bio-vcf 0.9.2 → 0.9.4

Sign up to get free protection for your applications and to get access to all the features.
Files changed (45) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +1 -21
  3. data/LICENSE.txt +1 -1
  4. data/README.md +107 -73
  5. data/RELEASE_NOTES.md +20 -0
  6. data/RELEASE_NOTES.md~ +11 -0
  7. data/VERSION +1 -1
  8. data/bin/bio-vcf +49 -30
  9. data/bio-vcf.gemspec +1 -1
  10. data/features/cli.feature +4 -1
  11. data/features/diff_count.feature +0 -1
  12. data/features/step_definitions/cli-feature.rb +13 -9
  13. data/features/step_definitions/diff_count.rb +1 -1
  14. data/features/step_definitions/somaticsniper.rb +1 -1
  15. data/lib/bio-vcf/pcows.rb +31 -25
  16. data/lib/bio-vcf/vcffile.rb +46 -0
  17. data/lib/bio-vcf/vcfgenotypefield.rb +20 -20
  18. data/lib/bio-vcf/vcfheader.rb +29 -0
  19. data/lib/bio-vcf/vcfrecord.rb +5 -3
  20. data/lib/bio-vcf/vcfsample.rb +3 -1
  21. data/test/data/input/empty.vcf +2 -0
  22. data/test/data/regression/empty-stderr.new +12 -0
  23. data/test/data/regression/empty.new +2 -0
  24. data/test/data/regression/empty.ref +2 -0
  25. data/test/data/regression/eval_once-stderr.new +2 -2
  26. data/test/data/regression/eval_r.info.dp-stderr.new +9 -7
  27. data/test/data/regression/ifilter_s.dp-stderr.new +9 -7
  28. data/test/data/regression/pass1-stderr.new +9 -7
  29. data/test/data/regression/r.info.dp-stderr.new +4 -8
  30. data/test/data/regression/r.info.dp.new +0 -33
  31. data/test/data/regression/rewrite.info.sample-stderr.new +9 -7
  32. data/test/data/regression/s.dp-stderr.new +9 -7
  33. data/test/data/regression/seval_s.dp-stderr.new +9 -7
  34. data/test/data/regression/sfilter_seval_s.dp-stderr.new +9 -7
  35. data/test/data/regression/thread4-stderr.new +9 -7
  36. data/test/data/regression/thread4_4-stderr.new +25 -44
  37. data/test/data/regression/thread4_4.new +0 -20
  38. data/test/data/regression/thread4_4_failed_filter-stderr.new +1 -1
  39. data/test/data/regression/thread4_4_failed_filter-stderr.ref +1 -1
  40. data/test/data/regression/vcf2json_full_header-stderr.new +9 -7
  41. data/test/data/regression/vcf2json_use_meta-stderr.new +9 -7
  42. metadata +11 -7
  43. data/features/#cli.feature# +0 -71
  44. data/features/filter.feature~ +0 -35
  45. data/test/stress/stress_test.sh~ +0 -8
data/test/data/regression/seval_s.dp-stderr.new CHANGED
@@ -1,8 +1,10 @@
1
- bio-vcf 0.9.2 (biogem Ruby 2.2.4 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=9387 to complete /tmp/bio-vcf_20160122-9385-1efdwsy/000001-bio-vcf
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=30651 to complete /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf
3
3
  Processing remaining output...
4
- Trying: [[9387, 1, "/tmp/bio-vcf_20160122-9385-1efdwsy/000001-bio-vcf"]]
5
- Set lock on [[9387, 1, "/tmp/bio-vcf_20160122-9385-1efdwsy/000001-bio-vcf"]]
6
- Processing output file /tmp/bio-vcf_20160122-9385-1efdwsy/000001-bio-vcf (blocking)
7
- Removing /tmp/bio-vcf_20160122-9385-1efdwsy/000001-bio-vcf
8
- Removing dir /tmp/bio-vcf_20160122-9385-1efdwsy
4
+ Trying: [[30651, 1, "/tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf"]]
5
+ Set lock on [[30651, 1, "/tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf"]]
6
+ Processing output file /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf (blocking)
7
+ Checking for output_lock on existing /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf
8
+ Trying to remove /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf.keep
9
+ Removing /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf.keep
10
+ Removing dir /tmp/bio-vcf_20201222-30649-gol7rw
data/test/data/regression/sfilter_seval_s.dp-stderr.new CHANGED
@@ -1,5 +1,5 @@
1
- bio-vcf 0.9.2 (biogem Ruby 2.2.4 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=9396 to complete /tmp/bio-vcf_20160122-9394-61zs8r/000001-bio-vcf
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=30660 to complete /tmp/bio-vcf_20201222-30658-19yukj0/000001-bio-vcf
3
3
  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
4
4
  [:filter, "s.dp>10"]
5
5
  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
@@ -9,8 +9,10 @@ Waiting up to 180 seconds for pid=9396 to complete /tmp/bio-vcf_20160122-9394-61
9
9
  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
10
10
  [:filter, "s.dp>10"]
11
11
  Processing remaining output...
12
- Trying: [[9396, 1, "/tmp/bio-vcf_20160122-9394-61zs8r/000001-bio-vcf"]]
13
- Set lock on [[9396, 1, "/tmp/bio-vcf_20160122-9394-61zs8r/000001-bio-vcf"]]
14
- Processing output file /tmp/bio-vcf_20160122-9394-61zs8r/000001-bio-vcf (blocking)
15
- Removing /tmp/bio-vcf_20160122-9394-61zs8r/000001-bio-vcf
16
- Removing dir /tmp/bio-vcf_20160122-9394-61zs8r
12
+ Trying: [[30660, 1, "/tmp/bio-vcf_20201222-30658-19yukj0/000001-bio-vcf"]]
13
+ Set lock on [[30660, 1, "/tmp/bio-vcf_20201222-30658-19yukj0/000001-bio-vcf"]]
14
+ Processing output file /tmp/bio-vcf_20201222-30658-19yukj0/000001-bio-vcf (blocking)
15
+ Checking for output_lock on existing /tmp/bio-vcf_20201222-30658-19yukj0/000001-bio-vcf
16
+ Trying to remove /tmp/bio-vcf_20201222-30658-19yukj0/000001-bio-vcf.keep
17
+ Removing /tmp/bio-vcf_20201222-30658-19yukj0/000001-bio-vcf.keep
18
+ Removing dir /tmp/bio-vcf_20201222-30658-19yukj0
data/test/data/regression/thread4-stderr.new CHANGED
@@ -1,8 +1,10 @@
1
- bio-vcf 0.9.2 (biogem Ruby 2.2.4 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=9256 to complete /tmp/bio-vcf_20160122-9254-1iksrje/000001-bio-vcf
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=30973 to complete /tmp/bio-vcf_20201222-30971-lfyqh6/000001-bio-vcf
3
3
  Processing remaining output...
4
- Trying: [[9256, 1, "/tmp/bio-vcf_20160122-9254-1iksrje/000001-bio-vcf"]]
5
- Set lock on [[9256, 1, "/tmp/bio-vcf_20160122-9254-1iksrje/000001-bio-vcf"]]
6
- Processing output file /tmp/bio-vcf_20160122-9254-1iksrje/000001-bio-vcf (blocking)
7
- Removing /tmp/bio-vcf_20160122-9254-1iksrje/000001-bio-vcf
8
- Removing dir /tmp/bio-vcf_20160122-9254-1iksrje
4
+ Trying: [[30973, 1, "/tmp/bio-vcf_20201222-30971-lfyqh6/000001-bio-vcf"]]
5
+ Set lock on [[30973, 1, "/tmp/bio-vcf_20201222-30971-lfyqh6/000001-bio-vcf"]]
6
+ Processing output file /tmp/bio-vcf_20201222-30971-lfyqh6/000001-bio-vcf (blocking)
7
+ Checking for output_lock on existing /tmp/bio-vcf_20201222-30971-lfyqh6/000001-bio-vcf
8
+ Trying to remove /tmp/bio-vcf_20201222-30971-lfyqh6/000001-bio-vcf.keep
9
+ Removing /tmp/bio-vcf_20201222-30971-lfyqh6/000001-bio-vcf.keep
10
+ Removing dir /tmp/bio-vcf_20201222-30971-lfyqh6
data/test/data/regression/thread4_4-stderr.new CHANGED
@@ -1,44 +1,25 @@
1
- bio-vcf 0.9.2 (biogem Ruby 2.2.4 with pcows) by Pjotr Prins 2015
2
- ..Set lock on [[9267, 1, "/tmp/bio-vcf_20160122-9264-14nbd6g/000001-bio-vcf"]]
3
- Processing output file /tmp/bio-vcf_20160122-9264-14nbd6g/000001-bio-vcf (non-blocking)
4
- .Checking for output_lock on existing /tmp/bio-vcf_20160122-9264-14nbd6g/000001-bio-vcf
5
- Removing /tmp/bio-vcf_20160122-9264-14nbd6g/000001-bio-vcf.keep
6
- Set lock on [[9272, 2, "/tmp/bio-vcf_20160122-9264-14nbd6g/000002-bio-vcf"]]
7
- Processing output file /tmp/bio-vcf_20160122-9264-14nbd6g/000002-bio-vcf (non-blocking)
8
- .Checking for output_lock on existing /tmp/bio-vcf_20160122-9264-14nbd6g/000002-bio-vcf
9
- Removing /tmp/bio-vcf_20160122-9264-14nbd6g/000002-bio-vcf.keep
10
- Set lock on [[9281, 3, "/tmp/bio-vcf_20160122-9264-14nbd6g/000003-bio-vcf"]]
11
- Processing output file /tmp/bio-vcf_20160122-9264-14nbd6g/000003-bio-vcf (non-blocking)
12
- .Checking for output_lock on existing /tmp/bio-vcf_20160122-9264-14nbd6g/000003-bio-vcf
13
- Removing /tmp/bio-vcf_20160122-9264-14nbd6g/000003-bio-vcf.keep
14
- Set lock on [[9290, 4, "/tmp/bio-vcf_20160122-9264-14nbd6g/000004-bio-vcf"]]
15
- Processing output file /tmp/bio-vcf_20160122-9264-14nbd6g/000004-bio-vcf (non-blocking)
16
- .Checking for output_lock on existing /tmp/bio-vcf_20160122-9264-14nbd6g/000004-bio-vcf
17
- Removing /tmp/bio-vcf_20160122-9264-14nbd6g/000004-bio-vcf.keep
18
- Set lock on [[9299, 5, "/tmp/bio-vcf_20160122-9264-14nbd6g/000005-bio-vcf"]]
19
- Processing output file /tmp/bio-vcf_20160122-9264-14nbd6g/000005-bio-vcf (non-blocking)
20
- .Checking for output_lock on existing /tmp/bio-vcf_20160122-9264-14nbd6g/000005-bio-vcf
21
- Removing /tmp/bio-vcf_20160122-9264-14nbd6g/000005-bio-vcf.keep
22
- Set lock on [[9308, 6, "/tmp/bio-vcf_20160122-9264-14nbd6g/000006-bio-vcf"]]
23
- Processing output file /tmp/bio-vcf_20160122-9264-14nbd6g/000006-bio-vcf (non-blocking)
24
- .Checking for output_lock on existing /tmp/bio-vcf_20160122-9264-14nbd6g/000006-bio-vcf
25
- Removing /tmp/bio-vcf_20160122-9264-14nbd6g/000006-bio-vcf.keep
26
- Set lock on [[9317, 7, "/tmp/bio-vcf_20160122-9264-14nbd6g/000007-bio-vcf"]]
27
- Processing output file /tmp/bio-vcf_20160122-9264-14nbd6g/000007-bio-vcf (non-blocking)
28
- .Checking for output_lock on existing /tmp/bio-vcf_20160122-9264-14nbd6g/000007-bio-vcf
29
- Removing /tmp/bio-vcf_20160122-9264-14nbd6g/000007-bio-vcf.keep
30
- Set lock on [[9326, 8, "/tmp/bio-vcf_20160122-9264-14nbd6g/000008-bio-vcf"]]
31
- Processing output file /tmp/bio-vcf_20160122-9264-14nbd6g/000008-bio-vcf (non-blocking)
32
- Waiting up to 180 seconds for pid=9343 to complete /tmp/bio-vcf_20160122-9264-14nbd6g/000010-bio-vcf
33
- Processing remaining output...
34
- Checking for output_lock on existing /tmp/bio-vcf_20160122-9264-14nbd6g/000008-bio-vcf
35
- Removing /tmp/bio-vcf_20160122-9264-14nbd6g/000008-bio-vcf.keep
36
- Set lock on [[9335, 9, "/tmp/bio-vcf_20160122-9264-14nbd6g/000009-bio-vcf"]]
37
- Processing output file /tmp/bio-vcf_20160122-9264-14nbd6g/000009-bio-vcf (non-blocking)
38
- Checking for output_lock on existing /tmp/bio-vcf_20160122-9264-14nbd6g/000009-bio-vcf
39
- Removing /tmp/bio-vcf_20160122-9264-14nbd6g/000009-bio-vcf.keep
40
- Set lock on [[9343, 10, "/tmp/bio-vcf_20160122-9264-14nbd6g/000010-bio-vcf"]]
41
- Processing output file /tmp/bio-vcf_20160122-9264-14nbd6g/000010-bio-vcf (non-blocking)
42
- Checking for output_lock on existing /tmp/bio-vcf_20160122-9264-14nbd6g/000010-bio-vcf
43
- Removing /tmp/bio-vcf_20160122-9264-14nbd6g/000010-bio-vcf.keep
44
- Removing dir /tmp/bio-vcf_20160122-9264-14nbd6g
1
+ bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
2
+ ..Set lock on [[30984, 1, "/tmp/bio-vcf_20201222-30981-rnkgf0/000001-bio-vcf"]]
3
+ Processing output file /tmp/bio-vcf_20201222-30981-rnkgf0/000001-bio-vcf (non-blocking)
4
+ .Checking for output_lock on existing /tmp/bio-vcf_20201222-30981-rnkgf0/000001-bio-vcf
5
+ Trying to remove /tmp/bio-vcf_20201222-30981-rnkgf0/000001-bio-vcf.keep
6
+ Removing /tmp/bio-vcf_20201222-30981-rnkgf0/000001-bio-vcf.keep
7
+ Set lock on [[30989, 2, "/tmp/bio-vcf_20201222-30981-rnkgf0/000002-bio-vcf"]]
8
+ Processing output file /tmp/bio-vcf_20201222-30981-rnkgf0/000002-bio-vcf (non-blocking)
9
+ .Checking for output_lock on existing /tmp/bio-vcf_20201222-30981-rnkgf0/000002-bio-vcf
10
+ Trying to remove /tmp/bio-vcf_20201222-30981-rnkgf0/000002-bio-vcf.keep
11
+ Removing /tmp/bio-vcf_20201222-30981-rnkgf0/000002-bio-vcf.keep
12
+ Set lock on [[30998, 3, "/tmp/bio-vcf_20201222-30981-rnkgf0/000003-bio-vcf"]]
13
+ Processing output file /tmp/bio-vcf_20201222-30981-rnkgf0/000003-bio-vcf (non-blocking)
14
+ .Checking for output_lock on existing /tmp/bio-vcf_20201222-30981-rnkgf0/000003-bio-vcf
15
+ .Checking for output_lock on existing /tmp/bio-vcf_20201222-30981-rnkgf0/000003-bio-vcf
16
+ Trying to remove /tmp/bio-vcf_20201222-30981-rnkgf0/000003-bio-vcf.keep
17
+ Removing /tmp/bio-vcf_20201222-30981-rnkgf0/000003-bio-vcf.keep
18
+ Set lock on [[31007, 4, "/tmp/bio-vcf_20201222-30981-rnkgf0/000004-bio-vcf"]]
19
+ Processing output file /tmp/bio-vcf_20201222-30981-rnkgf0/000004-bio-vcf (non-blocking)
20
+ .Checking for output_lock on existing /tmp/bio-vcf_20201222-30981-rnkgf0/000004-bio-vcf
21
+ .Waiting for slot (timeout=180)
22
+ ERROR:
23
+ Trying to remove /tmp/bio-vcf_20201222-30981-rnkgf0/000004-bio-vcf.keep
24
+ Removing /tmp/bio-vcf_20201222-30981-rnkgf0/000004-bio-vcf.keep
25
+ Removing dir /tmp/bio-vcf_20201222-30981-rnkgf0
data/test/data/regression/thread4_4.new CHANGED
@@ -128,23 +128,3 @@
128
128
  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
129
129
  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
130
130
  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
131
- 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
132
- 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
133
- 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
134
- 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
135
- 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
136
- 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
data/test/data/regression/thread4_4_failed_filter-stderr.new CHANGED
@@ -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
data/test/data/regression/thread4_4_failed_filter-stderr.ref CHANGED
@@ -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
data/test/data/regression/vcf2json_full_header-stderr.new CHANGED
@@ -1,8 +1,10 @@
1
- bio-vcf 0.9.2 (biogem Ruby 2.2.4 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=9418 to complete /tmp/bio-vcf_20160122-9416-1txay4y/000001-bio-vcf
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: [[9418, 1, "/tmp/bio-vcf_20160122-9416-1txay4y/000001-bio-vcf"]]
5
- Set lock on [[9418, 1, "/tmp/bio-vcf_20160122-9416-1txay4y/000001-bio-vcf"]]
6
- Processing output file /tmp/bio-vcf_20160122-9416-1txay4y/000001-bio-vcf (blocking)
7
- Removing /tmp/bio-vcf_20160122-9416-1txay4y/000001-bio-vcf
8
- Removing dir /tmp/bio-vcf_20160122-9416-1txay4y
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
data/test/data/regression/vcf2json_use_meta-stderr.new CHANGED
@@ -1,8 +1,10 @@
1
- bio-vcf 0.9.2 (biogem Ruby 2.2.4 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=9427 to complete /tmp/bio-vcf_20160122-9425-l2fs1h/000001-bio-vcf
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: [[9427, 1, "/tmp/bio-vcf_20160122-9425-l2fs1h/000001-bio-vcf"]]
5
- Set lock on [[9427, 1, "/tmp/bio-vcf_20160122-9425-l2fs1h/000001-bio-vcf"]]
6
- Processing output file /tmp/bio-vcf_20160122-9425-l2fs1h/000001-bio-vcf (blocking)
7
- Removing /tmp/bio-vcf_20160122-9425-l2fs1h/000001-bio-vcf
8
- Removing dir /tmp/bio-vcf_20160122-9425-l2fs1h
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: 0.9.2
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: 2016-01-22 00:00:00.000000000 Z
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/pjotrp/bioruby-vcf
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: 2.4.5.1
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
data/test/stress/stress_test.sh~ DELETED
@@ -1,8 +0,0 @@
1
- #! /bin/bash
2
- #
3
- # Stress test bio-vcf by running it on large files and comparing
4
- # results using threads
5
-
6
- input=test/data/input/multisample.vcf
7
-
8
- cat $input | ./bin/bio-vcf --num-threads 1 > stress_simple01.vcf