diff --git a/vcf/parser.py b/vcf/parser.py index bc51ee9..2124798 100644 --- a/vcf/parser.py +++ b/vcf/parser.py @@ -82,25 +82,25 @@ class _vcf_metadata_parser(object): def __init__(self): super(_vcf_metadata_parser, self).__init__() self.info_pattern = re.compile(r'''\#\#INFO=< - ID=(?P[^,]+), - Number=(?P-?\d+|\.|[AGR]), - Type=(?PInteger|Float|Flag|Character|String), + ID=(?P[^,]+),\s* + Number=(?P-?\d+|\.|[AGR]),\s* + Type=(?PInteger|Float|Flag|Character|String),\s* Description="(?P[^"]*)" - (?:,Source="(?P[^"]*)")? - (?:,Version="?(?P[^"]*)"?)? + (?:,\s*Source="(?P[^"]*)")? + (?:,\s*Version="?(?P[^"]*)"?)? >''', re.VERBOSE) self.filter_pattern = re.compile(r'''\#\#FILTER=< - ID=(?P[^,]+), + ID=(?P[^,]+),\s* Description="(?P[^"]*)" >''', re.VERBOSE) self.alt_pattern = re.compile(r'''\#\#ALT=< - ID=(?P[^,]+), + ID=(?P[^,]+),\s* Description="(?P[^"]*)" >''', re.VERBOSE) self.format_pattern = re.compile(r'''\#\#FORMAT=< - ID=(?P.+), - Number=(?P-?\d+|\.|[AGR]), - Type=(?P.+), + ID=(?P.+),\s* + Number=(?P-?\d+|\.|[AGR]),\s* + Type=(?P.+),\s* Description="(?P.*)" >''', re.VERBOSE) self.contig_pattern = re.compile(r'''\#\#contig=< diff --git a/vcf/test/metadata-whitespace.vcf b/vcf/test/metadata-whitespace.vcf new file mode 100644 index 0000000..c163f9a --- /dev/null +++ b/vcf/test/metadata-whitespace.vcf @@ -0,0 +1,56 @@ +##fileformat=VCFv4.2 +##FILTER= +##samtoolsVersion=1.0-17-gfaf4dd6+htslib-1.0-11-g830ea73 +##samtoolsCommand=samtools mpileup -u -t DP,DPR,DV,DP4,INFO/DPR,SP -f /data/archive/reference/Anopheles-arabiensis-Dongola_SCAFFOLDS_AaraD1.fa -r KB704451:0004153102-0004172483 huge_list_of_bam_files_removed +##reference=file:///data/archive/reference/Anopheles-arabiensis-Dongola_SCAFFOLDS_AaraD1.fa +##contig= +##ALT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##bcftools_callVersion=1.0-55-gc661821+htslib-1.0-11-g830ea73 +##bcftools_callCommand=call -m -vM -f GQ,GP +##SnpSiftVersion="SnpSift 3.6c (build 2014-05-20), by Pablo Cingolani" +##SnpSiftCmd="SnpSift varType - " +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LUPI059 MINE001 OKJ042 LUPI001 LUPI007 LUPI024 LUPI056 LUPI071 LUPI074 LUPI082 MINE040 MINE100 MINE101 MINE105 MINE111 OKJ017 OKJ045 OKJ070 SAGA066 SAGA107 SAGA131 SAGA133 SAGA134 SAGA141 2012L_LUPI_002 2012L_LUPI_015 2012L_LUPI_017 2012L_LUPI_018 2012L_LUPI_035 2012L_LUPI_062 2012L_LUPI_065 2012L_LUPI_077 2012L_LUPI_083 2012L_LUPI_116 2012L_LUPI_013 2012L_LUPI_041 2012L_LUPI_068 2012L_LUPI_096 2012L_LUPI_098 2012L_LUPI_101 2012L_LUPI_103 2012_LUPI_156 2012_LUPI_157 2012_LUPI_161 2012_LUPI_171 2012_LUPI_173 2012_LUPI_180 2012L_LUPI_010 2012L_LUPI_012 2012L_LUPI_021 2012L_LUPI_045 2012L_LUPI_047 2012L_LUPI_060 2012L_LUPI_061 2012L_LUPI_067 2012_LUPI_125 2012_LUPI_129 2012_LUPI_146 2012_LUPI_178 2012_LUPI_211 2012_LUPI_277 2012_LUPI_278 2012_LUPI_279 2012_LUPI_284 +KB704451 4157846 . N A,C 167.0 . DP=10;VDB=1.17174e-06;SGB=1.26353;MQ0F=0;DPR=0,6,4;AC=10,4;AN=14;DP4=0,0,10,0;MQ=60;SNP;VARTYPE=SNP,SNP GT:PL:DP:DV:SP:DP4:DPR:GP:GQ 1/2:74,23,14,57,0,54:4:4:0:0,0,4,0:0,3,1:144,56,16,90,0,57:16 1/2:26,26,26,3,3,0:1:1:0:0,0,1,0:0,0,1:95,58,28,36,2,3:3 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 1/1:26,3,0,26,3,26:1:1:0:0,0,1,0:0,1,0:96,36,2,60,3,29:3 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 1/1:26,3,0,26,3,26:1:1:0:0,0,1,0:0,1,0:96,36,2,60,3,29:3 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 1/2:26,26,26,3,3,0:1:1:0:0,0,1,0:0,0,1:95,58,28,36,2,3:3 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 1/1:26,3,0,26,3,26:1:1:0:0,0,1,0:0,1,0:96,36,2,60,3,29:3 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 1/2:26,26,26,3,3,0:1:1:0:0,0,1,0:0,0,1:95,58,28,36,2,3:3 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 +KB704451 4157870 . T C 275.0 . DP=243;VDB=0.00023935;SGB=29.4468;RPB=0.0368658;MQB=0.979612;MQSB=0.268441;BQB=0.99223;MQ0F=0;DPR=213,19;ICB=0.85092;HOB=0.0287274;AC=6;AN=118;DP4=201,12,19,1;MQ=53;SNP;VARTYPE=SNP GT:PL:DP:DV:SP:DP4:DPR:GP:GQ 0/0:0,66,255:22:0:0:20,2,0,0:22,0:0,75,279:75 0/0:0,12,120:4:0:0:4,0,0,0:4,0:0,21,144:21 1/1:193,36,0:12:12:0:0,0,12,0:0,12:168,20,0:20 0/0:0,9,95:3:0:0:3,0,0,0:3,0:0,18,119:18 0/1:78,0,110:7:3:0:3,1,3,0:4,3:68,0,125:68 0/0:0,3,40:1:0:0:1,0,0,0:1,0:0,12,64:12 0/0:0,6,72:2:0:0:2,0,0,0:2,0:0,15,96:15 0/0:0,9,90:3:0:0:3,0,0,0:3,0:0,18,114:18 0/0:0,12,122:4:0:0:4,0,0,0:4,0:0,21,146:21 0/0:0,9,97:3:0:0:3,0,0,0:3,0:0,18,121:18 0/0:0,15,122:5:0:0:5,0,0,0:5,0:0,24,146:24 0/0:0,6,71:2:0:0:2,0,0,0:2,0:0,15,95:15 0/0:0,6,58:2:0:0:2,0,0,0:2,0:0,15,82:15 0/0:0,18,155:6:0:0:6,0,0,0:6,0:0,27,179:27 0/0:0,3,39:1:0:0:1,0,0,0:1,0:0,12,63:12 0/1:35,3,0:1:1:0:0,0,1,0:0,1:23,0,12:12 0/0:0,9,87:3:0:0:3,0,0,0:3,0:0,18,111:18 0/1:47,0,104:6:2:0:4,0,2,0:4,2:37,0,119:37 0/0:0,21,160:7:0:0:7,0,0,0:7,0:0,30,184:30 0/0:0,6,35:2:0:0:2,0,0,0:2,0:0,15,59:15 0/0:0,12,98:4:0:0:4,0,0,0:4,0:0,21,122:21 0/0:0,6,70:2:0:0:2,0,0,0:2,0:0,15,94:15 0/0:0,6,66:2:0:0:2,0,0,0:2,0:0,15,90:15 0/0:0,12,122:4:0:0:4,0,0,0:4,0:0,21,146:21 0/0:0,3,29:1:0:0:0,1,0,0:1,0:0,12,53:12 0/0:0,6,72:2:0:0:2,0,0,0:2,0:0,15,96:15 0/0:0,9,76:3:0:0:3,0,0,0:3,0:0,18,100:18 0/0:0,15,136:5:0:0:5,0,0,0:5,0:0,24,160:24 0/0:0,30,182:10:0:0:10,0,0,0:10,0:0,39,206:39 0/0:0,6,66:2:0:0:2,0,0,0:2,0:0,15,90:15 0/0:0,6,69:2:0:0:2,0,0,0:2,0:0,15,93:15 0/0:0,27,152:9:0:0:9,0,0,0:9,0:0,36,176:36 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,94:2:0:0:2,0,0,0:2,0:0,15,118:15 0/0:0,21,195:7:0:0:5,2,0,0:7,0:0,30,219:30 0/0:0,9,92:3:0:0:2,1,0,0:3,0:0,18,116:18 0/1:33,0,18:2:1:0:0,1,1,0:1,1:23,0,33:23 0/0:0,3,35:1:0:0:1,0,0,0:1,0:0,12,59:12 0/0:0,9,91:3:0:0:3,0,0,0:3,0:0,18,115:18 0/0:0,3,36:1:0:0:1,0,0,0:1,0:0,12,60:12 0/0:0,30,212:10:0:0:9,1,0,0:10,0:0,39,236:39 0/0:0,9,89:3:0:0:3,0,0,0:3,0:0,18,113:18 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,21,195:7:0:0:7,0,0,0:7,0:0,30,219:30 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,9,97:3:0:0:2,1,0,0:3,0:0,18,121:18 0/0:0,9,93:3:0:0:3,0,0,0:3,0:0,18,117:18 0/0:0,9,116:3:0:0:3,0,0,0:3,0:0,18,140:18 0/0:0,6,71:2:0:0:1,1,0,0:2,0:0,15,95:15 0/0:0,9,89:3:0:0:3,0,0,0:3,0:0,18,113:18 0/0:0,33,175:11:0:0:11,0,0,0:11,0:0,42,199:42 0/0:0,6,63:2:0:0:2,0,0,0:2,0:0,15,87:15 0/0:0,21,145:7:0:0:7,0,0,0:7,0:0,30,169:30 0/0:0,3,39:1:0:0:0,1,0,0:1,0:0,12,63:12 0/0:0,9,84:3:0:0:3,0,0,0:3,0:0,18,108:18 0/0:0,3,13:1:0:0:1,0,0,0:1,0:0,12,37:12 0/0:0,3,23:1:0:0:1,0,0,0:1,0:0,12,47:12 0/0:0,12,106:4:0:0:4,0,0,0:4,0:0,21,130:21 0/0:0,3,36:1:0:0:1,0,0,0:1,0:0,12,60:12 0/0:0,9,94:3:0:0:3,0,0,0:3,0:0,18,118:18 0/0:0,6,67:2:0:0:2,0,0,0:2,0:0,15,91:15 0/0:2,5,27:2:1:0:1,0,0,1:1,0:0,12,49:12 +KB704451 4157877 . G A 999.0 . DP=250;VDB=6.58963e-09;SGB=31.659;RPB=0.0227135;MQB=0.410318;MQSB=0.139343;BQB=0.0767891;MQ0F=0;DPR=188,48;ICB=0.990841;HOB=0.00761276;AC=17;AN=118;DP4=176,12,45,3;MQ=55;SNP;VARTYPE=SNP GT:PL:DP:DV:SP:DP4:DPR:GP:GQ 0/1:159,0,202:22:9:0:12,1,8,1:13,9:154,0,212:127 0/0:0,12,120:4:0:0:4,0,0,0:4,0:0,16,134:16 0/0:0,51,207:17:0:0:17,0,0,0:17,0:0,55,221:55 0/0:0,9,98:3:0:0:3,0,0,0:3,0:0,13,112:13 0/1:123,0,61:8:5:0:3,0,4,1:3,5:118,0,71:71 0/0:0,3,38:1:0:0:0,1,0,0:1,0:0,7,52:7 0/1:68,0,29:3:2:0:1,0,1,1:1,2:63,0,39:39 0/0:0,6,69:2:0:0:2,0,0,0:2,0:0,10,83:10 0/0:0,12,119:4:0:0:4,0,0,0:4,0:0,16,133:16 0/1:34,0,34:2:1:0:1,0,1,0:1,1:29,0,44:29 0/1:24,0,99:5:1:0:4,0,1,0:4,1:19,0,109:19 0/1:34,0,28:2:1:0:1,0,1,0:1,1:29,0,38:29 0/0:0,6,58:2:0:0:2,0,0,0:2,0:0,10,72:10 0/1:122,0,57:7:4:0:3,0,4,0:3,4:117,0,67:67 0/0:0,3,41:1:0:0:1,0,0,0:1,0:0,7,55:7 0/0:0,3,29:1:0:0:1,0,0,0:1,0:0,7,43:7 0/0:0,12,105:4:0:0:4,0,0,0:4,0:0,16,119:16 0/0:0,18,144:6:0:0:6,0,0,0:6,0:0,22,158:22 0/1:118,0,63:8:5:0:3,0,5,0:3,5:113,0,73:73 0/0:0,6,34:2:0:0:2,0,0,0:2,0:0,10,48:10 0/0:0,15,131:5:0:0:5,0,0,0:5,0:0,19,145:19 0/0:0,6,72:2:0:0:2,0,0,0:2,0:0,10,86:10 0/0:0,6,89:2:0:0:2,0,0,0:2,0:0,10,103:10 1/1:124,12,0:4:4:0:0,0,4,0:0,4:112,4,2:4 0/0:0,3,34:1:0:0:0,1,0,0:1,0:0,7,48:7 0/0:0,6,73:2:0:0:2,0,0,0:2,0:0,10,87:10 0/0:0,9,91:3:0:0:3,0,0,0:3,0:0,13,105:13 0/0:0,15,138:5:0:0:5,0,0,0:5,0:0,19,152:19 0/0:0,30,179:10:0:0:10,0,0,0:10,0:0,34,193:34 0/0:0,6,65:2:0:0:2,0,0,0:2,0:0,10,79:10 0/0:0,6,70:2:0:0:2,0,0,0:2,0:0,10,84:10 0/0:0,27,155:9:0:0:9,0,0,0:9,0:0,31,169:31 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,94:2:0:0:2,0,0,0:2,0:0,10,108:10 0/0:0,15,161:5:0:0:3,2,0,0:5,0:0,19,175:19 0/0:0,6,72:2:0:0:1,1,0,0:2,0:0,10,86:10 0/0:0,6,65:2:0:0:1,1,0,0:2,0:0,10,79:10 0/1:36,3,0:1:1:0:0,0,1,0:0,1:29,0,7:7 0/0:0,9,93:3:0:0:3,0,0,0:3,0:0,13,107:13 0/0:0,3,34:1:0:0:1,0,0,0:1,0:0,7,48:7 0/1:87,0,137:10:4:0:5,1,4,0:6,4:82,0,147:82 0/1:57,0,26:3:2:0:1,0,2,0:1,2:52,0,36:35 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/1:139,0,73:7:4:0:3,0,4,0:3,4:134,0,83:83 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,75:2:0:0:1,1,0,0:2,0:0,10,89:10 0/1:90,9,0:3:3:0:0,0,3,0:0,3:79,2,3:3 0/0:0,9,98:3:0:0:3,0,0,0:3,0:0,13,112:13 0/0:0,6,72:2:0:0:1,1,0,0:2,0:0,10,86:10 0/0:0,9,88:3:0:0:3,0,0,0:3,0:0,13,102:13 0/0:0,33,173:11:0:0:11,0,0,0:11,0:0,37,187:37 0/0:0,6,57:2:0:0:2,0,0,0:2,0:0,10,71:10 0/0:0,15,125:5:0:0:5,0,0,0:5,0:0,19,139:19 0/0:0,6,61:2:0:0:1,1,0,0:2,0:0,10,75:10 0/1:24,0,51:3:1:0:2,0,1,0:2,1:19,0,61:19 0/0:0,3,30:1:0:0:1,0,0,0:1,0:0,7,44:7 0/0:0,3,23:1:0:0:1,0,0,0:1,0:0,7,37:7 0/0:0,12,105:4:0:0:4,0,0,0:4,0:0,16,119:16 0/0:0,3,35:1:0:0:1,0,0,0:1,0:0,7,49:7 0/1:25,0,61:3:1:0:2,0,1,0:2,1:20,0,71:20 0/0:0,6,67:2:0:0:2,0,0,0:2,0:0,10,81:10 0/0:0,3,8:1:0:0:0,1,0,0:1,0:0,7,22:7 +KB704451 4157907 . A C 278.0 . DP=295;VDB=0.241276;SGB=26.7514;RPB=0.676983;MQB=0.997838;MQSB=0.136536;BQB=0.45683;MQ0F=0;DPR=264,15;ICB=0.00518819;HOB=0.00237812;AC=4;AN=116;DP4=233,31,14,1;MQ=59;SNP;VARTYPE=SNP GT:PL:DP:DV:SP:DP4:DPR:GP:GQ 0/0:0,90,255:30:0:0:25,5,0,0:30,0:0,101,283:101 0/0:0,30,201:10:0:0:9,1,0,0:10,0:0,41,229:41 0/1:157,0,188:18:8:0:10,0,7,1:10,8:145,0,205:127 0/1:75,0,90:5:2:0:2,1,2,0:3,2:63,0,107:63 0/0:0,30,201:10:0:0:9,1,0,0:10,0:0,41,229:41 0/0:0,6,80:2:0:0:1,1,0,0:2,0:0,17,108:17 0/0:0,12,134:4:0:0:3,1,0,0:4,0:0,23,162:23 0/0:0,3,33:1:0:0:1,0,0,0:1,0:0,14,61:14 0/0:0,21,160:7:0:0:7,0,0,0:7,0:0,32,188:32 0/0:0,12,135:4:0:0:2,2,0,0:4,0:0,23,163:23 0/0:0,15,148:5:0:0:5,0,0,0:5,0:0,26,176:26 0/0:0,9,82:3:0:0:3,0,0,0:3,0:0,20,110:20 0/1:70,0,19:4:3:0:1,0,3,0:1,3:58,0,36:36 0/0:0,24,246:8:0:0:7,1,0,0:8,0:0,35,274:35 0/0:0,18,147:6:0:0:6,0,0,0:6,0:0,29,175:29 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,9,82:3:0:0:3,0,0,0:3,0:0,20,110:20 0/1:59,0,62:5:2:0:3,0,2,0:3,2:47,0,79:47 0/0:0,33,192:11:0:0:11,0,0,0:11,0:0,44,220:44 0/0:0,9,94:3:0:0:3,0,0,0:3,0:0,20,122:20 0/0:0,24,198:8:0:0:7,1,0,0:8,0:0,35,226:35 0/0:0,12,120:4:0:0:4,0,0,0:4,0:0,23,148:23 0/0:0,15,165:5:0:0:3,2,0,0:5,0:0,26,193:26 0/0:0,24,172:8:0:0:8,0,0,0:8,0:0,35,200:35 0/0:0,3,31:1:0:0:0,1,0,0:1,0:0,14,59:14 0/0:0,6,64:2:0:0:2,0,0,0:2,0:0,17,92:17 0/0:0,6,66:2:0:0:2,0,0,0:2,0:0,17,94:17 0/0:0,15,118:5:0:0:5,0,0,0:5,0:0,26,146:26 0/0:0,33,178:11:0:0:11,0,0,0:11,0:0,44,206:44 0/0:0,3,35:1:0:0:1,0,0,0:1,0:0,14,63:14 0/0:0,9,74:3:0:0:2,1,0,0:3,0:0,20,102:20 0/0:0,21,168:7:0:0:5,2,0,0:7,0:0,32,196:32 0/0:0,3,40:1:0:0:1,0,0,0:1,0:0,14,68:14 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,89:2:0:0:2,0,0,0:2,0:0,17,117:17 0/0:0,12,130:4:0:0:2,2,0,0:4,0:0,23,158:23 0/0:0,9,78:3:0:0:1,2,0,0:3,0:0,20,106:20 0/0:0,6,65:2:0:0:1,1,0,0:2,0:0,17,93:17 0/0:0,3,35:1:0:0:1,0,0,0:1,0:0,14,63:14 0/0:0,6,55:2:0:0:2,0,0,0:2,0:0,17,83:17 0/0:0,3,29:1:0:0:1,0,0,0:1,0:0,14,57:14 0/0:0,36,194:12:0:0:11,1,0,0:12,0:0,47,222:47 0/0:0,12,110:4:0:0:4,0,0,0:4,0:0,23,138:23 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,18,182:6:0:0:6,0,0,0:6,0:0,29,210:29 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,3,34:1:0:0:0,1,0,0:1,0:0,14,62:14 0/0:0,6,68:2:0:0:2,0,0,0:2,0:0,17,96:17 0/0:0,9,107:3:0:0:3,0,0,0:3,0:0,20,135:20 0/0:0,6,67:2:0:0:1,1,0,0:2,0:0,17,95:17 0/0:0,6,68:2:0:0:2,0,0,0:2,0:0,17,96:17 0/0:0,27,184:9:0:0:9,0,0,0:9,0:0,38,212:38 0/0:0,9,85:3:0:0:3,0,0,0:3,0:0,20,113:20 0/0:0,12,111:4:0:0:4,0,0,0:4,0:0,23,139:23 0/0:0,6,77:2:0:0:1,1,0,0:2,0:0,17,105:17 0/0:0,12,108:4:0:0:3,1,0,0:4,0:0,23,136:23 0/0:0,3,27:1:0:0:1,0,0,0:1,0:0,14,55:14 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,64:2:0:0:2,0,0,0:2,0:0,17,92:17 0/0:0,3,33:1:0:0:1,0,0,0:1,0:0,14,61:14 0/0:0,12,125:4:0:0:4,0,0,0:4,0:0,23,153:23 0/0:0,9,98:3:0:0:2,1,0,0:3,0:0,20,126:20 0/0:0,6,46:2:0:0:2,0,0,0:2,0:0,17,74:17 +KB704451 4157909 . T G 278.0 . DP=295;VDB=0.184881;SGB=22.7413;RPB=0.646301;MQB=0.998034;MQSB=0.200514;BQB=0.321842;MQ0F=0;DPR=247,15;ICB=0.00558284;HOB=0.00255102;AC=4;AN=112;DP4=218,29,15,1;MQ=59;SNP;VARTYPE=SNP GT:PL:DP:DV:SP:DP4:DPR:GP:GQ 0/0:0,87,255:29:0:0:24,5,0,0:29,0:0,97,282:97 0/0:0,27,183:9:0:0:9,0,0,0:9,0:0,37,210:37 0/1:156,0,167:19:8:0:11,0,7,1:11,8:145,0,183:127 0/1:75,0,107:5:2:0:2,1,2,0:3,2:64,0,123:64 0/0:0,27,191:9:0:0:8,1,0,0:9,0:0,37,218:37 0/0:0,6,80:2:0:0:1,1,0,0:2,0:0,16,107:16 0/0:0,12,119:4:0:0:3,1,0,0:4,0:0,22,146:22 0/0:0,3,34:1:0:0:1,0,0,0:1,0:0,13,61:13 0/0:0,15,126:5:0:0:5,0,0,0:5,0:0,25,153:25 0/0:0,12,132:4:0:0:2,2,0,0:4,0:0,22,159:22 0/0:0,12,133:4:0:0:4,0,0,0:4,0:0,22,160:22 0/0:0,6,67:2:0:0:2,0,0,0:2,0:0,16,94:16 0/1:79,9,0:3:3:0:0,0,3,0:0,3:60,0,8:8 0/0:0,21,230:7:0:0:6,1,0,0:7,0:0,31,257:31 0/0:0,18,144:6:0:0:6,0,0,0:6,0:0,28,171:28 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,53:2:0:0:2,0,0,0:2,0:0,16,80:16 0/1:59,0,64:5:2:0:3,0,2,0:3,2:48,0,80:48 0/0:0,33,180:11:0:0:11,0,0,0:11,0:0,43,207:43 0/0:0,12,110:4:0:0:4,0,0,0:4,0:0,22,137:22 0/0:0,24,190:8:0:0:7,1,0,0:8,0:0,34,217:34 0/0:0,12,110:4:0:0:4,0,0,0:4,0:0,22,137:22 0/0:0,15,164:5:0:0:3,2,0,0:5,0:0,25,191:25 0/0:0,24,161:8:0:0:8,0,0,0:8,0:0,34,188:34 0/0:0,3,32:1:0:0:0,1,0,0:1,0:0,13,59:13 0/0:0,6,63:2:0:0:2,0,0,0:2,0:0,16,90:16 0/0:0,6,65:2:0:0:2,0,0,0:2,0:0,16,92:16 0/0:0,15,121:5:0:0:5,0,0,0:5,0:0,25,148:25 0/0:0,30,174:10:0:0:10,0,0,0:10,0:0,40,201:40 0/0:0,3,34:1:0:0:1,0,0,0:1,0:0,13,61:13 0/0:0,6,63:2:0:0:2,0,0,0:2,0:0,16,90:16 0/0:0,21,164:7:0:0:5,2,0,0:7,0:0,31,191:31 0/0:0,3,37:1:0:0:1,0,0,0:1,0:0,13,64:13 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,89:2:0:0:2,0,0,0:2,0:0,16,116:16 0/0:0,12,128:4:0:0:2,2,0,0:4,0:0,22,155:22 0/0:0,9,94:3:0:0:1,2,0,0:3,0:0,19,121:19 0/0:0,6,63:2:0:0:1,1,0,0:2,0:0,16,90:16 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,56:2:0:0:2,0,0,0:2,0:0,16,83:16 0/0:0,3,34:1:0:0:1,0,0,0:1,0:0,13,61:13 0/0:0,36,193:12:0:0:11,1,0,0:12,0:0,46,220:46 0/0:0,12,108:4:0:0:4,0,0,0:4,0:0,22,135:22 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,18,168:6:0:0:6,0,0,0:6,0:0,28,195:28 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,3,31:1:0:0:0,1,0,0:1,0:0,13,58:13 0/0:0,6,47:2:0:0:2,0,0,0:2,0:0,16,74:16 0/0:8,11,65:2:1:0:1,0,1,0:1,0:0,13,84:13 0/0:0,6,64:2:0:0:1,1,0,0:2,0:0,16,91:16 0/0:0,3,34:1:0:0:1,0,0,0:1,0:0,13,61:13 0/0:0,27,177:9:0:0:9,0,0,0:9,0:0,37,204:37 0/0:0,6,50:2:0:0:2,0,0,0:2,0:0,16,77:16 0/0:0,12,101:4:0:0:4,0,0,0:4,0:0,22,128:22 0/0:0,6,65:2:0:0:1,1,0,0:2,0:0,16,92:16 0/0:0,12,100:4:0:0:3,1,0,0:4,0:0,22,127:22 0/0:0,3,31:1:0:0:1,0,0,0:1,0:0,13,58:13 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,9,84:3:0:0:3,0,0,0:3,0:0,19,111:19 0/0:0,3,32:1:0:0:1,0,0,0:1,0:0,13,59:13 0/0:0,12,104:4:0:0:4,0,0,0:4,0:0,22,131:22 0/0:0,6,66:2:0:0:1,1,0,0:2,0:0,16,93:16 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 +KB704451 4157927 . G A 4.88727 . DP=334;VDB=0.38;SGB=3.29913;RPB=0.454248;MQB=0.970588;MQSB=0.546099;BQB=0.215686;MQ0F=0;DPR=306,2;ICB=0.000310486;HOB=0.000153894;AC=1;AN=114;DP4=265,41,2,0;MQ=59;SNP;VARTYPE=SNP GT:PL:DP:DV:SP:DP4:DPR:GP:GQ 0/0:0,105,255:35:0:0:31,4,0,0:35,0:0,122,295:122 0/0:0,45,255:15:0:0:14,1,0,0:15,0:0,62,295:62 0/0:0,60,255:20:0:0:17,3,0,0:20,0:0,77,295:77 0/0:0,21,242:7:0:0:6,1,0,0:7,0:0,38,282:38 0/0:0,24,207:8:0:0:6,2,0,0:8,0:0,41,247:41 0/0:0,6,71:2:0:0:2,0,0,0:2,0:0,23,112:23 0/0:0,24,215:8:0:0:6,2,0,0:8,0:0,41,255:41 0/0:0,6,70:2:0:0:1,1,0,0:2,0:0,23,111:23 0/0:0,30,191:10:0:0:10,0,0,0:10,0:0,47,231:47 0/0:0,15,163:5:0:0:3,2,0,0:5,0:0,32,203:32 0/0:0,15,151:5:0:0:5,0,0,0:5,0:0,32,191:32 0/0:0,6,70:2:0:0:2,0,0,0:2,0:0,23,111:23 0/0:0,12,102:4:0:0:4,0,0,0:4,0:0,29,142:29 0/0:0,24,255:8:0:0:6,2,0,0:8,0:0,41,295:41 0/0:0,21,189:7:0:0:7,0,0,0:7,0:0,38,229:38 0/0:0,3,35:1:0:0:0,1,0,0:1,0:0,20,76:20 0/0:0,3,40:1:0:0:1,0,0,0:1,0:0,20,81:20 0/0:0,12,126:4:0:0:3,1,0,0:4,0:0,29,166:29 0/0:0,39,255:13:0:0:12,1,0,0:13,0:0,56,295:56 0/0:0,21,206:7:0:0:6,1,0,0:7,0:0,38,246:38 0/0:0,30,238:10:0:0:8,2,0,0:10,0:0,47,278:47 0/0:0,18,145:6:0:0:6,0,0,0:6,0:0,35,185:35 0/0:0,24,244:8:0:0:6,2,0,0:8,0:0,41,284:41 0/0:0,24,195:8:0:0:7,1,0,0:8,0:0,41,235:41 0/0:0,3,27:1:0:0:0,1,0,0:1,0:0,20,68:20 0/0:0,6,62:2:0:0:2,0,0,0:2,0:0,23,103:23 0/0:0,6,64:2:0:0:2,0,0,0:2,0:0,23,105:23 0/0:0,15,123:5:0:0:5,0,0,0:5,0:0,32,163:32 0/0:0,33,184:11:0:0:11,0,0,0:11,0:0,50,224:50 0/0:0,3,35:1:0:0:1,0,0,0:1,0:0,20,76:20 0/0:0,3,35:1:0:0:1,0,0,0:1,0:0,20,76:20 0/0:0,18,165:6:0:0:4,2,0,0:6,0:0,35,205:35 0/0:0,3,38:1:0:0:1,0,0,0:1,0:0,20,79:20 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,9,117:3:0:0:3,0,0,0:3,0:0,26,157:26 0/0:0,12,121:4:0:0:2,2,0,0:4,0:0,29,161:29 0/0:0,9,95:3:0:0:1,2,0,0:3,0:0,26,135:26 0/0:0,3,41:1:0:0:1,0,0,0:1,0:0,20,82:20 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,60:2:0:0:2,0,0,0:2,0:0,23,101:23 0/0:0,3,25:1:0:0:1,0,0,0:1,0:0,20,66:20 0/0:0,36,213:12:0:0:11,1,0,0:12,0:0,53,253:53 0/0:0,15,152:5:0:0:4,1,0,0:5,0:0,32,192:32 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,21,215:7:0:0:6,1,0,0:7,0:0,38,255:38 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,3,31:1:0:0:0,1,0,0:1,0:0,20,72:20 0/0:0,6,60:2:0:0:2,0,0,0:2,0:0,23,101:23 0/0:0,9,101:3:0:0:3,0,0,0:3,0:0,26,141:26 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,60:2:0:0:2,0,0,0:2,0:0,23,101:23 0/0:0,27,179:9:0:0:9,0,0,0:9,0:0,44,219:44 0/0:0,9,92:3:0:0:3,0,0,0:3,0:0,26,132:26 0/0:0,12,112:4:0:0:4,0,0,0:4,0:0,29,152:29 0/0:0,6,58:2:0:0:1,1,0,0:2,0:0,23,99:23 0/0:0,15,123:5:0:0:4,1,0,0:5,0:0,32,163:32 0/0:0,3,25:1:0:0:1,0,0,0:1,0:0,20,66:20 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,9,78:3:0:0:3,0,0,0:3,0:0,26,118:26 0/0:0,3,34:1:0:0:1,0,0,0:1,0:0,20,75:20 0/1:47,0,51:3:2:0:1,0,2,0:1,2:29,0,74:29 0/0:0,9,80:3:0:0:2,1,0,0:3,0:0,26,120:26 0/0:0,6,53:2:0:0:2,0,0,0:2,0:0,23,94:23 +KB704451 4157938 . ATTT ATTTT 650.0 . INDEL;IDV=18;IMF=0.428571;DP=361;VDB=0.773794;SGB=32.6744;MQSB=0.993251;MQ0F=0.00831025;DPR=115,60;ICB=0.929833;HOB=0.0258;AC=23;AN=100;DP4=98,17,48,12;MQ=59;INS;VARTYPE=INS GT:PL:DP:DV:SP:DP4:DPR:GP:GQ 0/1:124,0,7:19:16:0:3,0,13,3:3,16:123,0,13:13 0/1:14,3,0:1:1:0:0,0,1,0:0,1:12,1,5:4 0/0:0,9,55:3:0:0:3,0,0,0:3,0:0,9,62:9 0/0:0,21,146:7:0:0:5,2,0,0:7,0:0,21,153:21 0/0:0,18,126:6:0:0:4,2,0,0:6,0:0,18,133:18 0/0:0,6,56:2:0:0:2,0,0,0:2,0:0,7,63:7 0/0:0,9,87:3:0:0:2,1,0,0:3,0:0,9,94:9 1/1:46,9,0:3:3:0:0,0,1,2:0,3:40,4,1:4 0/0:0,27,155:9:0:0:8,1,0,0:9,0:0,27,162:27 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,57:2:0:0:2,0,0,0:2,0:0,7,64:7 0/1:24,3,0:1:1:0:0,0,1,0:0,1:22,1,5:5 0/0:0,3,32:1:0:0:1,0,0,0:1,0:1,5,40:5 0/0:0,9,84:3:0:0:2,1,0,0:3,0:0,9,91:9 0/0:0,15,111:5:0:0:5,0,0,0:5,0:0,15,118:15 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/1:32,6,0:2:2:0:0,0,1,1:0,2:28,2,3:3 0/0:0,6,55:2:0:0:2,0,0,0:2,0:0,7,62:7 0/1:63,0,61:7:4:0:3,0,3,1:3,4:62,0,67:61 0/0:0,24,154:8:0:0:7,1,0,0:8,0:0,24,161:24 0/1:16,0,94:7:2:0:5,0,2,0:5,2:15,0,100:15 0/1:61,0,101:9:4:0:4,1,3,1:5,4:60,0,107:60 0/0:0,3,31:1:0:0:1,0,0,0:1,0:1,5,39:5 0/1:13,3,0:1:1:0:0,0,0,1:0,1:11,1,5:4 0/1:16,0,47:3:1:0:2,0,1,0:2,1:15,0,53:15 0/0:0,3,32:1:0:0:1,0,0,0:1,0:1,5,40:5 0/1:46,0,57:5:2:0:3,0,2,0:3,2:45,0,63:45 0/1:50,0,12:6:5:0:1,0,5,0:1,5:49,0,18:18 0/0:0,3,30:1:0:0:1,0,0,0:1,0:1,5,38:5 0/0:0,3,4:1:0:0:1,0,0,0:1,0:1,5,12:4 0/1:18,0,98:5:1:0:2,2,1,0:4,1:17,0,104:17 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/1:15,0,26:2:1:0:1,0,1,0:1,1:14,0,32:14 0/1:20,0,26:2:1:0:1,0,0,1:1,1:19,0,32:19 0/0:0,6,60:2:0:0:1,1,0,0:2,0:0,7,67:7 0/0:0,3,32:1:0:0:1,0,0,0:1,0:1,5,40:5 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/1:33,3,0:1:1:0:0,0,1,0:0,1:31,1,5:5 0/1:82,6,0:7:6:0:1,0,5,1:1,6:78,2,3:3 0/0:0,15,126:5:0:0:4,1,0,0:5,0:0,15,133:15 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/1:34,6,0:2:2:0:0,0,2,0:0,2:30,2,3:3 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,6,50:2:0:0:1,1,0,0:2,0:0,7,57:7 0/0:0,3,28:1:0:0:1,0,0,0:1,0:1,5,36:5 0/0:0,6,57:2:0:0:2,0,0,0:2,0:0,7,64:7 0/0:0,18,124:6:0:0:5,1,0,0:6,0:0,18,131:18 0/1:53,6,0:2:2:0:0,0,2,0:0,2:49,2,3:3 0/0:0,12,96:4:0:0:4,0,0,0:4,0:0,12,103:12 0/1:25,3,0:1:1:0:0,0,1,0:0,1:23,1,5:5 1/1:61,9,0:3:3:0:0,0,2,1:0,3:55,4,1:4 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 0/0:0,3,31:1:0:0:0,1,0,0:1,0:1,5,39:5 0/0:0,6,56:2:0:0:2,0,0,0:2,0:0,7,63:7 0/0:0,3,29:1:0:0:1,0,0,0:1,0:1,5,37:5 0/0:0,3,32:1:0:0:1,0,0,0:1,0:1,5,40:5 0/0:0,9,87:3:0:0:2,1,0,0:3,0:0,9,94:9 ./.:0,0,0:0:0:0:0,0,0,0:0,0:0,0,0:0 +KB704451 4157940 . TTGTGTGTGTGTGT TTGTGTGTGTGTGTGTGT,TTTCTGTGTGTGTGTGT 999.0 . INDEL;IDV=7;IMF=0.5;DP=366;VDB=0.0431342;SGB=14.7456;MQSB=0.996953;MQ0F=0.010929;DPR=86,41,8;ICB=0.963728;HOB=0.02;AC=21,6;AN=90;DP4=70,16,39,10;MQ=58;INS;VARTYPE=INS,INS GT:PL:DP:DV:SP:DP4:DPR:GP:GQ 0/2:60,60,60,3,3,0:1:1:0:0,0,1,0:0,0,1:54,55,61,2,5,9:4 1/1:255,18,0,255,18,255:6:6:0:0,0,3,3:0,6,0:248,11,0,252,19,263:11 0/0:0,6,62,6,62,62:2:0:0:2,0,0,0:2,0,0:1,7,70,11,71,78:6 0/1:9,0,238,27,241,255:7:1:0:4,2,1,0:6,1,0:8,0,245,31,249,270:8 0/0:0,12,185,12,185,185:4:0:0:3,1,0,0:4,0,0:0,12,192,16,193,200:11 0/0:0,6,110,6,110,110:2:0:0:2,0,0,0:2,0,0:1,7,118,11,119,126:6 0/1:1,0,158,10,161,165:4:1:0:2,1,1,0:3,1,0:3,2,167,16,171,182:3 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/0:0,24,255,24,255,255:8:0:0:7,1,0,0:8,0,0:0,24,262,28,263,270:23 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/1:37,0,54,40,57,94:2:1:0:1,0,1,0:1,1,0:36,0,60,44,64,108:35 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/0:0,3,60,3,60,60:1:0:0:1,0,0,0:1,0,0:2,5,69,9,70,77:4 0/1:117,6,0,117,6,117:2:2:0:0,0,1,1:0,2,0:113,3,3,118,10,128:2 0/0:0,18,237,18,237,237:6:0:0:5,1,0,0:6,0,0:0,18,244,22,245,252:17 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/2:120,120,120,6,6,0:2:2:0:0,0,1,1:0,0,2:111,112,119,2,6,7:3 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 1/1:255,21,0,255,21,255:7:7:0:0,0,5,2:0,7,0:247,14,0,252,22,263:13 0/2:19,31,181,0,157,154:5:1:0:3,1,1,0:4,0,1:14,27,183,0,160,164:14 0/1:120,0,255,141,255,255:10:3:0:6,1,2,1:7,3,0:119,0,261,145,262,269:119 0/0:0,15,212,15,212,212:5:0:0:5,0,0,0:5,0,0:0,15,219,19,220,227:14 0/0:0,15,243,15,243,243:5:0:0:4,1,0,0:5,0,0:0,15,250,19,251,258:14 1/1:40,9,0,40,9,40:3:3:0:0,0,3,0:0,3,0:34,4,2,39,12,50:3 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/0:0,6,110,6,110,110:2:0:0:2,0,0,0:2,0,0:1,7,118,11,119,126:6 0/1:54,0,54,57,57,111:2:1:0:1,0,1,0:1,1,0:53,0,60,61,64,125:51 0/0:0,9,139,9,139,139:3:0:0:3,0,0,0:3,0,0:0,10,146,14,147,154:8 1/1:243,15,0,243,15,243:5:5:0:0,0,4,1:0,5,0:236,9,0,241,16,251:8 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/1:55,1,0,58,3,57:2:1:0:1,0,1,0:1,1,0:54,1,7,62,11,72:5 0/0:0,9,170,9,170,170:3:0:0:1,2,0,0:3,0,0:0,10,177,14,178,185:8 0/1:60,3,0,60,3,60:1:1:0:0,0,1,0:0,1,0:58,2,5,63,9,73:4 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/0:0,3,60,3,60,60:1:0:0:1,0,0,0:1,0,0:2,5,69,9,70,77:4 0/0:0,3,60,3,60,60:1:0:0:1,0,0,0:1,0,0:2,5,69,9,70,77:4 0/1:60,3,0,60,3,60:1:1:0:0,0,0,1:0,1,0:58,2,5,63,9,73:4 0/0:0,3,60,3,60,60:1:0:0:1,0,0,0:1,0,0:2,5,69,9,70,77:4 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/1:60,3,0,60,3,60:1:1:0:0,0,1,0:0,1,0:58,2,5,63,9,73:4 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/0:0,15,206,15,206,206:5:0:0:4,1,0,0:5,0,0:0,15,213,19,214,221:14 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 1/2:134,105,96,40,0,34:5:5:0:0,0,5,0:0,3,2:125,97,95,36,0,41:35 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/1:58,6,0,58,6,58:2:2:0:0,0,2,0:0,2,0:54,3,3,59,10,69:2 0/0:0,6,102,6,102,102:2:0:0:1,1,0,0:2,0,0:1,7,110,11,111,118:6 0/0:0,3,60,3,60,60:1:0:0:1,0,0,0:1,0,0:2,5,69,9,70,77:4 0/0:0,3,60,3,60,60:1:0:0:1,0,0,0:1,0,0:2,5,69,9,70,77:4 0/1:98,0,88,104,94,191:4:2:0:1,1,2,0:2,2,0:97,0,94,108,101,205:92 0/2:35,35,35,3,3,0:1:1:0:0,0,1,0:0,0,1:29,30,36,2,5,9:4 0/0:0,6,110,6,110,110:2:0:0:2,0,0,0:2,0,0:1,7,118,11,119,126:6 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/2:45,45,45,3,3,0:1:1:0:0,0,1,0:0,0,1:39,40,46,2,5,9:4 0/0:0,3,60,3,60,60:1:0:0:0,1,0,0:1,0,0:2,5,69,9,70,77:4 0/0:0,6,110,6,110,110:2:0:0:2,0,0,0:2,0,0:1,7,118,11,119,126:6 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 0/0:0,3,60,3,60,60:1:0:0:1,0,0,0:1,0,0:2,5,69,9,70,77:4 0/0:0,6,120,6,120,120:2:0:0:1,1,0,0:2,0,0:1,7,128,11,129,136:6 ./.:0,0,0,0,0,0:0:0:0:0,0,0,0:0,0,0:0,0,0,0,0,0:0 diff --git a/vcf/test/test_vcf.py b/vcf/test/test_vcf.py index 3782d12..729d6ee 100644 --- a/vcf/test/test_vcf.py +++ b/vcf/test/test_vcf.py @@ -457,6 +457,27 @@ def test_samples(self): self.assertEqual(self.reader.samples, self.samples) +class TestMetadataWhitespace(unittest.TestCase): + filename = 'metadata-whitespace.vcf' + def test_metadata_whitespace(self): + """ + Test parsing metadata header lines with whitespace. + """ + self.reader = vcf.Reader(fh(self.filename)) + + # Pick one INFO line and assert that we parsed it correctly. + info_indel = self.reader.infos['INDEL'] + assert info_indel.id == 'INDEL' + assert info_indel.num == 0 + assert info_indel.type == 'Flag' + assert info_indel.desc == 'Indicates that the variant is an INDEL.' + + # Test we can walk the file at least. + for r in self.reader: + for c in r: + pass + + class TestMixedFiltering(unittest.TestCase): filename = 'mixed-filtering.vcf' def test_mixed_filtering(self): @@ -1470,6 +1491,7 @@ def test_write_uncalled(self): suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestBcfToolsOutputWriter)) suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestWriterDictionaryMeta)) suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestSamplesSpace)) +suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestMetadataWhitespace)) suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestMixedFiltering)) suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestRecord)) suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestCall))