# HG changeset patch
# User iuc
# Date 1462224430 14400
# Node ID a531317a35278b993fa6c32faebe87cfbdb747e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
diff -r 000000000000 -r a531317a3527 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Mon May 02 17:27:10 2016 -0400
@@ -0,0 +1,21 @@
+# bcftools (v1.2)
+
+This aims to be a "faithful" rendering of the bcftool suite. I.e. options are
+presented essentially as closely to the command line version as is useful.
+
+This may not appeal to all, if you'd like to see smaller and more dedicated
+tools (e.g. "intersect", "union" and "complement" being separate tools instead
+of all of them included in the "isec" tool,) please feel free to file an issue.
+
+## TODO:
+
+- Galaxy needs datatypes for bcf and vcf files, block-gzipped and uncompressed.
+- Galaxy needs to automatically index those files with tabix
+
+## "Complete" Wrappers
+
+The wrappers were automatically generated in bulk. That doesn't get them 100%
+of the way there (e.g. meaningful test cases), so the rest of the process is a
+bit slower.
+
+- bcftools call
diff -r 000000000000 -r a531317a3527 bcftools_call.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_call.xml Mon May 02 17:27:10 2016 -0400
@@ -0,0 +1,159 @@
+
+
+ SNP/indel variant calling from VCF/BCF
+
+ call
+ macros.xml
+
+
+
+
+$output_file
+]]>
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diff -r 000000000000 -r a531317a3527 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon May 02 17:27:10 2016 -0400
@@ -0,0 +1,74 @@
+
+
+ 1.2
+
+
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+ bcftools
+
+
+
+ &1 | grep 'Version:']]>
+
+
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+ 10.1093/bioinformatics/btp352
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+#if $sec_default.regions_file:
+ --regions-file "${sec_default.regions_file}"
+#end if
+
+
+#if $sec_default.targets_file:
+ --targets-file "${sec_default.targets_file}"
+#end if
+
+
+#if $sec_default.samples_file:
+ --samples-file "${sec_default.samples_file}"
+#end if
+
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diff -r 000000000000 -r a531317a3527 test-data/mpileup.1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.1.out Mon May 02 17:27:10 2016 -0400
@@ -0,0 +1,40 @@
+##fileformat=VCFv4.2
+##FILTER=
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+##reference=file://xxx//mpileup.ref.fa.gz
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diff -r 000000000000 -r a531317a3527 test-data/mpileup.2.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.2.out Mon May 02 17:27:10 2016 -0400
@@ -0,0 +1,53 @@
+##fileformat=VCFv4.2
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+##reference=file://xxx//mpileup.ref.fa.gz
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diff -r 000000000000 -r a531317a3527 test-data/mpileup.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.vcf Mon May 02 17:27:10 2016 -0400
@@ -0,0 +1,4127 @@
+##fileformat=VCFv4.2
+##FILTER=
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=
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+17 22 . C 0 . DP=13;I16=13,0,0,0,511,20289,0,0,470,19210,0,0,223,4993,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,115:6:0 0,12,91:4:0 0,9,76:3:0
+17 23 . A 0 . DP=14;I16=14,0,0,0,513,19399,0,0,530,22810,0,0,223,4931,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,133:7:0 0,12,82:4:0 0,9,82:3:0
+17 24 . T 0 . DP=14;I16=14,0,0,0,534,20540,0,0,530,22810,0,0,224,4882,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,131:7:0 0,12,96:4:0 0,9,80:3:0
+17 25 . A 0 . DP=15;I16=15,0,0,0,561,21133,0,0,590,26410,0,0,225,4847,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,140:8:0 0,12,96:4:0 0,9,81:3:0
+17 26 . G 0 . DP=15;I16=15,0,0,0,591,23429,0,0,590,26410,0,0,227,4827,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,151:8:0 0,12,96:4:0 0,9,81:3:0
+17 27 . A 0 . DP=15;I16=15,0,0,0,588,23120,0,0,590,26410,0,0,229,4823,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,146:8:0 0,12,98:4:0 0,9,83:3:0
+17 28 . T 0 . DP=16;I16=16,0,0,0,605,23001,0,0,650,30010,0,0,231,4835,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,147:8:0 0,12,97:4:0 0,12,101:4:0
+17 29 . A 0 . DP=17;I16=17,0,0,0,615,22533,0,0,710,33610,0,0,234,4864,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,146:8:0 0,15,102:5:0 0,12,104:4:0
+17 30 . A 0 . DP=17;I16=17,0,0,0,660,25914,0,0,710,33610,0,0,238,4912,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,149:8:0 0,15,115:5:0 0,12,108:4:0
+17 31 . T 0 . DP=17;I16=17,0,0,0,656,25392,0,0,710,33610,0,0,242,4980,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,150:8:0 0,15,113:5:0 0,12,105:4:0
+17 32 . T 0 . DP=17;I16=17,0,0,0,605,21789,0,0,741,36369,0,0,247,5067,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,143:8:0 0,15,104:5:0 0,12,104:4:0
+17 33 . G 0 . DP=17;I16=17,0,0,0,659,25757,0,0,741,36369,0,0,252,5124,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,158:8:0 0,15,118:5:0 0,12,105:4:0
+17 34 . C 0 . DP=17;I16=17,0,0,0,658,25704,0,0,741,36369,0,0,257,5203,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,151:8:0 0,15,121:5:0 0,12,106:4:0
+17 35 . A 0 . DP=18;I16=18,0,0,0,677,25881,0,0,801,39969,0,0,262,5304,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,152:8:0 0,15,109:5:0 0,15,121:5:0
+17 36 . T 0 . DP=18;I16=18,0,0,0,678,25796,0,0,801,39969,0,0,268,5428,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,151:8:0 0,15,114:5:0 0,15,125:5:0
+17 37 . G 0 . DP=18;I16=18,0,0,0,685,26291,0,0,801,39969,0,0,274,5576,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,157:8:0 0,15,116:5:0 0,15,126:5:0
+17 38 . A 0 . DP=18;I16=18,0,0,0,697,27245,0,0,801,39969,0,0,280,5748,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,152:8:0 0,15,116:5:0 0,15,129:5:0
+17 39 . C 0 . DP=16;I16=16,0,0,0,591,22311,0,0,743,38287,0,0,288,5942,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,148:7:0 0,12,94:4:0 0,15,123:5:0
+17 40 . A 0 . DP=16;I16=16,0,0,0,630,24896,0,0,743,38287,0,0,295,6107,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,146:7:0 0,12,104:4:0 0,15,127:5:0
+17 41 . A 0 . DP=17;I16=17,0,0,0,645,24685,0,0,803,41887,0,0,302,6294,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,151:8:0 0,12,104:4:0 0,15,131:5:0
+17 42 . T 0 . DP=17;I16=17,0,0,0,618,23118,0,0,803,41887,0,0,310,6504,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,155:8:0 0,12,82:4:0 0,15,127:5:0
+17 43 . T 0 . DP=17;I16=17,0,0,0,631,23689,0,0,803,41887,0,0,318,6738,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,151:8:0 0,12,101:4:0 0,15,129:5:0
+17 44 . G 0 . DP=17;I16=17,0,0,0,664,26162,0,0,803,41887,0,0,324,6896,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,164:8:0 0,12,100:4:0 0,15,129:5:0
+17 45 . C 0 . DP=17;I16=17,0,0,0,657,25525,0,0,803,41887,0,0,329,7027,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,163:8:0 0,12,108:4:0 0,15,125:5:0
+17 46 . C 0 . DP=17;I16=17,0,0,0,646,25244,0,0,803,41887,0,0,334,7180,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,161:8:0 0,12,98:4:0 0,15,131:5:0
+17 47 . T 0 . DP=17;I16=17,0,0,0,700,28998,0,0,803,41887,0,0,339,7355,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,165:8:0 0,12,110:4:0 0,15,136:5:0
+17 48 . T 0 . DP=17;I16=17,0,0,0,648,25020,0,0,803,41887,0,0,343,7501,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,155:8:0 0,12,105:4:0 0,15,131:5:0
+17 49 . G 0 . DP=18;I16=18,0,0,0,686,26674,0,0,832,42728,0,0,346,7616,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,158:8:0 0,15,119:5:0 0,15,128:5:0
+17 50 . T 0 . DP=18;I16=17,0,0,0,650,24972,0,0,772,39128,0,0,332,7426,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,155:8:0 0,12,101:4:0 0,15,128:5:0
+17 51 . C 0 . DP=18;I16=18,0,0,0,681,26529,0,0,832,42728,0,0,353,7853,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,167:8:0 0,15,99:5:0 0,15,127:5:0
+17 52 . C 0 . DP=18;I16=17,0,0,0,645,24983,0,0,803,41887,0,0,353,7965,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,164:8:0 0,12,99:4:0 0,15,128:5:0
+17 53 . C 0 . DP=18;I16=18,0,0,0,687,26735,0,0,832,42728,0,0,359,8113,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,164:8:0 0,15,113:5:0 0,15,132:5:0
+17 54 . T 0 . DP=18;I16=18,0,0,0,736,30194,0,0,832,42728,0,0,361,8219,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,163:8:0 0,15,128:5:0 0,15,136:5:0
+17 55 . G 0 . DP=18;I16=18,0,0,0,674,26082,0,0,832,42728,0,0,362,8290,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,168:8:0 0,15,112:5:0 0,15,122:5:0
+17 56 . C 0 . DP=18;I16=18,0,0,0,701,27645,0,0,832,42728,0,0,363,8375,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,162:8:0 0,15,121:5:0 0,15,131:5:0
+17 57 . T 0 . DP=18;I16=17,0,0,0,694,29118,0,0,803,41887,0,0,356,8410,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,163:8:0 0,12,117:4:0 0,15,138:5:0
+17 58 . G 0 . DP=17;I16=16,0,0,0,616,24356,0,0,774,41046,0,0,356,8454,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,159:7:0 0,12,95:4:0 0,15,131:5:0
+17 59 . A 0 . DP=17;I16=17,0,0,0,656,26038,0,0,803,41887,0,0,366,8606,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,155:7:0 0,15,116:5:0 0,15,134:5:0
+17 60 . A 0 . DP=17;I16=17,0,0,0,663,26463,0,0,803,41887,0,0,367,8687,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,151:7:0 0,15,127:5:0 0,15,138:5:0
+17 61 . T 0 . DP=17;I16=16,0,0,0,605,23215,0,0,774,41046,0,0,355,8583,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,152:7:0 0,12,101:4:0 0,15,131:5:0
+17 62 . G 0 . DP=18;I16=17,0,0,0,646,24868,0,0,834,44646,0,0,353,8557,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,158:7:0 0,12,103:4:0 0,18,141:6:0
+17 63 . T 0 . DP=18;I16=17,0,0,0,590,21682,0,0,803,41887,0,0,341,8111,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,148:7:0 0,12,80:4:0 0,18,144:6:0
+17 64 . G 0 . DP=19;I16=19,0,0,0,696,26416,0,0,923,49087,0,0,366,8758,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,169:8:0 0,15,103:5:0 0,18,142:6:0
+17 65 . C 0 . DP=18;I16=18,0,0,0,686,26512,0,0,894,48246,0,0,367,8743,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,163:7:0 0,15,116:5:0 0,18,147:6:0
+17 66 . T 0 . DP=18;I16=17,0,0,0,691,28315,0,0,834,44646,0,0,342,8068,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,164:7:0 0,12,110:4:0 0,18,153:6:0
+17 67 . C 0 . DP=17;I16=17,0,0,0,645,25313,0,0,834,44646,0,0,341,7983,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,163:7:0 0,12,94:4:0 0,18,147:6:0
+17 68 . T 0 . DP=17;I16=17,0,0,0,691,28307,0,0,834,44646,0,0,339,7863,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,165:7:0 0,12,108:4:0 0,18,151:6:0
+17 69 . G 0 . DP=17;I16=17,0,0,0,657,25721,0,0,865,47405,0,0,338,7758,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,172:8:0 0,9,93:3:0 0,18,142:6:0
+17 70 . G 0 . DP=17;I16=16,0,0,0,575,21391,0,0,836,46564,0,0,317,7227,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,162:8:0 0,6,64:2:0 0,18,141:6:0
+17 71 . G 0 . DP=17;I16=15,0,0,0,571,21975,0,0,776,42964,0,0,307,7029,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,170:8:0 0,6,72:2:0 0,15,130:5:0
+17 72 . G 0 . DP=17;I16=15,0,0,0,572,22002,0,0,776,42964,0,0,305,6907,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,171:8:0 0,6,65:2:0 0,15,131:5:0
+17 73 . T 0 . DP=18;I16=16,0,0,0,623,25301,0,0,836,46564,0,0,314,6918,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,158:8:0 0,6,94:2:0 0,18,143:6:0
+17 74 . C 0 . DP=18;I16=17,0,0,0,674,28110,0,0,865,47405,0,0,338,7468,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,176:8:0 0,9,106:3:0 0,18,141:6:0
+17 75 . T 0 . DP=18;I16=16,0,0,0,685,30675,0,0,836,46564,0,0,312,6782,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,175:8:0 0,6,90:2:0 0,18,150:6:0
+17 76 . C 0 . DP=18;I16=17,0,0,0,683,29481,0,0,865,47405,0,0,336,7360,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,174:8:0 0,9,98:3:0 0,18,148:6:0
+17 77 . T 0 . DP=18;I16=16,0,0,0,710,33072,0,0,836,46564,0,0,310,6702,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,179:8:0 0,6,92:2:0 0,18,154:6:0
+17 78 . G 0 . DP=18;I16=16,0,0,0,692,31158,0,0,836,46564,0,0,309,6683,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,180:8:0 0,6,94:2:0 0,18,149:6:0
+17 79 . G 0 . DP=18;I16=15,0,0,0,605,26629,0,0,776,42964,0,0,283,6053,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,168:8:0 0,3,60:1:0 0,18,149:6:0
+17 80 . G 0 . DP=18;I16=17,0,0,0,688,30128,0,0,865,47405,0,0,332,7312,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,173:8:0 0,9,106:3:0 0,18,151:6:0
+17 81 . G 0 . DP=18;I16=16,0,0,0,631,27429,0,0,836,46564,0,0,326,7310,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,165:7:0 0,9,97:3:0 0,18,145:6:0
+17 82 . T 0 . DP=18;I16=15,0,0,0,559,22735,0,0,776,42964,0,0,280,6122,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,154:8:0 0,3,60:1:0 0,18,131:6:0
+17 83 . C 0 . DP=18;I16=16,0,0,0,622,27146,0,0,836,46564,0,0,304,6798,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,170:8:0 0,6,75:2:0 0,18,145:6:0
+17 84 . T 0 . DP=18;I16=17,0,0,0,705,32445,0,0,865,47405,0,0,328,7488,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,181:8:0 0,9,85:3:0 0,18,154:6:0
+17 85 . C 0 . DP=18;I16=17,0,0,0,708,31222,0,0,865,47405,0,0,327,7567,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,181:8:0 0,9,108:3:0 0,18,153:6:0
+17 86 . A 0 . DP=18;I16=17,0,0,0,692,29540,0,0,865,47405,0,0,326,7660,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,169:8:0 0,9,111:3:0 0,18,149:6:0
+17 87 . C 0 . DP=18;I16=17,0,0,0,683,29493,0,0,896,50164,0,0,326,7766,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,174:8:0 0,9,103:3:0 0,18,148:6:0
+17 88 . C 0 . DP=18;I16=17,0,0,0,703,31005,0,0,896,50164,0,0,326,7834,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,174:8:0 0,9,113:3:0 0,18,153:6:0
+17 89 . C 0 . DP=18;I16=17,0,0,0,697,30875,0,0,896,50164,0,0,326,7914,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,176:8:0 0,9,103:3:0 0,18,154:6:0
+17 90 . A 0 . DP=17;I16=16,0,0,0,668,29732,0,0,867,49323,0,0,326,7954,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,173:8:0 0,9,114:3:0 0,15,138:5:0
+17 91 . C 0 . DP=16;I16=15,0,0,0,613,26409,0,0,838,48482,0,0,327,8001,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,170:7:0 0,9,113:3:0 0,15,133:5:0
+17 92 . G 0 . DP=16;I16=15,0,0,0,499,18731,0,0,838,48482,0,0,328,8054,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,143:7:0 0,9,100:3:0 0,15,96:5:0
+17 93 . A 0 . DP=16;I16=15,0,0,0,635,28655,0,0,869,51241,0,0,329,8063,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,167:7:0 0,9,108:3:0 0,15,145:5:0
+17 94 . C 0 . DP=16;I16=15,0,0,0,607,25893,0,0,869,51241,0,0,331,8079,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,166:7:0 0,9,105:3:0 0,15,135:5:0
+17 95 . C 0 . DP=17;I16=15,0,0,0,615,26761,0,0,900,54000,0,0,306,7378,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,178:8:0 0,6,91:2:0 0,15,135:5:0
+17 96 . A 0 . DP=17;I16=16,0,0,0,625,26705,0,0,929,54841,0,0,332,7936,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,172:8:0 0,9,99:3:0 0,15,134:5:0
+17 97 . A 0 . DP=18;I16=17,0,0,0,675,29017,0,0,958,55682,0,0,333,7879,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,179:9:0 0,9,104:3:0 0,15,145:5:0
+17 98 . C 0 . DP=18;I16=17,0,0,0,655,27231,0,0,958,55682,0,0,333,7735,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,179:9:0 0,9,105:3:0 0,15,131:5:0
+17 99 . T 0 . DP=18;I16=17,0,0,0,720,32840,0,0,958,55682,0,0,333,7607,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,186:9:0 0,9,115:3:0 0,15,153:5:0
+17 100 . C 0 . DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,189:9:0 0,9,108:3:0 0,15,134:5:0
+17 101 . C 0 . DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,99:3:0 0,15,132:5:0
+17 102 . C 0 . DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,188:9:0 0,9,111:3:0 0,15,139:5:0
+17 103 . T 0 . DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,189:8:0 0,9,108:3:0 0,15,147:5:0
+17 104 . G 0 . DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,178:8:0 0,6,89:2:0 0,15,133:5:0
+17 105 . G 0 . DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,170:9:0 0,9,97:3:0 0,15,125:5:0
+17 106 . G 0 . DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,190:10:0 0,6,85:2:0 0,15,124:5:0
+17 107 . C 0 . DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,192:9:0 0,9,108:3:0 0,15,136:5:0
+17 108 . C 0 . DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,190:9:0 0,9,108:3:0 0,15,135:5:0
+17 109 . T 0 . DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,195:9:0 0,9,110:3:0 0,15,150:5:0
+17 110 . G 0 . DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,194:9:0 0,9,104:3:0 0,15,136:5:0
+17 111 . G 0 . DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,167:10:0 0,6,88:2:0 0,12,118:4:0
+17 112 . C 0 . DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,191:9:0 0,9,95:3:0 0,15,135:5:0
+17 113 . A 0 . DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,176:9:0 0,6,87:2:0 0,15,139:5:0
+17 114 . C 0 . DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,103:3:0 0,15,133:5:0
+17 115 . C 0 . DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,189:10:0 0,6,89:2:0 0,18,147:6:0
+17 116 . A 0 . DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,183:9:0 0,6,90:2:0 0,21,175:7:0
+17 117 . G 0 . DP=21;I16=17,1,0,0,723,31221,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,186:9:0 0,6,86:2:0 0,21,177:7:0
+17 118 . G 0 . DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,175:9:0 0,3,60:1:0 0,21,162:7:0
+17 119 . G 0 . DP=19;I16=16,1,0,0,629,26439,0,0,958,55682,0,0,267,5553,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,24,175:8:0 0,6,73:2:0 0,21,160:7:0
+17 120 . A 0 . DP=19;I16=16,1,0,0,672,29188,0,0,958,55682,0,0,264,5518,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,24,175:8:0 0,6,83:2:0 0,21,171:7:0
+17 121 . G 0 . DP=19;I16=16,1,0,0,662,28460,0,0,958,55682,0,0,260,5454,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,24,181:8:0 0,6,80:2:0 0,21,168:7:0
+17 122 . C 0 . DP=20;I16=17,1,0,0,716,31224,0,0,1018,59282,0,0,256,5410,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,24,181:8:0 0,9,99:3:0 0,21,178:7:0
+17 123 . T 0 . DP=18;I16=15,1,0,0,661,29997,0,0,898,52082,0,0,255,5385,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,21,167:7:0 0,9,112:3:0 0,18,166:6:0
+17 124 . T 0 . DP=19;I16=17,1,0,0,626,24802,0,0,987,56523,0,0,279,6003,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,27,154:9:0 0,9,104:3:0 0,18,154:6:0
+17 125 . A 0 . DP=18;I16=15,1,0,0,611,25689,0,0,898,52082,0,0,254,5340,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,21,154:7:0 0,9,104:3:0 0,18,162:6:0
+17 126 . A 0 . DP=18;I16=16,1,0,0,648,27366,0,0,927,52923,0,0,279,5947,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,24,162:8:0 0,9,107:3:0 0,18,174:6:0
+17 127 . C 0 . DP=18;I16=16,1,0,0,646,26972,0,0,927,52923,0,0,279,5949,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,24,163:8:0 0,9,109:3:0 0,18,160:6:0
+17 128 . A 0 . DP=18;I16=16,1,0,0,673,28797,0,0,927,52923,0,0,279,5971,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,24,169:8:0 0,9,111:3:0 0,18,162:6:0
+17 129 . A 0 . DP=17;I16=15,1,0,0,645,27891,0,0,867,49323,0,0,280,6012,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,24,168:8:0 0,9,113:3:0 0,15,159:5:0
+17 130 . A 0 . DP=17;I16=15,1,0,0,641,27295,0,0,867,49323,0,0,281,6071,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,24,169:8:0 0,9,113:3:0 0,15,152:5:0
+17 131 . C 0 . DP=16;I16=14,1,0,0,606,25732,0,0,838,48482,0,0,256,5472,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,21,167:7:0 0,9,110:3:0 0,15,147:5:0
+17 132 . A 0 . DP=16;I16=14,1,0,0,627,27579,0,0,838,48482,0,0,256,5514,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,21,169:7:0 0,9,110:3:0 0,15,151:5:0
+17 133 . T 0 . DP=15;I16=13,2,0,0,584,22816,0,0,838,48482,0,0,282,6196,0,0;QS=3,0;MQSB=0.576923;MQ0F=0 PL:DP:DV 0,21,163:7:0 0,9,105:3:0 0,15,150:5:0
+17 134 . C 0 . DP=15;I16=13,2,0,0,607,24653,0,0,838,48482,0,0,283,6267,0,0;QS=3,0;MQSB=0.576923;MQ0F=0 PL:DP:DV 0,21,177:7:0 0,9,105:3:0 0,15,152:5:0
+17 135 . T 0 . DP=15;I16=13,2,0,0,600,24178,0,0,838,48482,0,0,284,6352,0,0;QS=3,0;MQSB=0.576923;MQ0F=0 PL:DP:DV 0,21,173:7:0 0,9,106:3:0 0,15,156:5:0
+17 136 . G 0 . DP=15;I16=13,2,0,0,574,22258,0,0,838,48482,0,0,286,6450,0,0;QS=3,0;MQSB=0.576923;MQ0F=0 PL:DP:DV 0,21,172:7:0 0,9,105:3:0 0,15,134:5:0
+17 137 . T 0 . DP=15;I16=13,2,0,0,563,21377,0,0,838,48482,0,0,289,6561,0,0;QS=3,0;MQSB=0.576923;MQ0F=0 PL:DP:DV 0,21,160:7:0 0,9,104:3:0 0,15,139:5:0
+17 138 . C 0 . DP=15;I16=13,2,0,0,584,23088,0,0,838,48482,0,0,291,6637,0,0;QS=3,0;MQSB=0.576923;MQ0F=0 PL:DP:DV 0,21,172:7:0 0,9,108:3:0 0,15,142:5:0
+17 139 . C 0 . DP=15;I16=13,2,0,0,554,20790,0,0,838,48482,0,0,292,6680,0,0;QS=3,0;MQSB=0.576923;MQ0F=0 PL:DP:DV 0,21,161:7:0 0,9,106:3:0 0,15,143:5:0
+17 140 . A 0 . DP=15;I16=13,2,0,0,583,22789,0,0,838,48482,0,0,292,6690,0,0;QS=3,0;MQSB=0.576923;MQ0F=0 PL:DP:DV 0,21,163:7:0 0,9,107:3:0 0,15,153:5:0
+17 141 . G 0 . DP=14;I16=12,2,0,0,534,20750,0,0,778,44882,0,0,292,6664,0,0;QS=3,0;MQSB=0.583333;MQ0F=0 PL:DP:DV 0,18,158:6:0 0,9,108:3:0 0,15,142:5:0
+17 142 . C 0 . DP=14;I16=12,2,0,0,503,18593,0,0,778,44882,0,0,292,6650,0,0;QS=3,0;MQSB=0.583333;MQ0F=0 PL:DP:DV 0,18,157:6:0 0,9,97:3:0 0,15,129:5:0
+17 143 . G 0 . DP=14;I16=11,2,0,0,415,13657,0,0,718,41282,0,0,285,6599,0,0;QS=3,0;MQSB=0.590909;MQ0F=0 PL:DP:DV 0,18,128:6:0 0,9,95:3:0 0,12,97:4:0
+17 144 . A 0 . DP=14;I16=12,2,0,0,519,19725,0,0,778,44882,0,0,291,6609,0,0;QS=3,0;MQSB=0.583333;MQ0F=0 PL:DP:DV 0,18,152:6:0 0,9,105:3:0 0,15,129:5:0
+17 145 . A 0 . DP=14;I16=12,2,0,0,527,20289,0,0,778,44882,0,0,290,6584,0,0;QS=3,0;MQSB=0.583333;MQ0F=0 PL:DP:DV 0,18,153:6:0 0,9,106:3:0 0,15,138:5:0
+17 146 . T 0 . DP=14;I16=12,2,0,0,514,19484,0,0,778,44882,0,0,289,6573,0,0;QS=3,0;MQSB=0.583333;MQ0F=0 PL:DP:DV 0,18,152:6:0 0,9,103:3:0 0,15,128:5:0
+17 147 . A 0 . DP=14;I16=12,2,0,0,515,19213,0,0,778,44882,0,0,288,6576,0,0;QS=3,0;MQSB=0.583333;MQ0F=0 PL:DP:DV 0,18,150:6:0 0,9,99:3:0 0,15,140:5:0
+17 148 . C 0 . DP=14;I16=12,2,0,0,541,21019,0,0,778,44882,0,0,286,6542,0,0;QS=3,0;MQSB=0.583333;MQ0F=0 PL:DP:DV 0,18,157:6:0 0,9,106:3:0 0,15,146:5:0
+17 149 . C 0 . DP=14;I16=12,2,0,0,512,19326,0,0,778,44882,0,0,283,6471,0,0;QS=3,0;MQSB=0.583333;MQ0F=0 PL:DP:DV 0,18,148:6:0 0,9,109:3:0 0,15,140:5:0
+17 150 . T 0 . DP=13;I16=11,2,0,0,511,20251,0,0,749,44041,0,0,280,6362,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,18,153:6:0 0,6,84:2:0 0,15,152:5:0
+17 151 . G 0 . DP=13;I16=11,2,0,0,506,19826,0,0,749,44041,0,0,277,6263,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,18,157:6:0 0,6,84:2:0 0,15,144:5:0
+17 152 . C 0 . DP=14;I16=12,2,0,0,543,21283,0,0,809,47641,0,0,274,6174,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,168:7:0 0,6,84:2:0 0,15,146:5:0
+17 153 . A 0 . DP=14;I16=12,2,0,0,536,20594,0,0,809,47641,0,0,272,6096,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,156:7:0 0,6,81:2:0 0,15,153:5:0
+17 154 . T 0 . DP=14;I16=12,2,0,0,523,20051,0,0,809,47641,0,0,270,6030,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,159:7:0 0,6,83:2:0 0,15,139:5:0
+17 155 . C 0 . DP=14;I16=12,2,0,0,542,21254,0,0,809,47641,0,0,268,5976,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,172:7:0 0,6,85:2:0 0,15,139:5:0
+17 156 . C 0 . DP=14;I16=12,2,0,0,536,20884,0,0,809,47641,0,0,266,5934,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,163:7:0 0,6,84:2:0 0,15,150:5:0
+17 157 . C 0 . DP=14;I16=12,2,0,0,555,22081,0,0,809,47641,0,0,264,5904,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,169:7:0 0,6,85:2:0 0,15,149:5:0
+17 158 . T 0 . DP=14;I16=12,2,0,0,568,23154,0,0,809,47641,0,0,262,5886,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,170:7:0 0,6,84:2:0 0,15,159:5:0
+17 159 . A 0 . DP=15;I16=12,2,0,0,519,19467,0,0,809,47641,0,0,260,5880,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,157:7:0 0,6,83:2:0 0,15,135:5:0
+17 160 . G 0 . DP=15;I16=13,2,0,0,547,20633,0,0,869,51241,0,0,259,5887,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,165:7:0 0,6,85:2:0 0,18,139:6:0
+17 161 . A 0 . DP=15;I16=13,2,0,0,568,21610,0,0,869,51241,0,0,258,5908,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,157:7:0 0,6,83:2:0 0,18,162:6:0
+17 162 . A 0 . DP=15;I16=13,2,0,0,557,21139,0,0,869,51241,0,0,255,5843,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,147:7:0 0,6,87:2:0 0,18,167:6:0
+17 163 . G 0 . DP=14;I16=12,2,0,0,503,18645,0,0,809,47641,0,0,253,5791,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,21,153:7:0 0,6,79:2:0 0,15,138:5:0
+17 164 . T 0 . DP=14;I16=12,2,0,0,460,15968,0,0,809,47641,0,0,252,5750,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,18,131:6:0 0,6,79:2:0 0,18,136:6:0
+17 165 . G 0 . DP=14;I16=10,2,0,0,456,17460,0,0,689,40441,0,0,226,5094,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,18,149:6:0 0,6,80:2:0 0,12,122:4:0
+17 166 . A 0 . DP=14;I16=11,2,0,0,496,19138,0,0,749,44041,0,0,227,5077,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,18,145:6:0 0,6,82:2:0 0,15,148:5:0
+17 167 . A 0 . DP=14;I16=11,2,0,0,477,17851,0,0,749,44041,0,0,227,5071,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,18,132:6:0 0,6,86:2:0 0,15,147:5:0
+17 168 . G 0 . DP=14;I16=12,2,0,0,481,18015,0,0,809,47641,0,0,252,5702,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,18,145:6:0 0,6,82:2:0 0,18,140:6:0
+17 169 . C 0 . DP=13;I16=10,2,0,0,402,14224,0,0,689,40441,0,0,227,5045,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,15,106:5:0 0,6,76:2:0 0,15,145:5:0
+17 170 . C 0 . DP=13;I16=11,2,0,0,447,16383,0,0,749,44041,0,0,251,5601,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,15,128:5:0 0,6,80:2:0 0,18,143:6:0
+17 171 . A 0 . DP=13;I16=11,2,0,0,500,19366,0,0,749,44041,0,0,250,5546,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,15,134:5:0 0,6,81:2:0 0,18,166:6:0
+17 172 . C 0 . DP=13;I16=10,2,0,0,439,16395,0,0,689,40441,0,0,241,5441,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,15,138:5:0 0,6,75:2:0 0,15,129:5:0
+17 173 . C 0 . DP=13;I16=11,2,0,0,435,15225,0,0,749,44041,0,0,248,5478,0,0;QS=3,0;MQSB=0.5;MQ0F=0 PL:DP:DV 0,15,121:5:0 0,6,76:2:0 0,18,146:6:0
+17 174 . G 0 . DP=13;I16=11,1,0,0,351,10685,0,0,689,40441,0,0,238,5364,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,15,111:5:0 0,3,27:1:0 0,18,117:6:0
+17 175 . C 0 . DP=14;I16=13,1,0,0,511,19161,0,0,809,47641,0,0,249,5463,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,18,143:6:0 0,3,41:1:0 0,21,175:7:0
+17 176 . C 0 . DP=14;I16=13,1,0,0,489,17733,0,0,809,47641,0,0,251,5477,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,18,146:6:0 0,3,44:1:0 0,21,152:7:0
+17 177 . C 0 . DP=14;I16=13,1,0,0,488,17328,0,0,809,47641,0,0,253,5507,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,18,138:6:0 0,3,44:1:0 0,21,158:7:0
+17 178 . A 0 . DP=14;I16=13,1,0,0,519,19485,0,0,809,47641,0,0,254,5502,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,18,147:6:0 0,3,42:1:0 0,21,172:7:0
+17 179 . A 0 . DP=14;I16=13,1,0,0,478,17278,0,0,809,47641,0,0,255,5511,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,18,134:6:0 0,3,44:1:0 0,21,170:7:0
+17 180 . A 0 . DP=14;I16=12,1,0,0,425,14653,0,0,749,44041,0,0,250,5498,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,18,126:6:0 0,3,43:1:0 0,18,148:6:0
+17 181 . G 0 . DP=14;I16=11,1,0,0,450,17152,0,0,689,40441,0,0,233,5233,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,18,156:6:0 0,3,41:1:0 0,15,138:5:0
+17 182 . A 0 . DP=15;I16=14,1,0,0,515,18235,0,0,869,51241,0,0,258,5622,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,21,150:7:0 0,3,43:1:0 0,21,159:7:0
+17 183 . C 0 . DP=15;I16=13,1,0,0,483,17419,0,0,809,47641,0,0,235,5063,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,21,159:7:0 0,3,40:1:0 0,18,139:6:0
+17 184 . A 0 . DP=15;I16=14,1,0,0,535,19667,0,0,869,51241,0,0,262,5770,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,21,158:7:0 0,3,41:1:0 0,21,163:7:0
+17 185 . C 0 . DP=15;I16=13,1,0,0,487,17295,0,0,809,47641,0,0,238,5192,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,21,150:7:0 0,3,38:1:0 0,18,160:6:0
+17 186 . G 0 . DP=15;I16=12,1,0,0,381,11429,0,0,749,44041,0,0,239,5253,0,0;QS=3,0;MQSB=1;MQ0F=0 PL:DP:DV 0,18,117:6:0 0,3,32:1:0 0,18,124:6:0
+17 187 . C