# HG changeset patch
# User devteam
# Date 1480077019 18000
# Node ID 79f5d34da277f7ea190cadc10478f0d49e96a5c2

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus commit 5d67d705695dfee875bda85aa02ddf38924790a7

diff -r 000000000000 -r 79f5d34da277 test-data/output1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output1.fasta	Fri Nov 25 07:30:19 2016 -0500
@@ -0,0 +1,168 @@
+>Chromosome
+TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTT
+AACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTG
+ACCCCTCAGCAAAGGGCTTGGCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTT
+GCTCTGTTATCCGTGCCGAGCAGCTTTGTCCAAAACGAAATCGAGCGCCATCTGCGGGCC
+CCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGATCCAACTCGGGGTCCGCATC
+GCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGAAAATCCTGCT
+ACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG
+GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCACAATACCGATTCC
+GCTACCGCTGGCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGC
+GCCTCCAACCGGTTCGCGCACGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCT
+TACAACCCCCTGTTCATCTGGGGCGAGTCCGGTCTCGGCAAGACACACCTGCTACACGCG
+GCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGGTCAAATATGTCTCCACCGAG
+GAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGCATTCAAACGC
+AGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG
+GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATC
+GTCATCTCATCTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACC
+CGCTTTGAGTGGGGGCTGATCACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCC
+ATCTTGCGCAAGAAAGCACAGATGGAACGGCTCGCGGTCCCCGACGATGTCCTCGAACTC
+ATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGGGCGCGCTGATCCGGGTCACC
+GCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGATTGTGCTTCGC
+GATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC
+GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTG
+GCCCAGTCACGACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCC
+AAAATCGGCCAAGCGTTCGGCCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATC
+CTGTCCGAGATGGCCGAGCGCCGTGAGGTCTTTGATCACGTCAAAGAACTCACCACTCGC
+ATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCCGACAACGTTCTTAAAAAAAC
+TTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCTGTGCACAAAC
+CGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG
+ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACC
+TGCACCAAGACCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCT
+TCGTCGTTTGTTCTTGGAAAGACAGCGCTGGGGATCGTTCGCTGGATAACACCCGCATAA
+CTGGCTCGTCGCGGTGGGTCAGAGGTCAATGATGAACTTTCAAGTTGACGTGAGAAGCTC
+TACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGGGTCACGCGTCATGGGCGTTC
+GTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTCATCGTGAGGT
+GAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT
+TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGC
+CCGCGGTGCCGGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTT
+CCGGATTCGACTACGAGGTTTCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTG
+GAAGCGTTTTAGTTTCTGGCCGATTGTTGTCCGATATTACCCGGGCGTTGCCTAACAAGC
+CCGTAGACGTTCATGTCGAAGGTAACCGGGTCGCATTGACCTGCGGTAACGCCAGGTTTT
+CGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCGGAAGAGACCG
+GATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC
+GGGACGACACGTTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGG
+TTTTGGCCGCTACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGT
+CGCCAGATATCGAAGCGGCTGTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAG
+CGGGCATCGGCGGCTCTGACGTTCGTTTGTCGTTGGGTACTGGGCCGGGGGTGGGCAAGG
+ATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCACCACGCGACTTCTTGATGCCG
+AGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCCACCATGGACG
+TGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG
+TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGAC
+GAGCCGAGGAAGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACC
+CAACCTATCTAACGGACGGTTTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTA
+CGACTGCGGGTAAGCCTGCCTTGCTACGTCCGGTGTCCGGGGACGATCGCCCTGTGGCGG
+GTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGACTATGTCTATCTGTTGATGC
+CGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCGTCATTTGGGG
+CTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT
+TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACG
+ACGTTAGGTTCGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGT
+GCGGTGATCTCCACGATCGTGGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATC
+GCCACGGGGCGAGTCAACAAAGCGCGATTGAATCGATCATCGGTCCGAAGTACACGTGAT
+GTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGGATCTGGGGTTGGTTCGTGGG
+GATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAGGCCTGCGATC
+GCTGCGGTACGAGCCGAATATGAGAGGGTGTTGCGCCAGCGGACGGCGTTATTGAAGTCC
+GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGAC
+AGTCGTTTGGCGGAGCACGGGGCTGAACTGGTGGCCGCCCGCATCGATTTGGTCAACCAG
+TTGGCACCGGAAGTGAAGAAGGCATACCAGCTGTTGGCGCCGGAATCGCGATCGGCGTCT
+ATCGGTTATCGGGCCAGCATGGATGTAACCGGTCCCAGCGAGCAGTCAGATACCGATCGG
+CAATTGTTAGCAGCTCGGCTGTTGGCGGCGCTGGCGGCCCGTCGGGATGCCGAACTCGAG
+CGTGGGGTTTGTCTAGTTGGTCCGCACCGTGACGACCTAATACTGCGACTAGGCGATCAA
+CCCGCGAAAGGATTTGCTAGCCATGGGGAGGCGTGGTCGTTGGCGGTGGCACTGCGGTTG
+GCGGCCTATCAACTGTTACGCGTTGATGGTGGTGAGCCGGTGTTGTTGCTCGACGACGTG
+TTCGCCGAACTGGATGTCATGCGCCGTCGAGCGTTGGCGACGGCGGCCGAGTCCGCCGAA
+CAGGTGTTGGTGACTGCCGCGGTGCTCGAGGATATTCCCGCCGGCTGGGACGCCAGGCGG
+GTGCACATCGATGTGCGTGCCGATGACACCGGATCGATGTCGGTGGTTCTGCCATGACGG
+GTTCTGTTGACCGGCCCGACCAGAATCGCGGTGAGCGATCAATGAAGTCACCAGGGTTGG
+ATTTGGTCAGGCGCACCCTGGACGAAGCTCGTGCTGCTGCCCGCGCGCGCGGACAAGACG
+CCGGTCGAGGGCGGGTCGCTTCCGTTGCGTCGGGTCGGGTGGCCGGACGGCGACGAAGCT
+GGTCGGGTCCGGGGCCCGACATTCGTGATCCACAACCGCTGGGTAAGGCCGCTCGTGAGC
+TGGCAAAGAAACGCGGCTGGTCGGTGCGGGTCGCCGAGGGTATGGTGCTCGGCCAGTGGT
+CTGCGGTGGTCGGCCACCAGATCGCCGAACATGCACGCCCGACTGCGCTAAACGACGGGG
+TGTTGAGCGTGATTGCGGAGTCGACGGCGTGGGCGACGCAGTTGAGGATCATGCAGGCCC
+AGCTTCTGGCCAAGATCGCCGCAGCGGTTGGCAACGATGTGGTGCGATCGCTAAAGATCA
+CCGGGCCGGCGGCACCATCGTGGCGCAAGGGGCCTCGCCATATTGCCGGTAGGGGTCCGC
+GCGACACCTACGGATAACACGTCGATCGGCCCAGAACAAGGCGCTCCGGTCCCGGCCTGA
+GAGCCTCGAGGACGAAGCGGATCCGTATGCCGGACGTCGGGACGCACCAGGAAGAAAGAT
+GTCCGACGCACGGCGCGGTTAGATGGGTAAAAACGAGGCCAGAAGATCGGCCCTGGCGCC
+CGATCACGGTACAGTGGTGTGCGACCCCCTGCGGCGACTCAACCGCATGCACGCAACCCC
+TGAGGAGAGTATTCGGATCGTGGCTGCCCAGAAAAAGAAGGCCCAAGACGAATACGGCGC
+TGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGCAAACGTCCCGGCATGTACAT
+TGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCGACAACGCGGT
+CGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGG
+TGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACC
+GACCGTCGACGTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTA
+TGCGATATCTGGTGGTCTGCACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCG
+GCTCGAAGTCGAGATCAAGCGCGACGGGTACGAGTGGTCTCAGGTTTATGAGAAGTCGGA
+ACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACGGGGTCAACGGTGCGGTTCTG
+GGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCGCCCGCCGGCT
+GCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGAC
+CCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAG
+TGAACGCGCAGCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCC
+GGGTGGCCTGGTGGACTTCGTGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAG
+CATCGTGGACTTTTCCGGCAAGGGCACCGGGCACGAGGTGGAGATCGCGATGCAATGGAA
+CGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACCATCAACACCCACGAGGGCGG
+CACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGTACGCCAAGGA
+CCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT
+GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAA
+GTTGGGCAACACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAACGAACAGCTGACCCA
+CTGGTTTGAAGCCAACCCCACCGACGCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGC
+GCAAGCCCGTATCGCGGCACGTAAGGCACGAGAGTTGGTGCGGCGTAAGAGCGCCACCGA
+CATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCCACGGATCCGCGCAAGTCCGA
+ACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTCGCGATTCGAT
+GTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA
+CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCA
+CGACGAGTTCGATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGA
+TGTTGACGGCCAACATATTTCCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCC
+GCTCATCGAGAACGGGCATGTGTTTTTGGCACAACCGCCGCTGTACAAACTCAAGTGGCA
+GCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGCGACGGTCTGCTGGAGGCGGG
+GCTGAAGGCCGGGAAGAAGATCAACAAGGAAGACGGCATTCAGCGGTACAAGGGTCTAGG
+TGAAATGGACGCTAAGGAGTTGTGGGAGACCACCATGGATCCCTCGGTTCGTGTGTTGCG
+TCAAGTGACGCTGGACGACGCCGCCGCCGCCGACGAGTTGTTCTCCATCCTGATGGGCGA
+GGACGTCGACGCGCGGCGCAGCTTTATCACCCGCAACGCCAAGGATGTTCGGTTCCTGGA
+TGTCTAACGCAACCCTGCGTTCGATTGCAAACGAGGAATAGATGACAGACACGACGTTGC
+CGCCTGACGACTCGCTCGACCGGATCGAACCGGTTGACATCCAGCAGGAGATGCAGCGCA
+GCTACATCGACTATGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCGGAGGTGCGCGACG
+GGCTCAAGCCCGTGCATCGCCGGGTGCTCTATGCAATGTTCGATTCCGGCTTCCGCCCGG
+ACCGCAGCCACGCCAAGTCGGCCCGGTCGGTTGCCGAGACCATGGGCAACTACCACCCGC
+ACGGCGACGCGTCGATCTACGACACCCTGGTGCGCATGGCCCAGCCCTGGTCGCTGCGCT
+ACCCGCTGGTGGACGGCCAGGGCAACTTCGGCTCGCCAGGCAATGACCCACCGGCGGCGA
+TGAGGTACACCGAAGCCCGGCTGACCCCGTTGGCGATGGAGATGCTGAGGGAAATCGACG
+AGGAGACAGTCGATTTCATCCCTAACTACGACGGCCGGGTGCAAGAGCCGACGGTGCTAC
+CCAGCCGGTTCCCCAACCTGCTGGCCAACGGGTCAGGCGGCATCGCGGTCGGCATGGCAA
+CCAATATCCCGCCGCACAACCTGCGTGAGCTGGCCGACGCGGTGTTCTGGGCGCTGGAGA
+ATCACGACGCCGACGAAGAGGAGACCCTGGCCGCGGTCATGGGGCGGGTTAAAGGCCCGG
+ACTTCCCGACCGCCGGACTGATCGTCGGATCCCAGGGCACCGCTGATGCCTACAAAACTG
+GCCGCGGCTCCATTCGAATGCGCGGAGTTGTTGAGGTAGAAGAGGATTCCCGCGGTCGTA
+CCTCGCTGGTGATCACCGAGTTGCCGTATCAGGTCAACCACGACAACTTCATCACTTCGA
+TCGCCGAACAGGTCCGAGACGGCAAGCTGGCCGGCATTTCCAACATTGAGGACCAGTCTA
+GCGATCGGGTCGGTTTACGCATCGTCATCGAGATCAAGCGCGATGCGGTGGCCAAGGTGG
+TGATCAATAACCTTTACAAGCACACCCAGCTGCAGACCAGCTTTGGCGCCAACATGCTAG
+CGATCGTCGACGGGGTGCCGCGCACGCTGCGGCTGGACCAGCTGATCCGCTATTACGTTG
+ACCACCAACTCGACGTCATTGTGCGGCGCACCACCTACCGGCTGCGCAAGGCAAACGAGC
+GAGCCCACATTCTGCGCGGCCTGGTTAAAGCGCTCGACGCGCTGGACGAGGTCATTGCAC
+TGATCCGGGCGTCGGAGACCGTCGATATCGCCCGGGCCGGACTGATCGAGCTGCTCGACA
+TCGACGAGATCCAGGCCCAGGCAATCCTGGACATGCAGTTGCGGCGCCTGGCCGCACTGG
+AACGCCAGCGCATCATCGACGACCTGGCCAAAATCGAGGCCGAGATCGCCGATCTGGAAG
+ACATCCTGGCAAAACCCGAGCGGCAGCGTGGGATCGTGCGCGACGAACTCGCCGAAATCG
+TGGACAGGCACGGCGACGACCGGCGTACCCGGATCATCGCGGCCGACGGAGACGTCAGCG
+ACGAGGATTTGATCGCCCGCGAGGACGTCGTTGTCACTATCACCGAAACGGGATACGCCA
+AGCGCACCAAGACCGATCTGTATCGCAGCCAGAAACGCGGCGGCAAGGGCGTGCAGGGTG
+CGGGGTTGAAGCAGGACGACATCGTCGCGCACTTCTTCGTGTGCTCCACCCACGATTTGA
+TCCTGTTCTTCACCACCCAGGGACGGGTTTATCGGGCCAAGGCCTACGACTTGCCCGAGG
+CCTCCCGGACGGCGCGCGGGCAGCACGTGGCCAACCTGTTAGCCTTCCAGCCCGAGGAAC
+GCATCGCCCAGGTCATCCAGATTCGCGGCTACACCGACGCCCCGTACCTGGTGCTGGCCA
+CTCGCAACGGGCTGGTGAAAAAGTCCAAGCTGACCGACTTCGACTCCAATCGCTCGGGCG
+GAATCGTGGCGGTCAACCTGCGCGACAACGACGAGCTGGTCGGTGCGGTGCTGTGTTCGG
+CCGACGACGACCTGCTGCTGGTCTCGGCCAACGGGCAGTCCATCAGGTTCTCGGCGACCG
+ACGAGGCGCTGCGGCCAATGGGTCGTGCCACCTCGGGTGTGCAGGGCATGCGGTTCAATA
+TCGACGACCGGCTGCTGTCGCTGAACGTCGTGCGTGAAGGCACCTATCTGCTGGTGGCGA
+CGTCAGGGGGCTATGCGAAACGTACCGCGATCGAGGAATACCCGGTACAGGGCCGCGGCG
+GTAAAGGTGTGCTGACGGTCATGTACGACCGCCGGCGCGGCAGGTTGGTTGGGGCGTTGA
+TTGTCGACGACGACAGCGAGCTGTATGCCGTCACTTCCGGCGGTGGCGTGATCCGCACCG
+CGGCACGCCAGGTTCGCAAGGCGGGACGGCAGACCAAGGGTGTTCGGTTGATGAATCTGG
+GCGAGGGCGACACACTGTTGGCCATCGCGCGCAACGCCGAAGAAAGTGGCGACGATAATG
+CCGTGGACGCCAACGGCGCAGACCAGACGGGCAATTAATCAGGCTCGCCCGACGACGATG
+CGGATCGCGTAGCGATCTGAGGAGGAATCGGGCAGCTAGGCTCGGCAGCCGGGTACGAGT
+GTTAGGAGTCGGGGTGACTGCACCGAACGAGCCGGGGGCGCTCAGCAAGGGCGACGGCCC
+GAATGCGGATGGCTTGGTCGACCGTGGGGGCGCACATCGG
diff -r 000000000000 -r 79f5d34da277 test-data/reference.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.fasta	Fri Nov 25 07:30:19 2016 -0500
@@ -0,0 +1,168 @@
+>Chromosome
+TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTT
+AACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTG
+ACCCCTCAGCAAAGGGCTTGGCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTT
+GCTCTGTTATCCGTGCCGAGCAGCTTTGTCCAAAACGAAATCGAGCGCCATCTGCGGGCC
+CCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGATCCAACTCGGGGTCCGCATC
+GCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGAAAATCCTGCT
+ACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG
+GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCACAATACCGATTCC
+GCTACCGCTGGCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGC
+GCCTCCAACCGGTTCGCGCACGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCT
+TACAACCCCCTGTTCATCTGGGGCGAGTCCGGTCTCGGCAAGACACACCTGCTACACGCG
+GCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGGTCAAATATGTCTCCACCGAG
+GAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGCATTCAAACGC
+AGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG
+GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATC
+GTCATCTCATCTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACC
+CGCTTTGAGTGGGGGCTGATCACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCC
+ATCTTGCGCAAGAAAGCACAGATGGAACGGCTCGCGGTCCCCGACGATGTCCTCGAACTC
+ATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGGGCGCGCTGATCCGGGTCACC
+GCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGATTGTGCTTCGC
+GATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC
+GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTG
+GCCCAGTCACGACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCC
+AAAATCGGCCAAGCGTTCGGCCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATC
+CTGTCCGAGATGGCCGAGCGCCGTGAGGTCTTTGATCACGTCAAAGAACTCACCACTCGC
+ATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCCGACAACGTTCTTAAAAAAAC
+TTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCTGTGCACAAAC
+CGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG
+ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACC
+TGCACCAAGACCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCT
+TCGTCGTTTGTTCTTGGAAAGACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAA
+CTGGCTCGTCGCGGTGGGTCAGAGGTCAATGATGAACTTTCAAGTTGACGTGAGAAGCTC
+TACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGGGTCACGCGTCATGGGCATTC
+GTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTCATCGTGAGGT
+GAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT
+TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGC
+CCGCGGTGCCGGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTT
+CCGGATTCGACTACGAGGTTTCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTG
+GAAGCGTTTTAGTTTCTGGCCGATTGTTGTCCGATATTACCCGGGCGTTGCCTAACAAGC
+CCGTAGACGTTCATGTCGAAGGTAACCGGGTCGCATTGACCTGCGGTAACGCCAGGTTTT
+CGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCGGAAGAGACCG
+GATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC
+GGGACGACACGTTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGG
+TTTTGGCCGCTACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGT
+CGCCAGATATCGAAGCGGCTGTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAG
+CGGGCATCGGCGGCTCTGACGTTCGTTTGTCGTTGGGTACTGGGCCGGGGGTGGGCAAGG
+ATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCACCACGCGACTTCTTGATGCCG
+AGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCCACCATGGACG
+TGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG
+TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGAC
+GAGCCGAGGAAGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACC
+CAACCTATCTAACGGACGGTTTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTA
+CGACTGCGGGTAAGCCTGCCTTGCTACGTCCGGTGTCCGGGGACGATCGCCCTGTGGCGG
+GTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGACTATGTCTATCTGTTGATGC
+CGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCGTCATTTGGGG
+CTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT
+TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACG
+ACGTTAGGTTCGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGT
+GCGGTGATCTCCACGATCGTGGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATC
+GCCACGGGGCGAGTCAACAAAGCGCGATTGAATCGATCATCGGTCCGAAGTACACGTGAT
+GTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGGATCTGGGGTTGGTTCGTGGG
+GATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAGGCCTGCGATC
+GCTGCGGTACGAGCCGAATATGAGAGGGTGTTGCGCCAGCGGACGGCGTTATTGAAGTCC
+GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGAC
+AGTCGTTTGGCGGAGCACGGGGCTGAACTGGTGGCCGCCCGCATCGATTTGGTCAACCAG
+TTGGCACCGGAAGTGAAGAAGGCATACCAGCTGTTGGCGCCGGAATCGCGATCGGCGTCT
+ATCGGTTATCGGGCCAGCATGGATGTAACCGGTCCCAGCGAGCAGTCAGATATCGATCGG
+CAATTGTTAGCAGCTCGGCTGTTGGCGGCGCTGGCGGCCCGTCGGGATGCCGAACTCGAG
+CGTGGGGTTTGTCTAGTTGGTCCGCACCGTGACGACCTAATACTGCGACTAGGCGATCAA
+CCCGCGAAAGGATTTGCTAGCCATGGGGAGGCGTGGTCGTTGGCGGTGGCACTGCGGTTG
+GCGGCCTATCAACTGTTACGCGTTGATGGTGGTGAGCCGGTGTTGTTGCTCGACGACGTG
+TTCGCCGAACTGGATGTCATGCGCCGTCGAGCGTTGGCGACGGCGGCCGAGTCCGCCGAA
+CAGGTGTTGGTGACTGCCGCGGTGCTCGAGGATATTCCCGCCGGCTGGGACGCCAGGCGG
+GTGCACATCGATGTGCGTGCCGATGACACCGGATCGATGTCGGTGGTTCTGCCATGACGG
+GTTCTGTTGACCGGCCCGACCAGAATCGCGGTGAGCGATCAATGAAGTCACCAGGGTTGG
+ATTTGGTCAGGCGCACCCTGGACGAAGCTCGTGCTGCTGCCCGCGCGCGCGGACAAGACG
+CCGGTCGAGGGCGGGTCGCTTCCGTTGCGTCGGGTCGGGTGGCCGGACGGCGACGAAGCT
+GGTCGGGTCCGGGGCCCGACATTCGTGATCCACAACCGCTGGGTAAGGCCGCTCGTGAGC
+TGGCAAAGAAACGCGGCTGGTCGGTGCGGGTCGCCGAGGGTATGGTGCTCGGCCAGTGGT
+CTGCGGTGGTCGGCCACCAGATCGCCGAACATGCACGCCCGACTGCGCTAAACGACGGGG
+TGTTGAGCGTGATTGCGGAGTCGACGGCGTGGGCGACGCAGTTGAGGATCATGCAGGCCC
+AGCTTCTGGCCAAGATCGCCGCAGCGGTTGGCAACGATGTGGTGCGATCGCTAAAGATCA
+CCGGGCCGGCGGCACCATCGTGGCGCAAGGGGCCTCGCCATATTGCCGGTAGGGGTCCGC
+GCGACACCTACGGATAACACGTCGATCGGCCCAGAACAAGGCGCTCCGGTCCCGGCCTGA
+GAGCCTCGAGGACGAAGCGGATCCGTATGCCGGACGTCGGGACGCACCAGGAAGAAAGAT
+GTCCGACGCACGGCGCGGTTAGATGGGTAAAAACGAGGCCAGAAGATCGGCCCTGGCGCC
+CGATCACGGTACAGTGGTGTGCGACCCCCTGCGGCGACTCAACCGCATGCACGCAACCCC
+TGAGGAGAGTATTCGGATCGTGGCTGCCCAGAAAAAGAAGGCCCAAGACGAATACGGCGC
+TGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGCAAACGTCCCGGCATGTACAT
+TGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCGACAACGCGGT
+CGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGG
+TGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACC
+GACCGTCGACGTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTA
+TGCGATATCTGGTGGTCTGCACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCG
+GCTCGAAGTCGAGATCAAGCGCGACGGGTACGAGTGGTCTCAGGTTTATGAGAAGTCGGA
+ACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACGGGGTCAACGGTGCGGTTCTG
+GGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCGCCCGCCGGCT
+GCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGAC
+CCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAG
+TGAACGCGCAGCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCC
+GGGTGGCCTGGTGGACTTCGTGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAG
+CATCGTGGACTTTTCCGGCAAGGGCACCGGGCACGAGGTGGAGATCGCGATGCAATGGAA
+CGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACCATCAACACCCACGAGGGCGG
+CACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGTACGCCAAGGA
+CCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT
+GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAA
+GTTGGGCAACACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAACGAACAGCTGACCCA
+CTGGTTTGAAGCCAACCCCACCGACGCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGC
+GCAAGCCCGTATCGCGGCACGTAAGGCACGAGAGTTGGTGCGGCGTAAGAGCGCCACCGA
+CATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCCACGGATCCGCGCAAGTCCGA
+ACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTCGCGATTCGAT
+GTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA
+CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCA
+CGACGAGTTCGATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGA
+TGTTGACGGCCAACATATTTCCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCC
+GCTCATCGAGAACGGGCATGTGTTTTTGGCACAACCGCCGCTGTACAAACTCAAGTGGCA
+GCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGCGACGGTCTGCTGGAGGCGGG
+GCTGAAGGCCGGGAAGAAGATCAACAAGGAAGACGGCATTCAGCGGTACAAGGGTCTAGG
+TGAAATGGACGCTAAGGAGTTGTGGGAGACCACCATGGATCCCTCGGTTCGTGTGTTGCG
+TCAAGTGACGCTGGACGACGCCGCCGCCGCCGACGAGTTGTTCTCCATCCTGATGGGCGA
+GGACGTCGACGCGCGGCGCAGCTTTATCACCCGCAACGCCAAGGATGTTCGGTTCCTGGA
+TGTCTAACGCAACCCTGCGTTCGATTGCAAACGAGGAATAGATGACAGACACGACGTTGC
+CGCCTGACGACTCGCTCGACCGGATCGAACCGGTTGACATCGAGCAGGAGATGCAGCGCA
+GCTACATCGACTATGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCGGAGGTGCGCGACG
+GGCTCAAGCCCGTGCATCGCCGGGTGCTCTATGCAATGTTCGATTCCGGCTTCCGCCCGG
+ACCGCAGCCACGCCAAGTCGGCCCGGTCGGTTGCCGAGACCATGGGCAACTACCACCCGC
+ACGGCGACGCGTCGATCTACGACAGCCTGGTGCGCATGGCCCAGCCCTGGTCGCTGCGCT
+ACCCGCTGGTGGACGGCCAGGGCAACTTCGGCTCGCCAGGCAATGACCCACCGGCGGCGA
+TGAGGTACACCGAAGCCCGGCTGACCCCGTTGGCGATGGAGATGCTGAGGGAAATCGACG
+AGGAGACAGTCGATTTCATCCCTAACTACGACGGCCGGGTGCAAGAGCCGACGGTGCTAC
+CCAGCCGGTTCCCCAACCTGCTGGCCAACGGGTCAGGCGGCATCGCGGTCGGCATGGCAA
+CCAATATCCCGCCGCACAACCTGCGTGAGCTGGCCGACGCGGTGTTCTGGGCGCTGGAGA
+ATCACGACGCCGACGAAGAGGAGACCCTGGCCGCGGTCATGGGGCGGGTTAAAGGCCCGG
+ACTTCCCGACCGCCGGACTGATCGTCGGATCCCAGGGCACCGCTGATGCCTACAAAACTG
+GCCGCGGCTCCATTCGAATGCGCGGAGTTGTTGAGGTAGAAGAGGATTCCCGCGGTCGTA
+CCTCGCTGGTGATCACCGAGTTGCCGTATCAGGTCAACCACGACAACTTCATCACTTCGA
+TCGCCGAACAGGTCCGAGACGGCAAGCTGGCCGGCATTTCCAACATTGAGGACCAGTCTA
+GCGATCGGGTCGGTTTACGCATCGTCATCGAGATCAAGCGCGATGCGGTGGCCAAGGTGG
+TGATCAATAACCTTTACAAGCACACCCAGCTGCAGACCAGCTTTGGCGCCAACATGCTAG
+CGATCGTCGACGGGGTGCCGCGCACGCTGCGGCTGGACCAGCTGATCCGCTATTACGTTG
+ACCACCAACTCGACGTCATTGTGCGGCGCACCACCTACCGGCTGCGCAAGGCAAACGAGC
+GAGCCCACATTCTGCGCGGCCTGGTTAAAGCGCTCGACGCGCTGGACGAGGTCATTGCAC
+TGATCCGGGCGTCGGAGACCGTCGATATCGCCCGGGCCGGACTGATCGAGCTGCTCGACA
+TCGACGAGATCCAGGCCCAGGCAATCCTGGACATGCAGTTGCGGCGCCTGGCCGCACTGG
+AACGCCAGCGCATCATCGACGACCTGGCCAAAATCGAGGCCGAGATCGCCGATCTGGAAG
+ACATCCTGGCAAAACCCGAGCGGCAGCGTGGGATCGTGCGCGACGAACTCGCCGAAATCG
+TGGACAGGCACGGCGACGACCGGCGTACCCGGATCATCGCGGCCGACGGAGACGTCAGCG
+ACGAGGATTTGATCGCCCGCGAGGACGTCGTTGTCACTATCACCGAAACGGGATACGCCA
+AGCGCACCAAGACCGATCTGTATCGCAGCCAGAAACGCGGCGGCAAGGGCGTGCAGGGTG
+CGGGGTTGAAGCAGGACGACATCGTCGCGCACTTCTTCGTGTGCTCCACCCACGATTTGA
+TCCTGTTCTTCACCACCCAGGGACGGGTTTATCGGGCCAAGGCCTACGACTTGCCCGAGG
+CCTCCCGGACGGCGCGCGGGCAGCACGTGGCCAACCTGTTAGCCTTCCAGCCCGAGGAAC
+GCATCGCCCAGGTCATCCAGATTCGCGGCTACACCGACGCCCCGTACCTGGTGCTGGCCA
+CTCGCAACGGGCTGGTGAAAAAGTCCAAGCTGACCGACTTCGACTCCAATCGCTCGGGCG
+GAATCGTGGCGGTCAACCTGCGCGACAACGACGAGCTGGTCGGTGCGGTGCTGTGTTCGG
+CCGGCGACGACCTGCTGCTGGTCTCGGCCAACGGGCAGTCCATCAGGTTCTCGGCGACCG
+ACGAGGCGCTGCGGCCAATGGGTCGTGCCACCTCGGGTGTGCAGGGCATGCGGTTCAATA
+TCGACGACCGGCTGCTGTCGCTGAACGTCGTGCGTGAAGGCACCTATCTGCTGGTGGCGA
+CGTCAGGGGGCTATGCGAAACGTACCGCGATCGAGGAATACCCGGTACAGGGCCGCGGCG
+GTAAAGGTGTGCTGACGGTCATGTACGACCGCCGGCGCGGCAGGTTGGTTGGGGCGTTGA
+TTGTCGACGACGACAGCGAGCTGTATGCCGTCACTTCCGGCGGTGGCGTGATCCGCACCG
+CGGCACGCCAGGTTCGCAAGGCGGGACGGCAGACCAAGGGTGTTCGGTTGATGAATCTGG
+GCGAGGGCGACACACTGTTGGCCATCGCGCGCAACGCCGAAGAAAGTGGCGACGATAATG
+CCGTGGACGCCAACGGCGCAGACCAGACGGGCAATTAATCAGGCTCGCCCGACGACGATG
+CGGATCGCGTAGCGATCTGAGGAGGAATCGGGCAGCTAGGCTCGGCAGCCGGGTACGAGT
+GTTAGGAGTCGGGGTGACTGCACCGAACGAGCCGGGGGCGCTCAGCAAGGGCGACGGCCC
+GAATGCGGATGGCTTGGTCGACCGTGGGGGCGCACATCGG
diff -r 000000000000 -r 79f5d34da277 test-data/sample1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample1.vcf	Fri Nov 25 07:30:19 2016 -0500
@@ -0,0 +1,98 @@
+##fileformat=VCFv4.1
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Sun Jun 07 11:35:17 SAST 2015",Epoch=1433669717749,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[./R_2997_878#L6-_.R.bam.sorted_dedup.bam_realigned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=reference_H37Rv.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=4 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false doNotRunPhysicalPhasing=true pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive)
+##GVCFBlock=minGQ=1(inclusive),maxGQ=2(exclusive)
+##GVCFBlock=minGQ=10(inclusive),maxGQ=11(exclusive)
+##GVCFBlock=minGQ=11(inclusive),maxGQ=12(exclusive)
+##GVCFBlock=minGQ=12(inclusive),maxGQ=13(exclusive)
+##GVCFBlock=minGQ=13(inclusive),maxGQ=14(exclusive)
+##GVCFBlock=minGQ=14(inclusive),maxGQ=15(exclusive)
+##GVCFBlock=minGQ=15(inclusive),maxGQ=16(exclusive)
+##GVCFBlock=minGQ=16(inclusive),maxGQ=17(exclusive)
+##GVCFBlock=minGQ=17(inclusive),maxGQ=18(exclusive)
+##GVCFBlock=minGQ=18(inclusive),maxGQ=19(exclusive)
+##GVCFBlock=minGQ=19(inclusive),maxGQ=20(exclusive)
+##GVCFBlock=minGQ=2(inclusive),maxGQ=3(exclusive)
+##GVCFBlock=minGQ=20(inclusive),maxGQ=21(exclusive)
+##GVCFBlock=minGQ=21(inclusive),maxGQ=22(exclusive)
+##GVCFBlock=minGQ=22(inclusive),maxGQ=23(exclusive)
+##GVCFBlock=minGQ=23(inclusive),maxGQ=24(exclusive)
+##GVCFBlock=minGQ=24(inclusive),maxGQ=25(exclusive)
+##GVCFBlock=minGQ=25(inclusive),maxGQ=26(exclusive)
+##GVCFBlock=minGQ=26(inclusive),maxGQ=27(exclusive)
+##GVCFBlock=minGQ=27(inclusive),maxGQ=28(exclusive)
+##GVCFBlock=minGQ=28(inclusive),maxGQ=29(exclusive)
+##GVCFBlock=minGQ=29(inclusive),maxGQ=30(exclusive)
+##GVCFBlock=minGQ=3(inclusive),maxGQ=4(exclusive)
+##GVCFBlock=minGQ=30(inclusive),maxGQ=31(exclusive)
+##GVCFBlock=minGQ=31(inclusive),maxGQ=32(exclusive)
+##GVCFBlock=minGQ=32(inclusive),maxGQ=33(exclusive)
+##GVCFBlock=minGQ=33(inclusive),maxGQ=34(exclusive)
+##GVCFBlock=minGQ=34(inclusive),maxGQ=35(exclusive)
+##GVCFBlock=minGQ=35(inclusive),maxGQ=36(exclusive)
+##GVCFBlock=minGQ=36(inclusive),maxGQ=37(exclusive)
+##GVCFBlock=minGQ=37(inclusive),maxGQ=38(exclusive)
+##GVCFBlock=minGQ=38(inclusive),maxGQ=39(exclusive)
+##GVCFBlock=minGQ=39(inclusive),maxGQ=40(exclusive)
+##GVCFBlock=minGQ=4(inclusive),maxGQ=5(exclusive)
+##GVCFBlock=minGQ=40(inclusive),maxGQ=41(exclusive)
+##GVCFBlock=minGQ=41(inclusive),maxGQ=42(exclusive)
+##GVCFBlock=minGQ=42(inclusive),maxGQ=43(exclusive)
+##GVCFBlock=minGQ=43(inclusive),maxGQ=44(exclusive)
+##GVCFBlock=minGQ=44(inclusive),maxGQ=45(exclusive)
+##GVCFBlock=minGQ=45(inclusive),maxGQ=46(exclusive)
+##GVCFBlock=minGQ=46(inclusive),maxGQ=47(exclusive)
+##GVCFBlock=minGQ=47(inclusive),maxGQ=48(exclusive)
+##GVCFBlock=minGQ=48(inclusive),maxGQ=49(exclusive)
+##GVCFBlock=minGQ=49(inclusive),maxGQ=50(exclusive)
+##GVCFBlock=minGQ=5(inclusive),maxGQ=6(exclusive)
+##GVCFBlock=minGQ=50(inclusive),maxGQ=51(exclusive)
+##GVCFBlock=minGQ=51(inclusive),maxGQ=52(exclusive)
+##GVCFBlock=minGQ=52(inclusive),maxGQ=53(exclusive)
+##GVCFBlock=minGQ=53(inclusive),maxGQ=54(exclusive)
+##GVCFBlock=minGQ=54(inclusive),maxGQ=55(exclusive)
+##GVCFBlock=minGQ=55(inclusive),maxGQ=56(exclusive)
+##GVCFBlock=minGQ=56(inclusive),maxGQ=57(exclusive)
+##GVCFBlock=minGQ=57(inclusive),maxGQ=58(exclusive)
+##GVCFBlock=minGQ=58(inclusive),maxGQ=59(exclusive)
+##GVCFBlock=minGQ=59(inclusive),maxGQ=60(exclusive)
+##GVCFBlock=minGQ=6(inclusive),maxGQ=7(exclusive)
+##GVCFBlock=minGQ=60(inclusive),maxGQ=70(exclusive)
+##GVCFBlock=minGQ=7(inclusive),maxGQ=8(exclusive)
+##GVCFBlock=minGQ=70(inclusive),maxGQ=80(exclusive)
+##GVCFBlock=minGQ=8(inclusive),maxGQ=9(exclusive)
+##GVCFBlock=minGQ=80(inclusive),maxGQ=90(exclusive)
+##GVCFBlock=minGQ=9(inclusive),maxGQ=10(exclusive)
+##GVCFBlock=minGQ=90(inclusive),maxGQ=99(exclusive)
+##GVCFBlock=minGQ=99(inclusive),maxGQ=2147483647(exclusive)
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##contig=<ID=Chromosome,length=10000>
+##reference=file:///net/datasrv3hs.sanbi.ac.za/cip0/research/scratch/zahra/TB_wrk/TB_Variant_analysis/MDR/reference_H37Rv.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	./R_2997_878#L6-_.R
+Chromosome	1849	.	C	A,<NON_REF>	4546	.	DP=129;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,129,0:129:99:4576,0,4576:0,0,56,73
+Chromosome	1977	.	A	G,<NON_REF>	1957	.	DP=54;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,54,0:54:99:1987,0,1987:0,0,13,41
+Chromosome	4013	.	T	C,<NON_REF>	2397	.	DP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,66,0:66:99:2427,0,2427:0,0,31,35
+Chromosome	7362	.	G	C,<NON_REF>	2519	.	DP=68;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,68,0:68:99:2549,0,2549:0,0,28,40
+Chromosome	7585	.	G	C,<NON_REF>	1295	.	DP=36;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,36,0:36:99:1325,0,1325:0,0,26,10
+Chromosome	9304	.	G	A,<NON_REF>	1945	.	DP=58;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,58,0:58:99:1975,0,1975:0,0,23,35
diff -r 000000000000 -r 79f5d34da277 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Fri Nov 25 07:30:19 2016 -0500
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r 79f5d34da277 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Nov 25 07:30:19 2016 -0500
@@ -0,0 +1,6 @@
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r 79f5d34da277 vcftools_consensus.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcftools_consensus.xml	Fri Nov 25 07:30:19 2016 -0500
@@ -0,0 +1,78 @@
+<tool id="vcftools_consensus" name="Consensus" version="0.1.11">
+    <description>Apply VCF variants to a fasta file to create consensus sequence</description>
+
+    <requirements>
+        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="1.3.2">htslib</requirement>
+        <requirement type="package" version="0.1.11">vcftools</requirement>
+    </requirements>
+
+    <stdio>
+        <!--<regex match=".*" source="both" level="log" description="tool progress"/>-->
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+
+    <command>
+    <![CDATA[
+        ln -s '${variants}' variants.vcf &&
+        vcf-sort variants.vcf | bgzip -c > variants.sorted.vcf.gz &&
+
+        tabix -p vcf variants.sorted.vcf.gz  &&
+
+        #if $ref_genome_source.index_source == 'history':
+          ln -s '${ref_genome_source.ref_file}' reference.fasta &&
+          samtools faidx reference.fasta &&
+        #end if
+
+        cat
+        #if $ref_genome_source.index_source == 'builtin'
+          '${ ref_genome_source.reference_genome.fields.path }'
+        #else
+          reference.fasta
+        #end if
+        | vcf-consensus variants.sorted.vcf.gz > '${output}'
+    ]]>
+    </command>
+    <inputs>
+      <conditional name="ref_genome_source">
+        <param name="index_source" type="select" label="Reference genome source">
+          <option value="builtin">Built-in genome</option>
+          <option value="history">History</option>
+        </param>
+        <when value="builtin">
+          <param name="reference_genome" type="select">
+            <options from_data_table="fasta_indexes">
+              <filter column="2" type="sort_by" />
+              <validator message="No suitable reference genomes found" type="no_options" />
+            </options>
+          </param>
+        </when>
+        <when value="history">
+          <param name="ref_file" type="data" format="fasta" label="Reference genome" />
+        </when>
+      </conditional>
+      <param name="variants" label="Datasets containing Variants" type="data" format="vcf" />
+    </inputs>
+
+    <outputs>
+        <data name="output" format="fasta"/>
+    </outputs>
+
+    <tests>
+      <test>
+        <param name="index_source" value="history" />
+        <param ftype="fasta" name="ref_file" value="reference.fasta" />
+        <param ftype="vcf" name="variants" value="sample1.vcf" />
+        <output name="output" ftype="fasta" file="output1.fasta" />
+      </test>
+    </tests>
+
+    <help>
+        Please see the VCFtools `documentation`__ for help and further information.
+
+        .. __: http://vcftools.sourceforge.net/docs.html
+    </help>
+    <citations>
+      <citation type="doi">10.1093/bioinformatics/btr330</citation>
+    </citations>
+</tool>