Commit f4144949 authored by Sander Bollen's avatar Sander Bollen
Browse files

Adding MergeAllelesTest and dependencies

parent a91aa4a6
@HD VN:1.4 SO:unsorted
@SQ SN:chrQ LN:16571 M5:94445ec460a68206ae9781f71697d3db UR:file:/home/ahbbollen/fake_chrQ.fa
>chrQ
TCGGCATCTAGAAACTCCAAGTCTGCAGATCTATAACACACGAGGGTATTCAGCCCTAAAGCATTGCGTCTAGGCATGGGTCTTTAATCTCGCCCCGGCAACCTCTACGCGAGCTCCTACCAGTCAACGTGATTGATCCCTCGTACCTAGCATATTCCACGGCGTTTCATAGCCTTGACGGGCACCTTATCCATTTTTACCTAGTTTGACATTAATTGCTTCAAGACTACTGCGGTACGGGTCCCTGCATCCAGAAAGGATGACAAAAAGTGTGACAGTGCGTTCAATCCATAGATTCCCGTCGGTGCGAGGGCTGAAGTTGAGCCCTACAACCCGGCGATAAAAATTGTAACCCTATGCATTGCGTCAAGTTAAGACCCTCCATCTTCGCCACGCGATAGGAATTTGAAACATCGGCGTGCTTAGAAAGGCTATTAGCGCGGGTGGCCTGATCGGTATCCGATAAAGGCGTTGCCACAAATTTTGCCGATTGACCTGCAATTACATCGGGTAAGTGCATTTCCGCCGTTAGAGTATTAAGTCATGACGTTTTCGACATGGGCATTTAATTGGCCCAAGGTGGAATATTCCTGATGTGCCTAAGTATGAGCTCCCCATGAGAATTTGAAGATCATGAAGACTTGAGTCAATTCTAAATGTAGTTACCATCACTTAAGTTCGTTCGCCTTCTGGGCAGGCTATGTCTAACGAGCGACGTCCGCAGTGTGACAATCTAGATATTGGTTGAGCAGGAATACCAAGGAGGTGCTTGAAGTTTCTCTTATGGAACCAACTTCAATCAATAGGTAGTCTCCGTTTCGTTTCCACTGAGACATTTGTGCAGTGGCACAGTATGTGGTCGTAAGCGCATGGTGTTGTTGGAACGAAGACTCTCACTTTTGTTTCCTTTGGTAGTTTAATTTAGCAGTATCCTGGTCGTTGACCAATTTGTGAATCTCCACGGTCTCTCTTTATCAGTCATACCTCTTAAACCGGCTTCCGCTCCTGCGCACATTTATATCCTACTTTCCGTCAATGTGAAAGAGAGATCAACATAATTTCGCGCACGATCTGTCCCATTTCAGACGCCATCGACGGGTCCCGCCTTCACAAAAAACCTGCCACCATGCAGTAGGTACCTCCATATGCTGAGCGTCCGTTACCGGAAGGGTTAAGTCACTGTTTAAAGGATAAGGCGAGGTTTCCCTTGGTGGTGTACTACTGCTCACGTTCCTGCTTTACTCTCCGAGTATTGTTTTAAAAGTGGGCACGCTGGAACGCAGCACCCTATAAGAAGACTCAGTTAGGTCCCCTTCACGAGCATGTTTGAGCTCTCGGACCTAAGACGTCCGAACTCGGTTACGACGGTTAAAGACAAAGCTCCCAGCATGGTATCAGAAGCCACCACGCGTGAGGATGGCGGGGCCCTGGGCACATTGGCCCCGAATTCTTCGCCCACTTAAGTCGGACTCACCACGGGAGACTACGCCCTAACCGGATAATATCTTTTAGATACCATACAGGGTGCAACCATCGCGGCGTCAGCTGAATGTGAGGACAGAGCCCCACACACAGCACTAACAGATCCATGATTTTACTTCGTTTGGGCGACGTGCGAGCCTATTCGGCCTGTCGGACTTTGTGTAGATTCGGGATTTGACCTAGCGTATAGGCCTTTGGTATACTCGAATTATCAGGGTCAAACTACCCTCAAGGAATCCTATTTCAGACGGACGTTTGCCACCCCGGAACGTTGTCGGATCGCTTCTTGCCGCAGGAGATTCATGGAGTGATAATCGCTGGACTCACAAGTGTCAGCGGACTTTCGGTGTCTTGTGGCCTACTTGCAGTGAACACCACCAAACGAGTAGTATTATGGATTGCCGGCGTGTGTTTGTGGCCATGATTGGTTGATGCGACGGCCTAGATTCTCCTACGGGAATCTACCAGGCCCAAAAGCGCTGACTTTTATGTATTTGAGGGGCCGAAATTACATAGTAACCCAGAACAAATACCCGTTAGTTATAAAGTGAGCGCATAAGTTTGGTCGATCCGGCAGTCGAACCATTGCGGTCGGACATATCCGCAGTAGTACACTAAGGCGGAATAGACTGCCGAGTCAACGCTCCCTCATTCTTGCTACCTTAGATCTCGCAGGTTCGACCATTGCTGAAGCCGCTGAATTACACGAGTTGTTTTGTTAACCCCCGGAATGTAGTTCGTACGCCTCAACTGATTCTTCAAAAGCTCACTGCACGTGACTTGTCATGTGTTCCTAAAACATACCTCATCTGTGGGTCTGGTCCCATAAGCATGGAATGTCCGTCGACGCAACATGGAAACCCACTCGCTCGCTATACGTTTATGGTGAGACAGAAACACACTGTATTAGACTGCCACTGATAGCCCCAGTAGCAAGGTGATGTGGCAGGCATGGTACCCAAACGTCTATCGTTTTGGGAACCAAGGGGAGTGCTAATAGGTCCGGCCACGTAGAATGACATAACCTCCAGAGGAGCGCAGGAGTTGATGCATTAAAAGATCCATACTAAACGTTAGCTTAATGCCTTCAAGGCACCAGCTACCTCCATGACAAGGAGATTTCGGAAGGGGTAAGATTTACTTCTGTCCCAAAAGGGTAATGACCCGTAGGGATGGAATCATTGATGAACTCTAAAGGGACTCAGCCGACTAGCCGAGAGGGCTGGACGATCATTTGATGGGAGAATACGCATACATCTAAGTGTCAAGTATTAAATCGGTAATCTCCGTAAAGGCGTGAAGTTCACAGGGCGCAGTTTCCAGTTACTCCAAGAAACTACCGGTTCAGTTATCGCTTCCGGTGCCTTCACAGCAAACATCATTCGCTCAAGAAAGTGCTGTCGCTGCGTGTGGATATTTCCCCCTCGTTCTGGAAAGTGCTCTCAGCGACGCACGTAAACATGCTGGCGACGAGAGAGGCGTCAACACGGTCCGTTACCAAACTGCGGCATTTACCACGAACCTGATTGCAAAGTGAGATTTCCGTAAGGAGGTTAGCCAAATATTACGTAGAGTGTTCCACACCAAATCCGTCGTCCACATTCGCGACGGCAGTCTAGACGTGTAATTCCCCGGATAATCCAGTTACTACATGCTGATGCAGTCATAGTGCACGCAAATGCGCAACTTAACAAGCACGACCTGAAACAGAGAACCCCTGTGTAGTCAATATAGGATGACGGACACACACACTTGCTGCTGCAATCTTACATTCTGCGAACGAGTGCAAAGTTGAAATCATGACGAACAGCCTTGCTTTTCAGAGTCTCTATCGAACTCCTTTACACCTCCATATCTACTTGCAAATCACACTAGAGGGGCGCAGCTTACTCACTGAGAGATGGTCTACCTAATCGATTTTCGGTGAACTTTGAGTACAGCATTGAGTCTGGAGGGTTCCACTACTTTATCGTACCGGTCCGACATGATTTCTTATCGAATAGATGTTGAGATGGACATTAATAAGCATAGTACGTCTCGATCGATGGCTACCTTTACGTCTATGAGTGCTTACATAAGGTCTCTCGTAAGTCATGGTCCCGCGGGGCTCGCGCAACATTGTGGATTAATGACTCCAGTGACGCATGTTCGATTCGCATGAAGTAGGTGGCGCGTATTCATACATGAATAGTAGGCAGAACGAGCACATTGGACCGATCTTGGAGGTTGGGCTTGAGGTCCCGCACTGATAGTTTACGGCCATGAAGACGACAATTGTCAATACTTCTCTATCCTGAGCGAATGCTGACGGGGGCCAGGCGGAAAAGTGCGACACAGTCTACTGATTACGTGTAGTACGTGGCTAAGCATATTCCCGGGTTCGCAAACATAGGTCTCTGATGGGGTATGGGTAAGAAATCTGAAGGTTGCGTCTCTCACCACGGTCAGGATACCGAATCAGCTCATAAGAGTTACAAACGCGCAAATGAAGGCCTAGTCCACAGGGGTGTCATTCGCACGAGCTGGGCTTAGAATCACTGTTTTCGGTCGCACCTGTAGGGGGACATGGGACGGATTTCACAACAAAAAAGCATCTCTCATGATTCGATTCAGATAGAGGAGAGGAGGTAAATGCCAACAAATCTATTCTTTAGTACCGCCTGACGGAACGTATTTAATCCTCGCCTCAGATCGACACCGCAGGGTAGCTGAAGACGTCCGTTCTTAGACATTTAGTCGATCATTTGTTATGAAACAGAACTAGGAGTCCGTGCCCTTCAGGCCGGCTCAGGGGCACCTACCTCCAGATCGCCCAGGTTGGGTTTATTAGGCGCCGAAAAGTTACTGCCCTATCAGCCCCTCCAATCCGACCTACGGACATCATCCCACTGGCTCGCAAAATATAAATTGCGGATGGGAAAGGATAAGGAAAATCATTACCTACACAGAAGGACAATGTCAGTTCCAAATAACACTGATACTTTCGGAGCAACTTGGTCCGGAAATGTAAGTACGACTATAGCCCTTTCGACCAACGCCGACAGTCCTATTTGGACGCCGAGAGAGGCGACGGGTAGCCGAATGTAAAGCTCTCGGGTCGCTCTTGGCGGAATGCGCTGCGGGTCCTACCCTAAACCCTTACCACCACCAACTTCGTTAGGAGCCGTATAGATTACAGCTCCCGCAAAATTAGAGAGGAATCTGAGTTATTAGCTGAGGACCCCGCATTTTCTGCGACGGCGTAGCTGCAGTGACGTACGATATGAGTTCCCGACTGTGAGGGAGTCCCAGTCGTGACTCCCTACAACGGCTCCAGATATTGTTACTTATGGTCAATATGCCCCGACCGCCCATTGTCTCGAGTACAGTCTTCCCCAAAGTTAAGCTGTGCATTACCTTACCGTTTTAGGTCCAGCTGGTAGCACCGAATGCTGCGCAATCCGAGCCCCCGAAATAGACTACGTGTCCACGGTCAATTGTCATGGGTAGCAGAGCTCAAAGAGGAGAAACGTGCCCCGTAAACCTATTAGATCTCGGTTGATAAATATCAGGCCACAGCAGGCTGCCCGATGCTTGTTTGAACAACAACTTCGGGAGCCGCGGTCCTTGGTTCTCCCGATATTCGGCCGCACCGAACGGTACGCGTCATCGCGAGGTGCGTTCTCGCAGCAAGAAATATTTGTTGTTGTTGTCTTCCTTCCGCATAGGAAACCTTAAGCGGTACCTTTCTACGAAGTTGAACCCTAGAAGCACGTGTAACAATTTTTTTTACGCTACACCCGGATCTGCTTCCATCTGTTGATCATATGAGCCTAATGTGACTAATCTGTGCCGTCGATTGAAAATTCGTTCTGAACCTAATCACATGAATTAAAATTAGGGCGAGAATTGGCTCCTTTTGGGCCGTAATCCTTCAAAGGGTTAACCGAATTTAGCCTCCACGGTGACACAAACTCCCATAGGTAAGGCAAACCCAATAACGAGGAAGCCTTGCCCACAGCATGTTTGATAAATACCCTTAGGGTAATATCGCGTGCAATACTGAAGCCGCTCTTCTAGCATCCGTGTTTGACATACTATGACCTTGAAGCCTGCCGCAGCTTCTAGGTCATCCAAGTAGATCAAAACGCCATGTTGTGGATCCATGCATCTTCCCAGTGAACATGGATCTTAGTGTGACAGGCGAGGAGCGGCGAACACTATCGGTGTGGCAAGCTCGGGCCTTCGTACGTTGTGGAAGTATGCGAATAAGGAGACCGTAATGTATCAAGTTCTTAAGAGCCTTGGTACCGTTGCAATTCGGCATGTTCCTACAGAGACACTCCGTGTTTGTCATCCGTCATAGATCTATGGCGTAGTTAGCGCCTCTGAAGTAGTTGTCCATTCAGCAGGCATTGCTTAGGGAGTTTCTGGCGCTTGCCGCTCAAGATGCTCACGGGCCTAAGTAGCACGGCAACCTTTTGACAAAGCATTTTATAAACTGAGCATATTGGCCCGAAACTAATCCAGCAAAGGGTGAAGACCTGTCAGCGGGCCCAGAGTGTGAACGGTCTACTGCGCGGTACATAAGTGGCGTAATCCATCAACAAGACCTACACGACCTGAATGATTTCCAACAACTTTATATGCTTTTCCGCATCTCGAGAGTACCGGAATCTATGCAATCTCCCAAGGATCCGTAGATTTGAAATTCAATCCGACGGGGTAAGGTTGCCGCGCCGGTTAGCTAATGTGCGGATTTATAGTCTTTTTCCCAGAAGGCGTAGTTAGTTTCGCACCTAACTACGACACATACTTGGGTCGACTGTTGAAGGTGGTAAGTTGCGAGCAGTCCGCCGCTCTCACGCGCCGAACCACGTTCATATCGGCAAAGTTGCGCGATGACCTATAGGTGTGCAAAGCTCGTCCGACATTGGGATTGGATTCACGTACATACGTTAGTATCATGGGTAAGCTTCCATGTCAGCCTCGTGTATAGCACCGGTGCGCCGCGCGTTAAGGATTCTATGCCCAGCAAATGTGCCAACGTTGTGGGGAGAAAAGTGTAGTTGGATGCGATCGTGACATCGGCACACCGAAACTCTGCAGCCAGTCCCGCTAATCTCATTGGCACCGGGTAAGAGATTACCTTTGGTTAGGAATCGCGTGCGACGTACTGCACGAAAACAGTGCCTGAACCGAGGTGTTTACTTAGATGGTTCTAGACCCAGCATGTTCCTCACTGGAACCTGACGTCGGTACGTGATCCTCTATACCTCCTTTTCGGTATTGGCCTGGCAGCTACTCTAACTGTTTGGGCCGCGCCGATTTCTCGAGTCCACACGGCGAGGTCAGCAAAATTGCCAGTTAGTGGATGTTGGGATCTCAACGCATTACCATGAGAGTTCTTGGTTTACCCGTTAACATCGCTGCGCACGGTGTGAAAAGCCTGTTTCTTTGGCCCCCATCATCTTCGGCCCGCAGATCTCAGATCAATGATGTAAGGTTGCGGCGGCAAAGACTAGACTTGAGTCGTGAGATGGTGCTTTGCTGAGGCCGTCTCCTATAGCTTATTCTAGGACTTTCCGCAAACCACCCGACGTGCGGCTGTCCACGATCGGATTCCATTCTGTCTCGGAGCATACAGCACTAGATTTGCCGCTTGAAAAATGTTCCATAACCATGATTTCAACCCCATCTAGTCGGCAGGCACAGCTGAGAACAGCGAAGGGCGTCGTGAAGGGCATTGCCCGTAGTGTTTCAGACGTGCTAGAGACTAAATCAACTATCTGCACTCGTAGCCTGGCGTGTGAGATGTCACCACGATGTGCCTAGAGGAGTGATTATGAACATGTATTACCACGTCCGGGTGTCGACGGCTATATGGCTAACATTTCTTATGGCTAGACGTGCTTGGAAAGGTTCCCCAGCCTTCTGTTTCCCGGTGCTTTCCACGAGTCTGGAGTTCTGGTAATTAACTACATGGCGTTAACGCGGAGGTAACCCCCAGTCATTGCATTGCAGGTAGGGCTTAGGTGCAATATAATTCACCAAGGCGCGGATTCCTCACGATTGTTACGAAGACACCCGGAGGGTTTCAGTATGGCTTGAGAAGTGTACGTTTTTCCGGCCAGGGTGTAACTATAACCAACACATGTTTGGCCACGGGCTAAGTCGGTCCGCACGACTGATTTCCCCCGCCCATGTGTTTGGGAGCAATAAACTGCGTCTGCCAAGAGTAACAACTCGAGTAGAGAAGGGAAGTCTCAGACTATTTTGCAAATCAGACTGTAAGGCTCAACAGCCATACAGCTTGCCCTACTACTGAATACTAGCGTAGCGTGGCCACATAGGAAAGACTTCATGTCTTCTAATAACCTTTTACCTCCAACGTCCCCGCCGTCTTCACGCGGTCCAACGATGAGGAAACAACCACCCCTATCTTCCGCGGAGTGGTTCACACGACCCCCGGCGTTAACGCGCACGTTGTTGTCTTTCGGGACGGCACTACCCCCAAATGCCCAGACCCAGTGCTAGCGATATTCAAACGCCGTCCGGTAAGTCCTGACGTTTTTCAACTGGATGCACTGGCGACACGTAGTTCGCAAGGCGTCCATGAGAGGTTTTAACCGTCATGTTTCCGTATCACGTCTTATGTCTGTCTCTATTCTCAGCGAAATTCTCATCATAGGGCGGAGACTATCTGAAGGCCAGCGAATACAAGATTTAATATCAAATATAGCATGGGGGCCAACAGAGGCCCCCCTGGTGCTGACGAATTATCGTGATATTAGTACAGCTGTCTGCAATGCCATTTCGAAGGCTTTTTGTTCGTATCACTGCTCTATGCATAGCGGTCACTATGACCTCTCAGCTTGACTCACCCGAATGACCAATTGTGGTCCAGCACTCCCTCATCTTCCCCCATTAACGATACGTTGGGCACCATCGGTGTGAGCTACCCGTTACAGTCATAGAATCGTTCTTTGCGTTGTACGCGGCACGGAGGTGACCGGGAAAAGCGCCGCGAAGGCCCCGCACTGAATAAAGCTAGTATTAGCGTCTGTCAAAGTGTTTTGACACCTAATTCGCTTCCAAGTCCCAATATCTAATCTAGCCTGCTTTGGGCCAACATCTCATTGCGTTATGCTAATGAAGAGGGTGCGGGATCACATCCGCTCTTCTCTTCCTATACACAGCGGACATTCGGGTTGGACGTTTGGAGTGATAATTTATCGTTAGGGATAAGTATGTCGGCGCTTAGTAGTATAGCCCGCTGACCAGCGTTCGATTTCGAACCTTACTGGACATTCTCAATAACTACTGATCATGACGTTTTCCTCAGTTCCTAGCCTTGACAACTAGCCACAGTCAGCATGGTAGAGAGCGTTGAGCCGGGGATAGCCAGGCTATTAAGACAAAGACCCTCGGGCCCCTTAATGCGCGTCAAGTCTGACGGTTTGAGTGCGGAGCAGTAAGCGCTTTGGTATAACCGTGACGTAGCAGATCCATGCTTCGCCCGCTTCCACCTGAGAGATACTAGCCTCTTTCGCACTTTGTAGGATTACGGGCAGCGAAATATTTATCCTGTGCGGCGAGCCCGCTTCGGTTTCGAGCTCTATCAGTGCGCGGTTGGCACTCCAACGCACGATAACATATACCCGCCCACAAGGCCATGCAGGTTTAACCTCCTATTCTGATTGTACCTGGCTGACTTTACGGTACCCACCAGCGCAGGATTAATAGCCTAATTATGCTAACCGGTGCTAGTCTAACTGCTGTTACTAGTCCGCCCCAGCTACCCCACGGGTCAGTAACTGCACCAGCAAGCATGGTTCTCCTCCTGAAGTTGTACGTTCGAGAACCCCGTATCGAGTTGGTATATAAATTAAGGGTTGTCTAAAACAGAAGCCTATTCCGCTATCATCGGTGTAATAACTGATCGCGCCGTGGTTAAATGGAGGAGCACCCGCATGGATACATCGCTAGCGTCTTGTAACTCTCTGGGGGCCTAGTATGGAACGGAACAATGACATCATTGCTTACGGGGCCCGCACTTAGCTGTCGCGTATCGCAAATCATATGGCATGTCAGTCCCGACATCACGAAAATGACCCCATCTGAGGTGGTCGGGAGGCGAACAGTCGAATATGATGTATGCACCCGCAACTTAATGTTCAAAGGCGGGCGAAATGCCTTCTCCCGTCCGGACTATCCTGAGTGCTAGCCGCGAGTCTGTAAAGGTTGACGCAACCATATAGCACGCAGAAAAATCACTCTCACACCATGAGAACCATGGCGGCACGCTGTCTACTTTGTCTGACAGGCTACGGAAGGAATGGTACATACGTACAAACGGATGATATGATATCGGTCATTGCCTATTGTGACGCTACCCTACTGCATCACCCCCTTAGAATGCGTTGGACGCTCTATAGCAGATCCTCCATCCAGTGGAAGTCTCGTCGCCGTGGTTTGCCTTAACGACCGTTGGAGAGAGCAGGACAGAAATATCGCCCTTTTGAGCGCATTATTTGGAATCGAGGTAAGTCAGTGCGGCATAATCGCGCCTCGTGAGCGGAACAGTTTTTGATCCCACCCGCTAAATGCCAAGGTGCTGTAACCTGGGCGCGACACCAAAAGACCACGTGCTGTATGAAGCATGTGTTCTAGCGCACTCTCAACCGTTACCCCGAGAGTAAAATGTTAGTTGTAGGCCGATTCTGCAATGGTAATTGGCGGAGTGTCTAGGGAAATGTTTCGGTCATACTTAACCGGCTACCTCTTCCTCCCTCAGATTCGGTCTGAGATGAGATATACTGGGTGAGTTGAGTCGCCCTGTATCGTTGCGGCGCTCGTGGACCAGACAGACAGTTCCCGTTTATCTCTGCTTCTAGATGGAGGGTCGCCTCCGTGTTAACGCCGGCGAAGGTAGTCGCAGCTGAAGTTGTGATGCACAATCAGGTGAGCCTTTTAAGTATGGTCCTACGGACGTGAACAGCTGGGCCCAGTCATTTAGTACGGGGGGTTTACCTATAAGGATACGGTAAGAACGTCATCTATCCGTCCCACTGGAGTCCGAGGGGTTCGTGTCTACACGGATTACTTATCATGCACACACGTCTACGGTCATGCATAAAGTTGTGCAGCGCAGCAATCGGAGCGGAGTTACACCATCTCCCTATTAACAAGGCACTTATTAGTACTTACCCCGTTATAGAGCTCTCATCTTATCGATAGAGCGCAGTCCTAAGTATTGGCTCGAGTGATTCGCTCCTCAGCCCTTGATTGTAACTCCCCCGATTGCAGGTTGTATGGTGAGTAAAATCTCTGCGCCCTTCTGTTCGGATAAAGAACCCCGACCACTAATGCCCGCCTGCTTGTTGGGCGGTAAATGGGTAACGGAACATGGACTATGAGTGCGATGATGGTCAATAGAATTACCTTATTACGCAGTAAAAGGAATGACGCAGACAGGTATTTGTCGACGATTGCTTCGAACCTGGCAAAATGGGGAGGTATCCTGTCATGTTCATCTGTAAAACAACTCCTGCCTCTTCGTAGAGGACACACACTGTGGGCCTTTAGCCTTTAGCAGCCCATTGGGGCTTACCAGCTGTCGTCATGGGGTATCATTAAGATCCATGCGCCCCCGAAACTTACTGCAAAACAATATGGCTTAAAGGTAAAGGGACCATCAGGAGAATGCTTAAGAGCGACATATAGATACGTATTTAATTAATTTATGTTAACGCAACCATCTCGCAGGAGTCGCATAGCATATTGCCGGGTGATAGTTAATGCACTGTGCTTCCGTGTTTATATAAAATAAGCAGTAACCTCTGACAGGTTGAGACTCCAACAAGTGCTCCGGGTATTTACCTTCTACCATGGCGTTCTAATATCACGAAAGAGAAATTGTGTGTACCGATGCCAGGTGACCGCCCGCGTGCGCCAACGACGCAATCTAGAGCATCCACGCTGAATTGGGGAACTCTTGCCGTTCGTCGCATGGTGTACTTGGTACCACTCGATATGCCTGATTAGGTTTGGCCGTAGCACGTAAGGTAGTGACTTTCCATTCAAGCTAGCGAAGCGACACCACCACAGTGCCCGGTCAAAATAACCCACACCTGGCCAGCATAGAGGCTAAAATAGCTACAGTGCGCTAATCGAGTGTTTTTGCATCGGCTCGTGGCTGGTGGACTCGGGACAGCTTAGAACTAACTCTGGTGTACAAACGCGATCGTAGCTCTCGCGACTTACTCACCGGAGTAGGTTAGATGGACAAGACCTAACCCGAAGCCTAAATCGCCCTGAGTGTTAGCCGCCATTCAATTCTATGGTTTATCGGGGGCGTCTATGGCTGCGACAGTATGGAGGCCCGTTATGGGCACCCGAGTATCGTACCATAGTAATCCCATATTCCTCTTCGAGCGACTATTGGATCAACATACCTACAGGGTAGTATGAATGTTCTTGATTACAGAAACCATGGAATCGGCGCATTCTATGTTTCACTTCCGAATAACAGTGAGCAAGGCATGCCCTTGACAAGGATCATCCCGACAGCAAGCCGATCGGGCCCTAGAGCCCGACCCCCAAACAGAACACCGGCCACGTAGTTGCTGGGACTAAACAAAGGTGTGTTTCCATAAAAGGAAATCTTCAAGTGTATTGTTGAGTCGTAACGCTTATATTTATGGCCCAATGGGCGTTGCGAGCACAGTAGCAGGCCTAGATGAATGCCTAGGCCACGATCGGGGGGAGGCTCATTGAACGTACTGCCATACCAAGCCCCCGTATGCTATGGCAGGAGGGGTTCTCTTCGTATAGAGCGAGGGTCTCTACGCCAAGCAGCATTCCCGTGTTGGGTGGCCAATGGGGCTCACTAGAAACTCGGTTTTTTTAGCGAAGGAATGAGCAAACTCGTGAAAGGTGGTACACACCAGTTGCGGCCGATTTGTTGTAGCAACAAGGTTTGAAGAATTGAGTAGATGGGCCAATTTACCTCCTATTTAGCGAGTGAGATGGCGCATGTTTATTCAGACTCCATGTGGGGTAGAGGCTAATCGTTTAGTAGCAATAACCCCGCGGGGCAAGAGACCGTAATAACTTGAATCTGTGGTAGCTATGAATATGTGCTTCGCCCTAAGTGTTATGTAACAAGAGTGATCCAGGGGCTCAGATCACACTTAGTACGATCCGCTACTGAAATGCGGCCGCGGGCTTGCACGCTGGACATAAGTCGGATAATCAATTGCCTACGACAGGTTCAGCCATAAGGCTTGGCTCCTAACACACTCATGATGTCTGGCTTTTACTCGTGCCCGGACATAAACGTATGCTCAAACGCGAGACAGGGGAGGGTCAGCACCGTTTAGATCTATAAGGCCTACCGGTAATATGGATCGACAACAAACAGATGCTATAGGGATACCTACTCCTTTGGACCCACATGTAGATGAAGGCAAACACGCAGAGCAAAGGAGAGTAGTCCACCCGGTATAAGTTTGTGCTTTGAATTCTGGCTACGCAGACTTGCACTCTGTCCCGGCATTCACTATACTTCTCCGGAAGTCCTTTAAGAAATGTCCGCGCTCATGTGGTTCCCGTTGCTCAGGGGCCAACTCAAGTAGATCTTTAAGGCGCAGTCGACCACAGGCTACTAGATACGAGTTATACTTATCCGGACATCTGGCTAAATACTTGGATACGATACTTCCCCAGTCGTGAGAACGAAGCTAATACAGATCGAATTTCGATGGTTCAGGCAGGCAGTTCTCAGGAGGCAAGGTGTTAAATAGTTTCGGAGGCTCTTTCGTACGATCAGGGTCTACTACCCTAGGGCATTTTGACTTTGGATTAAATATGCAAAATGCAAGGCCGATTGTGATCAGTACTGATACTCCAACTGGACCACCTTCAGACCCTTCGAGGGGACCTAGACGACGGGAACCCTTCCAGCGGGTGATACCAGTTAGAGCAAGTCACAAACACGATTCAGCCCCCGGGGTTTATGACGTACCATGCGAGTAATAATGCACGTATACGGAGCTCTTCCACCGAGCGATGGCATTTCGGGGCGAGGTAGTTGTCTTTCATTGGCATCGCACAACCCCCATCCTCTTAATTGGCATCGTCTCCAGCTGGAAAGAATTTGAGTGAGCATGTCGCCCCTATTATTCCGTTGCCAATAAAGTGTCTCAACTTTTGGCGAAGGTTTTAACGCATACAAGGAGAAGCCGCGAGACGTCTGTACCGCTGATCTGGACGCAAAGTGCTCGGACTGCCGCTGAGTTATCCTGGACGCCATGATTAGAGCCGTCGTCACTACCTGCATACATGGGCCGATAGAGTACTGCAACCAACAACTCACTTAAGCTCCACAACGGCTGGACACTTCCGAGAGCGGTCTTACACAAACGTTAGGTCCTGGGCCGCCGACCTTACCGCTAGTTAGTGAGAGCCAGTTAAAATTATGAACGCTCGGAACCTTCCCAACAGTGGCCGCAGCCTTCCTTGACGCCTAGCACATCTGGTTTATACTCGGGTATGCCGTAGATCGGTAACCTAGGGAACGACCCTGTGGGTTTAACACCCGAGTGCGTAATCAAGCCTAGAGGCCATCTCAACTCGAGAGGTCTCCTGACAAAGAGGCGCCCGATGAATCATCCAGAGGCGTCTGGCGGTCCTACGAGAGTGGCTTTGGATGCCTGCCCCTTGGATGGATCTGTCTTTAATCGGCGCCAATACCTAGCACTGCTAGGCTCCAGACTGTGTTTACATGCCGTAACCCTGATACTCGCAGAAACGTTGCTGGAAATTCCTAGCAGCTGAAACCATTCCCCGTAACGTACTAGTACGCTAAGAGAGAGTCTCTCCTGGCCCTGATGAGTGTGTTCTCATCTGGGGCACGATACAAGAATCGGAACGAACGCAATGCCGAAGTCCCTTGTACCTTAATTTGGGCGACGCAGATAGACCCAAAGATCGCGGACTACGGAAACTAGCATAGGACCTGTGTCGAGAAGGTTCGAGCAGGTAGTGACACGCAGCGCGGTGGCCGGCGGGGTGGCACATTGCGGGTCAATACTGGTAGTAGCCACTCTTTGGACATAGCGGCGGACCAGCGCCTAGAATGTCTCATTCTCATTTTGTTCCGTGGCACGTTACGTAATGACGGCCCGCCAGCACCTGTGTATGGACTTGTAGCTCGGGCCTCTGGTCCTGGCACGACAAGGCACCAGCCAGTAATCTCTCCTAAGGCGCTAGCGTGCATAGCGCGTCTGCCTACCGCCAGAGAACGCGTCATCTGCAAGACGTCCCAGCGTAGTGAATTGTAACTGCAAGCGTTCTCTTACGGTCATAGTGCCGATTTTGAGCAGTAATGGAAGCAGCAAAATGCCGCCCAAGCGATTCGCAAACTTCTAACAGAGCTACAGCCGGACACGACGCGGTGGTGCTCGCGGTTGGTGATCTTATGATATTAACGCCCATAGCGGCCATCTTAATCGACACCATGTTCGTTTTGGCAGGCCTTGTGGTAAACACGTGCTAGTGGCACCACCCATGCCCGTGCCCATACATCCAAACCGAGAGAAAGCCTATTTAAGCGAAAACCACAACTTCGAGGTTTCACCCCCTGCCATTGATAAAGCGAGGAGTACCCCCGATGCCGGGAAGCGTCCGCACCCATTTCTTTCGTTCTGGAATCCTCGGGCGACTTCTCGAAGATACTGTGCTCACGACCTGGAGTATCATGAACAATCGGAGGAAAATGAGTAATTGTCGAGTCGTTGTTAGACGGCACTTCCGTCCGGCCCAACTGTTCTCGGATACGTGTCCCGTGGTCAATGCTCTAAACCGGCTGCCGGCGACTCAGTTCACTGAGACAAATTCTGATGCTTTCGAAGCAAGGATGCGCCCAGAGCAGAGCTGCCCAGATGAGGTTAAGAACGTAACTATAATCGATCAGCCATTCGGCTTAAGGGGCCCCGGCGAAACGCGAAACACTTGGCACATGGACGCTTCACGCGCAACAGTAGTTGTCTCTTTCGTGAGCCACCGTAGCAGCTAGAAAGGCCTATCCAGTGATGCTTTATGACTGAGTGTCGAATCTAGGTATAGCATAGACTGGCTGATCGGGCGGGTCGGCCCACCCGTCTCGGTCGAGCGGTTCTGACTTTGGGTGGCTGTGTGAACCCAACTGCAGATGGAGTTGAATGGGTACACCCTATGCGAGGCCTCGTCTTTACACCAAATCGGGGCCCTGTGAAGTGCCACTCTTTTCCAGCCGGCAGCCGCTCAGTCTGATTTTGCTTGTACATGTCGTGTGCGAACGTTCCGGGAGGCTTCCGTGTTCCAAATACCGTGTTCTCATATTCGGTCCATCTACCGACGGAGAGTTGGGATGCCCGGGCCCGGAAATATAATTTAAACTCGTGGCCAAGAATTTAGCATGTTGTAAACATGAGAGACAGGGCCGGGCTAAAACATTACCCCTGAGTAATGTAGAGCCACAACTGAACATAACATTGGGATCTAACGCACGCAATCAGTGTAGCTTCAGCCCACCCTCTAAATTTCCCCCGGACAACTGGATTATCACCTGCGTCACGCGATAATTGCTCGCATCTCACCAACACACTTCGACAAATCTGGAGTCTCCCTGGTCCGTACGTCCAAAACCGTTTAAATGGGCGGGTGTGTCGTGAACCAATCTCCTCTTCCATTTGTCACATACTGGCGATGACATCCTTTTACTTGAATTATTCATCCGGGCACCAGCCGCTTTCCCTACGATCCCCGACACTCGGGGCTTCGGGAGTTGCCCGCCAAAAAACCGACAAACCAAACTATACAATCAATCCCATCTAGATGTAGGGGACTGAGGCTCTAAGCTATGCGCCTACTATACTTTGTAGGTATCAAACTACGCTTGAAGATAGTTGATAAGGAAGCGAATTGATCGAGTACCGTATCTTCAGTCCGACTCCCGTTCGAACGCAGCACGCTAACATGGTCCACTGGCATTCTTACTAAATACCTAGTTCACTTCTACATGAGGAGTGTCTGGGCCGGACTCACCTTTGATTAGATAACTGAAG
package nl.lumc.sasc.biopet.tools
import java.nio.file.Paths
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
import scala.util.Random
/**
* Created by ahbbollen on 10-4-15.
*/
class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
import MergeAlleles._
private def resourcePath(p: String): String = {
Paths.get(getClass.getResource(p).toURI).toString
}
val vepped_path = resourcePath("/chrQ.vcf.gz")
val reference = resourcePath("/fake_chrQ.fa")
// These two have to created
// resourcepath copies files to another directory
// hence we need to supply all needed files
val dict = resourcePath("/fake_chrQ.dict")
val fai = resourcePath("/fake_chrQ.fa.fai")
val rand = new Random()
@Test def testOutputTypeVcf() = {
val tmp_path = "/tmp/MergeAlleles_" + rand.nextString(10) + ".vcf"
val arguments = Array("-I", vepped_path, "-o", tmp_path, "-R", reference)
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
val tmp_path = "/tmp/MergeAlleles_" + rand.nextString(10) + ".vcf.gz"
val arguments = Array("-I", vepped_path, "-o", tmp_path, "-R", reference)
main(arguments)
}
@Test def testOutputTypeBcf() = {
val tmp_path = "/tmp/MergeAlleles_" + rand.nextString(10) + ".bcf"
val arguments = Array("-I", vepped_path, "-o", tmp_path, "-R", reference)
main(arguments)
}
}
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