0000 0 0 3.000 1 1.1 9 9 TTTCAGGGCCAAGGGCCCAG GGGAGGGGTGAGCAGGGGCC 11:402284-410793 SNV 0 0
7+
NA21144.chrom11.Duplicates testbed 11 407708 407708 A C 6 6 0 0 6 0 C/C 1.0000 0;0 21.7 1 33.5 1 60.0 5.000 1.0000 0 0 3.000 1 1.0 5 5 CCAGCCGGGCCGCACAGAGC CCCGGGGGCTAACCCCTCCC 11:402284-410793 SNV 0 0
8+
NA21144.chrom11.Duplicates testbed 11 409815 409815 G A 15 6 6 3 3 3 G/A 0.4000 2;2 35.5 1 37.5 1 60.0 12.000 0.4286 0 6 4.000 1 -3.3 6 14 CAATGTGGAGCCAGCCTGAG GGCAGGAGGTGGGAGTGGGG 11:402284-410793 SNV 0 0
9+
NA21144.chrom11.Duplicates testbed 11 408352 408352 C A 6 5 1 0 1 4 C/A 0.8333 0;2 17.8 1 38.4 1 60.0 10.000 0.8333 0 3 2.000 1 1.0 5 6 GCCAAGAGAAGTGACCTGAA CTGGAGGGGATGCAGATTTG 11:402284-410793 SNV 0 0
10+
NA21144.chrom11.Duplicates testbed 11 409385 409385 C G 10 9 0 0 4 5 G/G 0.9000 0;2 17.2 1 37.9 1 60.0 18.000 1.0000 0 1 2.000 2 1.0 9 9 ACCTTCCACCTGGATGGGCA AGCTGGGAGCCTGGAGCAGT 11:402284-410793 SNV 0 0
11+
NA21144.chrom11.Duplicates testbed 11 410462 410462 A G 7 7 0 0 2 5 G/G 1.0000 0;2 21.0 1 36.7 1 53.4 14.000 1.0000 0 0 1.000 1 1.1 7 7 GATGTAACCTACACCATGGG GATGCCCAGCTCTGACCATG 11:402284-410793 SNV 0 0
12+
NA21144.chrom11.Duplicates testbed 11 404317 404317 C T 7 4 1 2 2 2 C/T 0.5714 2;2 24.5 1 33.2 1 60.0 3.000 0.5000 0 1 2.000 1 1.5 3 6 AACAAGCTCCACCGTGACTT CGGGCGGTACGTTTCCCGAG 11:402284-410793 SNV 0 0
13+
NA21144.chrom11.Duplicates testbed 11 403880 403880 G C 8 3 2 3 2 1 G/C 0.3750 2;2 24.3 1 29.7 1 60.0 2.000 0.2857 0 0 4.000 1 2.0 2 7 CCAGCTCCCTGGGGGAGGCA GGGACCCCAGGTGCCCAGGT 11:402284-410793 SNV 0 0
14+
NA21144.chrom11.Duplicates testbed 11 406473 406473 A C 10 10 0 0 6 4 C/C 1.0000 0;2 24.3 1 32.5 1 56.9 9.000 1.0000 0 0 2.000 1 2.8 9 9 GTCTGGGGGTCTCCTTCCAC GGCCTGTACTGCACCTTCCG 11:402284-410793 SNV 0 0
15+
NA21144.chrom11.Duplicates testbed 11 406483 406483 T C 10 10 0 0 6 4 C/C 1.0000 0;2 26.1 1 33.4 1 57.7 20.000 1.0000 0 0 1.000 1 2.5 10 10 CTCCTTCCACAGGCCTGTAC GCACCTTCCGCGGCAGCGCC 11:402284-410793 SNV 0 0
16+
NA21144.chrom11.Duplicates testbed 11 403939 403939 A G 8 8 0 0 4 4 G/G 1.0000 0;2 21.9 1 28.8 1 56.1 7.000 1.0000 0 0 1.000 1 2.1 7 7 AGACTGACCCCCGGCCTCCC CAGCCACGAAGGTGGTGAGC 11:402284-410793 SNV 0 0
17+
NA21144.chrom11.Duplicates testbed 11 404468 404468 G A 5 4 1 0 2 2 G/A 0.8000 0;2 39.0 1 37.8 1 60.0 8.000 0.8000 0 1 3.000 1 1.2 4 5 ACACCCAGCACACTGCAGGA GGACAGCGGGCAGAGGGCCA 11:402284-410793 SNV 0 0
18+
NA21144.chrom11.Duplicates testbed 11 409592 409592 G A 11 2 4 5 1 1 G/A 0.1818 2;2 29.5 1 36.0 1 60.0 4.000 0.1818 0 0 1.000 1 1.0 2 11 CACATCGGCCACACCCTGCT TGGGCCCCAGCAGTGCCCAC 11:402284-410793 SNV 0 0

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