bio-vcf 0.9.2 → 0.9.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +5 -5
- data/.travis.yml +1 -21
- data/LICENSE.txt +1 -1
- data/README.md +107 -73
- data/RELEASE_NOTES.md +20 -0
- data/RELEASE_NOTES.md~ +11 -0
- data/VERSION +1 -1
- data/bin/bio-vcf +49 -30
- data/bio-vcf.gemspec +1 -1
- data/features/cli.feature +4 -1
- data/features/diff_count.feature +0 -1
- data/features/step_definitions/cli-feature.rb +13 -9
- data/features/step_definitions/diff_count.rb +1 -1
- data/features/step_definitions/somaticsniper.rb +1 -1
- data/lib/bio-vcf/pcows.rb +31 -25
- data/lib/bio-vcf/vcffile.rb +46 -0
- data/lib/bio-vcf/vcfgenotypefield.rb +20 -20
- data/lib/bio-vcf/vcfheader.rb +29 -0
- data/lib/bio-vcf/vcfrecord.rb +5 -3
- data/lib/bio-vcf/vcfsample.rb +3 -1
- data/test/data/input/empty.vcf +2 -0
- data/test/data/regression/empty-stderr.new +12 -0
- data/test/data/regression/empty.new +2 -0
- data/test/data/regression/empty.ref +2 -0
- data/test/data/regression/eval_once-stderr.new +2 -2
- data/test/data/regression/eval_r.info.dp-stderr.new +9 -7
- data/test/data/regression/ifilter_s.dp-stderr.new +9 -7
- data/test/data/regression/pass1-stderr.new +9 -7
- data/test/data/regression/r.info.dp-stderr.new +4 -8
- data/test/data/regression/r.info.dp.new +0 -33
- data/test/data/regression/rewrite.info.sample-stderr.new +9 -7
- data/test/data/regression/s.dp-stderr.new +9 -7
- data/test/data/regression/seval_s.dp-stderr.new +9 -7
- data/test/data/regression/sfilter_seval_s.dp-stderr.new +9 -7
- data/test/data/regression/thread4-stderr.new +9 -7
- data/test/data/regression/thread4_4-stderr.new +25 -44
- data/test/data/regression/thread4_4.new +0 -20
- data/test/data/regression/thread4_4_failed_filter-stderr.new +1 -1
- data/test/data/regression/thread4_4_failed_filter-stderr.ref +1 -1
- data/test/data/regression/vcf2json_full_header-stderr.new +9 -7
- data/test/data/regression/vcf2json_use_meta-stderr.new +9 -7
- metadata +11 -7
- data/features/#cli.feature# +0 -71
- data/features/filter.feature~ +0 -35
- data/test/stress/stress_test.sh~ +0 -8
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bio-vcf 0.9.
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Waiting up to 180 seconds for pid=
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bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
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Waiting up to 180 seconds for pid=30651 to complete /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf
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Processing output file /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf (blocking)
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bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
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Waiting up to 180 seconds for pid=30660 to complete /tmp/bio-vcf_20201222-30658-19yukj0/000001-bio-vcf
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[:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
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bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
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Waiting up to 180 seconds for pid=30973 to complete /tmp/bio-vcf_20201222-30971-lfyqh6/000001-bio-vcf
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1 13118 . A G 2317.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437 GT:AD:DP:GQ:PL 0/1:21,13:34:95:95,0,277 0/1:82,47:129:99:444,0,1445 0/1:65,36:101:99:412,0,1179 0/1:92,53:145:99:455,0,1989 0/1:58,40:99:99:312,0,1216 0/1:52,33:85:99:186,0,1000 0/1:61,47:108:99:453,0,1079
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1 13178 . G A 72.69 . AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383 GT:AD:DP:GQ:PL 0/1:49,3:52:11:11,0,292 0/0:161,11:172:60:0,60,1328 0/1:122,15:137:99:99,0,936 0/0:164,8:172:99:0,112,1436 0/0:120,9:129:62:0,62,771 0/0:113,6:119:12:0,12,885 0/0:138,10:148:99:0,112,1596
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1 13302 . C T 1067.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193 GT:AD:DP:GQ:PL 0/0:26,10:36:41:0,41,616 0/1:91,45:136:99:183,0,2085 0/1:71,28:99:86:86,0,1557 0/1:96,50:146:99:333,0,2098 0/1:55,34:90:99:283,0,1321 0/1:47,18:65:99:157,0,943 0/1:89,28:117:67:67,0,1921
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1 13757 . G A 271.89 . AC=2;AF=0.143;AN=14;BaseQRankSum=2.916;DP=1149;Dels=0.00;FS=11.172;HaplotypeScore=7.1466;MLEAC=2;MLEAF=0.143;MQ=18.17;MQ0=374;MQRankSum=3.990;QD=0.87;ReadPosRankSum=1.309 GT:AD:DP:GQ:PL 0/0:47,4:53:16:0,16,344 0/0:185,16:201:60:0,60,2690 0/1:157,24:181:99:162,0,2556 0/0:232,18:250:99:0,137,3600 0/0:139,13:152:15:0,15,2266 0/1:114,16:130:99:147,0,1525 0/0:168,14:182:2:0,2,2230
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1 13868 . A G 1481.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=2.036;DP=1108;Dels=0.00;FS=4.601;HaplotypeScore=6.7136;MLEAC=7;MLEAF=0.500;MQ=13.23;MQ0=622;MQRankSum=1.659;QD=1.34;ReadPosRankSum=0.283 GT:AD:DP:GQ:PL 0/1:60,15:75:80:80,0,568 0/1:146,46:192:99:289,0,1030 0/1:146,36:182:99:203,0,1001 0/1:172,52:224:99:222,0,1150 0/1:106,36:142:99:181,0,621 0/1:79,32:111:99:126,0,467 0/1:129,38:167:99:420,0,767
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1 13896 . C A 389.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=-0.743;DP=830;Dels=0.00;FS=0.000;HaplotypeScore=1.6931;MLEAC=6;MLEAF=0.429;MQ=11.88;MQ0=518;MQRankSum=-1.292;QD=0.54;ReadPosRankSum=0.433 GT:AD:DP:GQ:PL 0/1:50,12:62:99:107,0,367 0/1:107,28:135:40:40,0,660 0/1:120,23:143:37:37,0,675 0/1:144,31:175:99:172,0,690 0/0:98,14:112:42:0,42,577 0/1:65,16:81:34:34,0,290 0/1:102,19:121:41:41,0,677
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1 14354 . C A 109.72 . AC=3;AF=0.250;AN=12;BaseQRankSum=-2.527;DP=764;Dels=0.00;FS=0.000;HaplotypeScore=0.3231;MLEAC=3;MLEAF=0.250;MQ=5.02;MQ0=710;MQRankSum=1.079;QD=0.47;ReadPosRankSum=-0.178 GT:AD:DP:GQ:PL 0/1:36,7:43:68:68,0,75 0/0:141,17:158:9:0,9,86 0/1:103,12:115:42:42,0,72 0/0:132,13:145:21:0,21,201 ./. 0/1:62,10:72:38:38,0,117 0/0:108,11:119:9:0,9,86
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1 14464 . A T 3945.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=0.104;DP=809;Dels=0.00;FS=38.588;HaplotypeScore=5.8354;MLEAC=7;MLEAF=0.500;MQ=23.21;MQ0=241;MQRankSum=6.859;QD=4.88;ReadPosRankSum=-0.294 GT:AD:DP:GQ:PL 0/1:41,10:51:99:183,0,569 0/1:107,48:155:99:829,0,1388 0/1:99,42:141:99:691,0,1103 0/1:114,36:150:99:454,0,1544 0/1:48,35:83:99:781,0,561 0/1:64,25:89:99:409,0,781 0/1:102,38:140:99:638,0,1310
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-
1 14673 . G C 1012.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.674;DP=754;Dels=0.00;FS=115.496;HaplotypeScore=14.9167;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=268;MQRankSum=-1.459;QD=1.34;ReadPosRankSum=-3.039 GT:AD:DP:GQ:PL 0/1:28,8:36:34:34,0,409 0/1:117,25:142:99:125,0,1964 0/1:87,30:117:99:214,0,1506 0/1:130,27:157:99:193,0,2076 0/1:77,18:95:99:114,0,1273 0/1:49,27:76:99:200,0,719 0/1:103,28:131:99:172,0,1620
|
|
137
|
-
1 14699 . C G 64.65 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.064;DP=719;Dels=0.00;FS=29.480;HaplotypeScore=5.5900;MLEAC=2;MLEAF=0.143;MQ=24.79;MQ0=233;MQRankSum=-8.066;QD=0.27;ReadPosRankSum=-0.696 GT:AD:DP:GQ:PL 0/0:35,6:43:51:0,51,720 0/1:91,37:128:59:59,0,1859 0/0:80,29:109:99:0,101,1700 0/0:113,34:147:14:0,14,1987 0/0:72,26:98:37:0,37,1319 0/0:53,25:78:78:0,78,1035 0/1:84,30:114:44:44,0,1326
|
|
138
|
-
1 14907 . A G 9688.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.299;DP=1083;Dels=0.00;FS=20.983;HaplotypeScore=11.4413;MLEAC=7;MLEAF=0.500;MQ=33.27;MQ0=51;MQRankSum=1.076;QD=8.95;ReadPosRankSum=0.653 GT:AD:DP:GQ:PL 0/1:27,30:57:99:603,0,550 0/1:117,99:216:99:2024,0,2888 0/1:91,71:162:99:1489,0,1990 0/1:119,86:205:99:1876,0,2588 0/1:100,53:153:99:1001,0,2297 0/1:59,59:118:99:1240,0,1241 0/1:91,67:158:99:1495,0,2003
|
|
139
|
-
1 14930 . A G 8665.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-13.760;DP=1092;Dels=0.00;FS=17.240;HaplotypeScore=20.0469;MLEAC=7;MLEAF=0.500;MQ=34.72;MQ0=22;MQRankSum=1.127;QD=7.94;ReadPosRankSum=0.785 GT:AD:DP:GQ:PL 0/1:32,36:68:99:609,0,659 0/1:123,92:216:99:1636,0,3225 0/1:92,78:170:99:1449,0,2202 0/1:123,86:210:99:1748,0,3028 0/1:85,50:136:99:802,0,2117 0/1:62,63:125:99:1072,0,1437 0/1:92,71:164:99:1389,0,2055
|
|
140
|
-
1 14933 . G A 248.54 . AC=3;AF=0.214;AN=14;BaseQRankSum=1.588;DP=1089;Dels=0.00;FS=14.333;HaplotypeScore=19.7793;MLEAC=3;MLEAF=0.214;MQ=34.91;MQ0=18;MQRankSum=1.439;QD=0.45;ReadPosRankSum=0.752 GT:AD:DP:GQ:PL 0/0:59,9:68:1:0,1,1361 0/1:192,24:216:99:125,0,4941 0/0:160,9:169:99:0,142,4118 0/1:191,21:212:39:39,0,4848 0/0:126,6:132:99:0,210,3367 0/1:113,15:128:99:124,0,2578 0/0:154,10:164:99:0,158,3934
|
|
141
|
-
1 14948 . G A 570.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.167;DP=1050;Dels=0.00;FS=11.131;HaplotypeScore=6.4398;MLEAC=7;MLEAF=0.500;MQ=32.69;MQ0=53;MQRankSum=0.017;QD=0.54;ReadPosRankSum=-1.181 GT:AD:DP:GQ:PL 0/1:56,7:63:79:79,0,1134 0/1:168,24:192:70:70,0,3900 0/1:160,21:181:99:147,0,3515 0/1:188,23:211:57:57,0,4113 0/1:115,14:129:32:32,0,2406 0/1:103,18:121:99:173,0,2016 0/1:132,21:153:52:52,0,2861
|
|
142
|
-
1 14976 . G A 195.07 . AC=3;AF=0.214;AN=14;BaseQRankSum=7.340;DP=939;Dels=0.00;FS=32.492;HaplotypeScore=4.6786;MLEAC=3;MLEAF=0.214;MQ=27.87;MQ0=167;MQRankSum=1.477;QD=0.53;ReadPosRankSum=-0.560 GT:AD:DP:GQ:PL 0/1:50,6:56:12:12,0,929 0/0:152,14:166:81:0,81,3159 0/0:152,9:161:99:0,113,2885 0/1:174,22:196:99:127,0,3211 0/0:100,9:109:97:0,97,1900 0/1:103,13:116:97:97,0,1548 0/0:122,13:135:55:0,55,2246
|
|
143
|
-
1 15118 . A G 2503.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.645;DP=1004;Dels=0.00;FS=0.313;HaplotypeScore=4.1078;MLEAC=7;MLEAF=0.500;MQ=21.49;MQ0=207;MQRankSum=-0.007;QD=2.49;ReadPosRankSum=-0.291 GT:AD:DP:GQ:PL 0/1:38,8:46:50:50,0,575 0/1:148,50:198:99:671,0,2598 0/1:97,32:129:99:358,0,1911 0/1:176,53:230:99:700,0,2989 0/1:91,19:113:99:146,0,1741 0/1:92,31:126:99:347,0,1543 0/1:126,30:158:99:271,0,2193
|
|
144
|
-
1 15190 . G A 2564.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=11.094;DP=1090;Dels=0.00;FS=0.297;HaplotypeScore=4.3151;MLEAC=7;MLEAF=0.500;MQ=26.11;MQ0=187;MQRankSum=-0.724;QD=2.35;ReadPosRankSum=0.530 GT:AD:DP:GQ:PL 0/1:42,11:53:99:177,0,696 0/1:157,51:208:99:839,0,3145 0/1:142,28:170:91:91,0,2919 0/1:160,40:200:99:499,0,2815 0/1:109,17:126:99:167,0,2363 0/1:111,34:145:99:554,0,2268 0/1:141,38:179:99:277,0,2827
|
|
145
|
-
1 15211 . T G 14032.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-11.292;DP=992;Dels=0.00;FS=0.281;HaplotypeScore=11.0809;MLEAC=7;MLEAF=0.500;MQ=27.20;MQ0=159;MQRankSum=3.859;QD=14.15;ReadPosRankSum=-1.972 GT:AD:DP:GQ:PL 0/1:19,35:54:99:858,0,183 0/1:63,120:183:99:2771,0,960 0/1:50,111:161:99:2213,0,740 0/1:58,113:171:99:2326,0,685 0/1:39,81:120:99:1707,0,678 0/1:38,96:134:99:2126,0,499 0/1:61,107:168:99:2071,0,895
|
|
146
|
-
1 15274 . A G,T 8909.81 . AC=7,7;AF=0.500,0.500;AN=14;BaseQRankSum=2.416;DP=636;Dels=0.00;FS=0.000;HaplotypeScore=5.1061;MLEAC=7,7;MLEAF=0.500,0.500;MQ=22.77;MQ0=195;MQRankSum=2.299;QD=14.01;ReadPosRankSum=1.707 GT:AD:DP:GQ:PL 1/2:1,14,22:37:99:717,494,467,224,0,170 1/2:1,45,75:121:99:1922,1334,1265,588,0,441 1/2:0,31,71:102:99:1960,1563,1515,396,0,222 1/2:1,59,77:137:99:2009,1376,1298,633,0,486 1/2:0,18,52:71:62:938,789,771,149,0,62 1/2:0,29,38:67:99:1141,883,853,258,0,162 1/2:0,38,60:98:99:1464,1064,1016,399,0,285
|
|
147
|
-
1 15447 . A G 109.56 . AC=3;AF=0.214;AN=14;BaseQRankSum=-9.704;DP=1213;Dels=0.00;FS=0.000;HaplotypeScore=16.4636;MLEAC=3;MLEAF=0.214;MQ=19.12;MQ0=346;MQRankSum=-0.997;QD=0.20;ReadPosRankSum=-1.088 GT:AD:DP:GQ:PL 0/0:42,4:46:34:0,34,690 0/0:220,22:242:99:0,99,3639 0/0:167,16:183:42:0,42,2582 0/1:201,25:226:78:78,0,2854 0/1:121,16:137:39:39,0,1877 0/0:160,13:173:99:0,139,2724 0/1:157,18:175:34:34,0,2472
|
|
148
|
-
1 15688 . C T 54.29 . AC=2;AF=0.143;AN=14;BaseQRankSum=-8.686;DP=904;Dels=0.00;FS=11.971;HaplotypeScore=3.1454;MLEAC=2;MLEAF=0.143;MQ=16.75;MQ0=361;MQRankSum=-0.069;QD=0.16;ReadPosRankSum=0.355 GT:AD:DP:GQ:PL 0/0:34,3:37:15:0,15,335 0/0:166,16:182:61:0,61,2190 0/1:131,16:147:69:69,0,1563 0/1:167,17:184:22:22,0,1894 0/0:88,12:100:15:0,15,1099 0/0:88,13:101:1:0,1,1126 0/0:132,16:148:18:0,18,1706
|
|
149
|
-
1 16068 . T C 377.22 . AC=4;AF=0.286;AN=14;BaseQRankSum=-7.618;DP=398;Dels=0.00;FS=12.349;HaplotypeScore=1.8069;MLEAC=4;MLEAF=0.286;MQ=26.64;MQ0=64;MQRankSum=-4.589;QD=1.80;ReadPosRankSum=-0.448 GT:AD:DP:GQ:PL 0/1:18,15:33:99:182,0,404 0/0:51,6:57:31:0,31,815 0/1:52,16:68:64:64,0,1101 0/0:68,13:81:99:0,99,1505 0/0:41,8:49:51:0,51,1010 0/1:40,9:49:21:21,0,702 0/1:38,19:58:99:153,0,760
|
|
150
|
-
1 16103 . T G 2348.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-1.646;DP=526;Dels=0.00;FS=2.577;HaplotypeScore=0.9645;MLEAC=7;MLEAF=0.500;MQ=26.64;MQ0=82;MQRankSum=-2.736;QD=4.47;ReadPosRankSum=-2.044 GT:AD:DP:GQ:PL 0/1:21,29:50:99:504,0,450 0/1:55,24:79:99:209,0,838 0/1:49,37:86:99:456,0,1002 0/1:74,32:106:99:193,0,1519 0/1:41,19:60:99:141,0,740 0/1:38,23:61:99:257,0,548 0/1:38,46:84:99:628,0,641
|
|
@@ -2,4 +2,4 @@ Unknown field name <t> in record, did you mean r.info.t?
|
|
|
2
2
|
Unknown field name <t> in record, did you mean r.info.t?
|
|
3
3
|
Unknown field name <t> in record, did you mean r.info.t?
|
|
4
4
|
Unknown field name <t> in record, did you mean r.info.t?
|
|
5
|
-
execution expired
|
|
5
|
+
ERROR: execution expired
|
|
@@ -2,4 +2,4 @@ Unknown field name <t> in record, did you mean r.info.t?
|
|
|
2
2
|
Unknown field name <t> in record, did you mean r.info.t?
|
|
3
3
|
Unknown field name <t> in record, did you mean r.info.t?
|
|
4
4
|
Unknown field name <t> in record, did you mean r.info.t?
|
|
5
|
-
execution expired
|
|
5
|
+
ERROR: execution expired
|
|
@@ -1,8 +1,10 @@
|
|
|
1
|
-
bio-vcf 0.9.
|
|
2
|
-
Waiting up to 180 seconds for pid=
|
|
1
|
+
bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
|
|
2
|
+
Waiting up to 180 seconds for pid=30682 to complete /tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf
|
|
3
3
|
Processing remaining output...
|
|
4
|
-
Trying: [[
|
|
5
|
-
Set lock on [[
|
|
6
|
-
Processing output file /tmp/bio-
|
|
7
|
-
|
|
8
|
-
|
|
4
|
+
Trying: [[30682, 1, "/tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf"]]
|
|
5
|
+
Set lock on [[30682, 1, "/tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf"]]
|
|
6
|
+
Processing output file /tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf (blocking)
|
|
7
|
+
Checking for output_lock on existing /tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf
|
|
8
|
+
Trying to remove /tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf.keep
|
|
9
|
+
Removing /tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf.keep
|
|
10
|
+
Removing dir /tmp/bio-vcf_20201222-30680-iio5eo
|
|
@@ -1,8 +1,10 @@
|
|
|
1
|
-
bio-vcf 0.9.
|
|
2
|
-
Waiting up to 180 seconds for pid=
|
|
1
|
+
bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
|
|
2
|
+
Waiting up to 180 seconds for pid=30691 to complete /tmp/bio-vcf_20201222-30689-1bguuj5/000001-bio-vcf
|
|
3
3
|
Processing remaining output...
|
|
4
|
-
Trying: [[
|
|
5
|
-
Set lock on [[
|
|
6
|
-
Processing output file /tmp/bio-
|
|
7
|
-
|
|
8
|
-
|
|
4
|
+
Trying: [[30691, 1, "/tmp/bio-vcf_20201222-30689-1bguuj5/000001-bio-vcf"]]
|
|
5
|
+
Set lock on [[30691, 1, "/tmp/bio-vcf_20201222-30689-1bguuj5/000001-bio-vcf"]]
|
|
6
|
+
Processing output file /tmp/bio-vcf_20201222-30689-1bguuj5/000001-bio-vcf (blocking)
|
|
7
|
+
Checking for output_lock on existing /tmp/bio-vcf_20201222-30689-1bguuj5/000001-bio-vcf
|
|
8
|
+
Trying to remove /tmp/bio-vcf_20201222-30689-1bguuj5/000001-bio-vcf.keep
|
|
9
|
+
Removing /tmp/bio-vcf_20201222-30689-1bguuj5/000001-bio-vcf.keep
|
|
10
|
+
Removing dir /tmp/bio-vcf_20201222-30689-1bguuj5
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: bio-vcf
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.9.
|
|
4
|
+
version: 0.9.4
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Pjotr Prins
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date:
|
|
11
|
+
date: 2020-12-22 00:00:00.000000000 Z
|
|
12
12
|
dependencies: []
|
|
13
13
|
description: Smart lazy multi-threaded parser for VCF format with useful filtering
|
|
14
14
|
and output rewriting (JSON, RDF etc.)
|
|
@@ -25,16 +25,16 @@ files:
|
|
|
25
25
|
- Gemfile.lock
|
|
26
26
|
- LICENSE.txt
|
|
27
27
|
- README.md
|
|
28
|
+
- RELEASE_NOTES.md
|
|
29
|
+
- RELEASE_NOTES.md~
|
|
28
30
|
- Rakefile
|
|
29
31
|
- TAGS
|
|
30
32
|
- VERSION
|
|
31
33
|
- bin/bio-vcf
|
|
32
34
|
- bio-vcf.gemspec
|
|
33
|
-
- features/#cli.feature#
|
|
34
35
|
- features/cli.feature
|
|
35
36
|
- features/diff_count.feature
|
|
36
37
|
- features/filter.feature
|
|
37
|
-
- features/filter.feature~
|
|
38
38
|
- features/multisample.feature
|
|
39
39
|
- features/sfilter.feature
|
|
40
40
|
- features/somaticsniper.feature
|
|
@@ -54,6 +54,7 @@ files:
|
|
|
54
54
|
- lib/bio-vcf/utils.rb
|
|
55
55
|
- lib/bio-vcf/variant.rb
|
|
56
56
|
- lib/bio-vcf/vcf.rb
|
|
57
|
+
- lib/bio-vcf/vcffile.rb
|
|
57
58
|
- lib/bio-vcf/vcfgenotypefield.rb
|
|
58
59
|
- lib/bio-vcf/vcfheader.rb
|
|
59
60
|
- lib/bio-vcf/vcfheader_line.rb
|
|
@@ -71,11 +72,15 @@ files:
|
|
|
71
72
|
- template/vcf2rdf.erb
|
|
72
73
|
- template/vcf2rdf_header.erb
|
|
73
74
|
- test/data/input/dbsnp.vcf
|
|
75
|
+
- test/data/input/empty.vcf
|
|
74
76
|
- test/data/input/gatk_exome.vcf
|
|
75
77
|
- test/data/input/gatk_wgs.vcf
|
|
76
78
|
- test/data/input/multisample.vcf
|
|
77
79
|
- test/data/input/somaticsniper.vcf
|
|
78
80
|
- test/data/input/test.bed
|
|
81
|
+
- test/data/regression/empty-stderr.new
|
|
82
|
+
- test/data/regression/empty.new
|
|
83
|
+
- test/data/regression/empty.ref
|
|
79
84
|
- test/data/regression/eval_once-stderr.new
|
|
80
85
|
- test/data/regression/eval_once.new
|
|
81
86
|
- test/data/regression/eval_once.ref
|
|
@@ -120,9 +125,8 @@ files:
|
|
|
120
125
|
- test/data/regression/vcf2json_use_meta.ref
|
|
121
126
|
- test/performance/metrics.md
|
|
122
127
|
- test/stress/stress_test.sh
|
|
123
|
-
- test/stress/stress_test.sh~
|
|
124
128
|
- test/tmp/test.vcf
|
|
125
|
-
homepage: http://github.com/
|
|
129
|
+
homepage: http://github.com/vcflib/bio-vcf
|
|
126
130
|
licenses:
|
|
127
131
|
- MIT
|
|
128
132
|
metadata: {}
|
|
@@ -142,7 +146,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
142
146
|
version: '0'
|
|
143
147
|
requirements: []
|
|
144
148
|
rubyforge_project:
|
|
145
|
-
rubygems_version: 2.
|
|
149
|
+
rubygems_version: 2.7.6.2
|
|
146
150
|
signing_key:
|
|
147
151
|
specification_version: 4
|
|
148
152
|
summary: Fast multi-purpose multi-threaded VCF parser
|
data/features/#cli.feature#
DELETED
|
@@ -1,71 +0,0 @@
|
|
|
1
|
-
@cli
|
|
2
|
-
Feature: Command-line interface (CLI)
|
|
3
|
-
|
|
4
|
-
bio-vcf has a powerful command line interface. Here we regression test features.
|
|
5
|
-
|
|
6
|
-
Scenario: Test the info filter using dp
|
|
7
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
8
|
-
When I execute "./bin/bio-vcf -i --filter 'r.info.dp>100'"
|
|
9
|
-
Then I expect the named output to match the named output "r.info.dp"
|
|
10
|
-
|
|
11
|
-
Scenario: Test the info filter using dp and threads
|
|
12
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
13
|
-
When I execute "./bin/bio-vcf -i --num-threads 4 --filter 'r.info.dp>2'"
|
|
14
|
-
Then I expect the named output to match the named output "thread4"
|
|
15
|
-
|
|
16
|
-
Scenario: Test the info filter using dp and threads with lines
|
|
17
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
18
|
-
When I execute "./bin/bio-vcf -i --num-threads 4 --thread-lines 4 --filter 'r.info.dp>2'"
|
|
19
|
-
Then I expect the named output to match the named output "thread4_4"
|
|
20
|
-
|
|
21
|
-
Scenario: Test the sample filter using dp
|
|
22
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
23
|
-
When I execute "./bin/bio-vcf -i --sfilter 's.dp>20'"
|
|
24
|
-
Then I expect the named output to match the named output "s.dp"
|
|
25
|
-
|
|
26
|
-
Scenario: Test the include sample filter using dp
|
|
27
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
28
|
-
When I execute "./bin/bio-vcf -i --ifilter 's.dp>100' --seval s.dp"
|
|
29
|
-
Then I expect the named output to match the named output "ifilter_s.dp"
|
|
30
|
-
|
|
31
|
-
Scenario: Test the info eval using dp
|
|
32
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
33
|
-
When I execute "./bin/bio-vcf -i --eval 'r.info.dp'"
|
|
34
|
-
Then I expect the named output to match the named output "eval_r.info.dp"
|
|
35
|
-
|
|
36
|
-
Scenario: Test the sample eval using dp
|
|
37
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
38
|
-
When I execute "./bin/bio-vcf -i --seval 's.dp'"
|
|
39
|
-
Then I expect the named output to match the named output "seval_s.dp"
|
|
40
|
-
|
|
41
|
-
Scenario: Test the sample filter + eval using dp
|
|
42
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
43
|
-
When I execute "./bin/bio-vcf -i --sfilter 's.dp>10' --seval 's.dp'"
|
|
44
|
-
Then I expect the named output to match the named output "sfilter_seval_s.dp"
|
|
45
|
-
|
|
46
|
-
Scenario: Rewrite an info field
|
|
47
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
48
|
-
When I execute "./bin/bio-vcf --rewrite rec.info[\'sample\']=\'XXXXX\'"
|
|
49
|
-
Then I expect the named output to match the named output "rewrite.info.sample"
|
|
50
|
-
|
|
51
|
-
Scenario: Test eval-once
|
|
52
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
53
|
-
When I execute "./bin/bio-vcf --eval-once header.meta[\'GATKCommandLine\']"
|
|
54
|
-
Then I expect the named output to match the named output "eval_once"
|
|
55
|
-
|
|
56
|
-
Scenario: Test JSON output with header meta data
|
|
57
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
58
|
-
When I execute "./bin/bio-vcf --template template/vcf2json_full_header.erb"
|
|
59
|
-
Then I expect the named output to match the named output "vcf2json_full_header"
|
|
60
|
-
|
|
61
|
-
Scenario: Test JSON output with header meta data and query samples
|
|
62
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
63
|
-
When I execute "./bin/bio-vcf --template template/vcf2json_use_meta.erb"
|
|
64
|
-
Then I expect the named output to match the named output "vcf2json_use_meta"
|
|
65
|
-
|
|
66
|
-
Scenario: Test deadlock on failed filter with threads
|
|
67
|
-
Given I have input file(s) named "test/data/input/multisample.vcf"
|
|
68
|
-
When I execute "./bin/bio-vcf -q --timeout 4 --num-threads 4 --thread-lines 4 --filter 't.info.dp>2'"
|
|
69
|
-
Then I expect an error and the named output to match the named output "thread4_4_failed_filter" in under 30 seconds
|
|
70
|
-
|
|
71
|
-
|
data/features/filter.feature~
DELETED
|
@@ -1,35 +0,0 @@
|
|
|
1
|
-
@meta
|
|
2
|
-
Feature: Parsing VCF meta information from the header
|
|
3
|
-
|
|
4
|
-
Take a header and parse that information as defined by the VCF standard.
|
|
5
|
-
|
|
6
|
-
Scenario: When parsing a header line
|
|
7
|
-
|
|
8
|
-
Given the VCF header lines
|
|
9
|
-
"""
|
|
10
|
-
##fileformat=VCFv4.1
|
|
11
|
-
##fileDate=20140121
|
|
12
|
-
##phasing=none
|
|
13
|
-
##reference=file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta
|
|
14
|
-
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
|
|
15
|
-
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
|
|
16
|
-
##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
|
|
17
|
-
##INFO=<ID=PM,Number=0,Type=Flag,Description="Variant is Precious(Clinical,Pubmed Cited)">
|
|
18
|
-
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
|
|
19
|
-
"""
|
|
20
|
-
When I parse the VCF header
|
|
21
|
-
Then I expect vcf.columns to be [CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO','FORMAT','NORMAL','TUMOR']
|
|
22
|
-
And I expect vcf.fileformat to be "VCFv4.1"
|
|
23
|
-
And I expect vcf.fileDate to be "20140121"
|
|
24
|
-
And I expect vcf.field['fileDate'] to be "20140121"
|
|
25
|
-
And I expect vcf.phasing to be "none"
|
|
26
|
-
And I expect vcf.reference to be "file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta"
|
|
27
|
-
And I expect vcf.format['GT'] to be {"ID"=>"GT", "Number"=>"1", "Type"=>"String", "Description"=>"Genotype"}
|
|
28
|
-
And I expect vcf.format['DP'] to be {"ID"=>"DP", "Number"=>"1", "Type"=>"Integer", "Description"=>"Total read depth"}
|
|
29
|
-
And I expect vcf.format['DP4'] to be {"ID"=>"DP4", "Number"=>"4", "Type"=>"Integer", "Description"=>"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"}
|
|
30
|
-
And I expect vcf.info['PM'] to be {"ID"=>"PM", "Number"=>"0", "Type"=>"Flag", "Description"=>"Variant is Precious(Clinical,Pubmed Cited)"}'
|
|
31
|
-
And I expect vcf.meta to contain all header meta information
|
|
32
|
-
|
|
33
|
-
Scenario: When parsing the header of somatic_sniper.vcf
|
|
34
|
-
|
|
35
|
-
Do something
|