bio-vcf 0.9.0 → 0.9.2

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.
Files changed (36) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +2 -3
  3. data/Gemfile.lock +44 -0
  4. data/README.md +151 -28
  5. data/VERSION +1 -1
  6. data/bin/bio-vcf +47 -15
  7. data/bio-vcf.gemspec +4 -21
  8. data/features/#cli.feature# +71 -0
  9. data/features/cli.feature +3 -3
  10. data/features/filter.feature +12 -0
  11. data/features/filter.feature~ +35 -0
  12. data/features/somaticsniper.feature +2 -0
  13. data/features/step_definitions/cli-feature.rb +5 -0
  14. data/features/step_definitions/somaticsniper.rb +8 -0
  15. data/lib/bio-vcf/pcows.rb +123 -36
  16. data/lib/bio-vcf/vcfgenotypefield.rb +1 -1
  17. data/lib/bio-vcf/vcfrecord.rb +21 -0
  18. data/lib/bio-vcf/vcfsample.rb +13 -0
  19. data/test/data/regression/eval_once-stderr.new +2 -1
  20. data/test/data/regression/eval_r.info.dp-stderr.new +8 -4
  21. data/test/data/regression/ifilter_s.dp-stderr.new +8 -4
  22. data/test/data/regression/pass1-stderr.new +8 -0
  23. data/test/data/regression/pass1.new +88 -0
  24. data/test/data/regression/pass1.ref +88 -0
  25. data/test/data/regression/r.info.dp-stderr.new +8 -4
  26. data/test/data/regression/rewrite.info.sample-stderr.new +8 -4
  27. data/test/data/regression/s.dp-stderr.new +8 -4
  28. data/test/data/regression/seval_s.dp-stderr.new +8 -4
  29. data/test/data/regression/sfilter_seval_s.dp-stderr.new +8 -4
  30. data/test/data/regression/thread4-stderr.new +8 -4
  31. data/test/data/regression/thread4_4-stderr.new +44 -15
  32. data/test/data/regression/vcf2json_full_header-stderr.new +8 -4
  33. data/test/data/regression/vcf2json_use_meta-stderr.new +8 -4
  34. data/test/stress/stress_test.sh +15 -0
  35. data/test/stress/stress_test.sh~ +8 -0
  36. metadata +14 -5
data/lib/bio-vcf/vcfgenotypefield.rb CHANGED
@@ -154,7 +154,7 @@ module BioVcf
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  def gti?
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  not VcfValue::empty?(fetch_value("GT"))
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  end
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-
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+
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  def gti
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  gt.split(/[\/\|]/).map { |g| g.to_i }
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  end
data/lib/bio-vcf/vcfrecord.rb CHANGED
@@ -210,6 +210,12 @@ module BioVcf
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  list.each { |i| yield VcfSample::Sample.new(self,sample_by_index(i.to_i)) }
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  end
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+ def samples
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+ list = []
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+ each_sample { |s| list << s }
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+ list
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+ end
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+
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  def missing_samples?
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  @fields[9..-1].each { |sample|
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  return true if VcfSample::empty?(sample)
@@ -287,6 +293,21 @@ module BioVcf
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  end
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  end
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295
 
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+ def add_to_filter_field str
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+ filter = @fields[6]
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+ if not filter or filter == '.' or filter == 'PASS'
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+ filter = str
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+ else
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+ values = filter.split(/;/)
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+ if not values.include?(str)
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+ filter = filter +';'+str
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+ end
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+ end
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+ filter = '.' if filter == nil or filter == ''
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+ @fields[6] = filter
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+ filter
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+ end
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+
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  # Return the sample
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  def method_missing(m, *args, &block)
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  name = m.to_s
data/lib/bio-vcf/vcfsample.rb CHANGED
@@ -43,6 +43,19 @@ module BioVcf
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  v.split(/[\/\|]/).map{ |v| (v=='.' ? nil : v.to_i) }
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  end
45
45
 
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+ def gtindex
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+ v = fetch_values("GT")
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+ return case v
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+ when nil then nil
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+ when './.' then nil
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+ when '0/0' then 0
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+ when '0/1' then 1
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+ when '1/1' then 2
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+ else
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+ raise "Unknown genotype #{v}"
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+ end
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+ end
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+
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  # Split GT into into a nucleode sequence
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  def gts
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  gti.map { |i| (i ? @rec.get_gt(i) : nil) }
data/test/data/regression/eval_once-stderr.new CHANGED
@@ -1 +1,2 @@
1
- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
1
+ bio-vcf 0.9.2 (biogem Ruby 2.2.4 with pcows) by Pjotr Prins 2015
2
+ Removing dir /tmp/bio-vcf_20160122-9412-5yf2ot
data/test/data/regression/eval_r.info.dp-stderr.new CHANGED
@@ -1,4 +1,8 @@
1
- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=3644 to complete
3
- OK pid=3644, processing /tmp/bio-vcf_20150816-3642-1j5rn5y/000001-bio-vcf
4
- Processing /tmp/bio-vcf_20150816-3642-1j5rn5y/000001-bio-vcf
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=9378 to complete /tmp/bio-vcf_20160122-9376-640z88/000001-bio-vcf
3
+ Processing remaining output...
4
+ Trying: [[9378, 1, "/tmp/bio-vcf_20160122-9376-640z88/000001-bio-vcf"]]
5
+ Set lock on [[9378, 1, "/tmp/bio-vcf_20160122-9376-640z88/000001-bio-vcf"]]
6
+ Processing output file /tmp/bio-vcf_20160122-9376-640z88/000001-bio-vcf (blocking)
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+ Removing /tmp/bio-vcf_20160122-9376-640z88/000001-bio-vcf
8
+ Removing dir /tmp/bio-vcf_20160122-9376-640z88
data/test/data/regression/ifilter_s.dp-stderr.new CHANGED
@@ -1,5 +1,5 @@
1
- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=3632 to complete
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=9369 to complete /tmp/bio-vcf_20160122-9367-zhp98h/000001-bio-vcf
3
3
  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
4
4
  [:filter, "s.dp>100"]
5
5
  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
@@ -24,5 +24,9 @@ Waiting up to 180 seconds for pid=3632 to complete
24
24
  [:filter, "s.dp>100"]
25
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  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
26
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  [:filter, "s.dp>100"]
27
- OK pid=3632, processing /tmp/bio-vcf_20150816-3629-1g0u53a/000001-bio-vcf
28
- Processing /tmp/bio-vcf_20150816-3629-1g0u53a/000001-bio-vcf
27
+ Processing remaining output...
28
+ Trying: [[9369, 1, "/tmp/bio-vcf_20160122-9367-zhp98h/000001-bio-vcf"]]
29
+ Set lock on [[9369, 1, "/tmp/bio-vcf_20160122-9367-zhp98h/000001-bio-vcf"]]
30
+ Processing output file /tmp/bio-vcf_20160122-9367-zhp98h/000001-bio-vcf (blocking)
31
+ Removing /tmp/bio-vcf_20160122-9367-zhp98h/000001-bio-vcf
32
+ Removing dir /tmp/bio-vcf_20160122-9367-zhp98h
data/test/data/regression/pass1-stderr.new ADDED
@@ -0,0 +1,8 @@
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=9462 to complete /tmp/bio-vcf_20160122-9460-14lv2wl/000001-bio-vcf
3
+ Processing remaining output...
4
+ Trying: [[9462, 1, "/tmp/bio-vcf_20160122-9460-14lv2wl/000001-bio-vcf"]]
5
+ Set lock on [[9462, 1, "/tmp/bio-vcf_20160122-9460-14lv2wl/000001-bio-vcf"]]
6
+ Processing output file /tmp/bio-vcf_20160122-9460-14lv2wl/000001-bio-vcf (blocking)
7
+ Removing /tmp/bio-vcf_20160122-9460-14lv2wl/000001-bio-vcf
8
+ Removing dir /tmp/bio-vcf_20160122-9460-14lv2wl
data/test/data/regression/pass1.new ADDED
@@ -0,0 +1,88 @@
1
+ ##fileformat=VCFv4.1
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+ ##fileDate=20140121
3
+ ##phasing=none
4
+ ##reference=file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta
5
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
6
+ ##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
7
+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
8
+ ##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
9
+ ##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
10
+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
11
+ ##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
12
+ ##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
13
+ ##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality">
14
+ ##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality across all reads">
15
+ ##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
16
+ ##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown">
17
+ ##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score">
18
+ ##FILTER=<ID=PASS,Description="r.normal.dp>5 and r.tumor.dp>7">
19
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
20
+ 1 1636394 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:17:12,5,0,0:0,17,0,0:75:36:0:56:37:37:0:. 0/1:0/1:6:3,1,1,1:0,4,0,2:29:36:29:60,60:37:37,37:2:36
21
+ 1 36217006 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:21:9,12,0,0:0,21,0,0:90:31:0:60:37:37:0:. 0/1:0/1:6:2,2,0,2:0,4,0,2:24:31:24:60,53:37:37,37:2:31
22
+ 1 46527674 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:6,3,0,0:0,0,9,0:54:37:0:60:37:37:0:. 0/1:0/1:4:2,0,0,2:2,0,2,0:30:37:30:60,60:37:37,37:2:34
23
+ 1 108417572 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,7,0,0:48:42:0:41:37:37:0:. 0/1:0/1:4:2,0,1,1:0,2,0,2:30:42:35:60,60:37:37,37:2:31
24
+ 1 155170305 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:5,4,0,0:0,9,0,0:54:34:0:59:37:37:0:. 0/1:0/1:6:3,1,2,0:0,4,0,2:27:34:27:44,60:37:37,37:2:32
25
+ 1 155449089 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:5,4,0,0:0,0,9,0:54:37:0:60:37:37:0:. 0/1:0/1:4:1,1,0,2:2,0,2,0:30:37:30:60,60:37:37,37:2:34
26
+ 1 169847826 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:6,3,0,0:0,0,9,0:54:37:0:60:37:37:0:. 0/1:0/1:4:2,0,2,0:2,0,2,0:30:37:30:60,60:37:37,37:2:34
27
+ 1 203098164 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:3,7,0,0:0,10,0,0:57:40:0:53:37:37:0:. 0/1:0/1:3:1,0,2,0:0,1,0,2:1:40:33:60,60:37:37,37:2:37
28
+ 2 39213209 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:16:8,8,0,0:0,0,16,0:75:42:0:56:37:37:0:. 0/1:0/1:4:2,0,1,1:2,0,2,0:30:42:35:60,59:37:37,37:2:42
29
+ 2 86691250 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:6,2,0,0:0,0,8,0:51:42:0:59:37:37:0:. 0/1:0/1:4:2,0,1,1:2,0,2,0:30:42:35:60,60:37:37,37:2:33
30
+ 2 88874243 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:17:12,5,0,0:0,0,17,0:78:34:0:59:37:37:0:. 0/1:0/1:5:2,1,0,2:2,0,3,0:27:34:27:60,60:37:37,37:2:34
31
+ 2 121728044 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:6,3,0,0:0,0,9,0:54:42:0:55:37:37:0:. 0/1:0/1:4:1,1,1,1:2,0,2,0:35:42:35:60,57:37:37,37:2:36
32
+ 2 170062591 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:4,5,0,0:0,0,9,0:54:39:0:60:37:37:0:. 0/1:0/1:5:2,1,1,1:2,0,3,0:32:39:32:60,60:37:37,37:2:35
33
+ 2 216257844 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:2,5,0,0:0,0,7,0:48:40:0:60:37:37:0:. 0/1:0/1:3:1,0,0,2:2,0,1,0:1:40:33:60,60:37:37,37:2:30
34
+ 2 222322623 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:15:6,9,0,0:0,15,0,0:72:33:0:60:37:37:0:. 0/1:0/1:7:4,1,1,1:0,5,0,2:26:33:26:60,60:37:37,37:2:33
35
+ 3 25675413 . A T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:6,2,0,0:8,0,0,0:51:32:0:59:37:37:0:. 0/1:0/1:4:1,1,0,2:2,0,0,2:6:32:25:34,37:37:37,37:2:30
36
+ 3 36779638 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:13:8,5,0,0:0,13,0,0:66:36:0:60:37:37:0:. 0/1:0/1:6:1,3,1,1:0,4,0,2:29:36:29:60,60:37:37,37:2:36
37
+ 3 123458847 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:4,6,0,0:0,0,0,10:54:39:0:41:37:37:0:. 0/1:0/1:5:1,2,1,1:0,2,0,3:32:39:32:55,45:37:37,37:2:35
38
+ 3 124351308 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:7,1,0,0:0,0,8,0:51:42:0:58:37:37:0:. 0/1:0/1:4:1,1,1,1:2,0,2,0:35:42:35:60,60:37:37,37:2:33
39
+ 3 142171996 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:8,2,0,0:0,10,0,0:57:37:0:59:37:37:0:. 0/1:0/1:4:0,2,2,0:0,2,0,2:30:37:30:60,60:37:37,37:2:35
40
+ 3 189526168 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:23:11,12,0,0:0,0,23,0:96:36:0:59:37:37:0:. 0/1:0/1:6:1,3,1,1:2,0,4,0:29:36:29:60,60:37:37,37:2:36
41
+ 4 82058553 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:6,1,0,0:0,7,0,0:48:37:0:60:37:37:0:. 0/1:0/1:4:2,0,2,0:0,2,0,2:30:37:30:60,60:37:37,37:2:30
42
+ 4 122769998 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:7,0,0,0:0,7,0,0:48:40:0:54:37:37:0:. 0/1:0/1:3:1,0,2,0:0,1,0,2:1:40:33:60,60:37:37,37:2:30
43
+ 5 13850856 . G C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:3,5,0,0:0,0,8,0:51:40:0:51:37:37:0:. 0/1:0/1:3:0,1,2,0:0,2,1,0:1:40:33:49,60:37:37,37:2:33
44
+ 5 132038609 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:12:10,2,0,0:0,12,0,0:63:33:0:58:37:37:0:. 0/1:0/1:7:3,2,1,1:0,5,0,2:26:33:26:60,60:37:37,37:2:33
45
+ 5 137756599 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:13:7,6,0,0:0,13,0,0:66:31:0:60:37:37:0:. 0/1:0/1:6:2,2,2,0:0,4,0,2:24:31:24:60,60:37:37,37:2:31
46
+ 5 141974902 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:9,5,0,0:0,14,0,0:69:40:0:60:37:37:0:. 0/1:0/1:3:1,0,2,0:0,1,0,2:1:40:33:60,60:37:37,37:2:40
47
+ 6 2749400 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:8,2,0,0:0,10,0,0:57:35:0:60:37:37:0:. 0/1:0/1:4:2,0,0,2:0,2,0,2:28:35:28:60,39:37:37,37:2:34
48
+ 7 95217113 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,0,7,0:48:36:0:60:37:37:0:. 0/1:0/1:6:1,3,1,1:2,0,4,0:29:36:29:60,60:37:37,37:2:30
49
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data/test/data/regression/pass1.ref ADDED
@@ -0,0 +1,88 @@
1
+ ##fileformat=VCFv4.1
2
+ ##fileDate=20140121
3
+ ##phasing=none
4
+ ##reference=file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta
5
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
6
+ ##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
7
+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
8
+ ##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
9
+ ##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
10
+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
11
+ ##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
12
+ ##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
13
+ ##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality">
14
+ ##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality across all reads">
15
+ ##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
16
+ ##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown">
17
+ ##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score">
18
+ ##FILTER=<ID=PASS,Description="r.normal.dp>5 and r.tumor.dp>7">
19
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
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data/test/data/regression/r.info.dp-stderr.new CHANGED
@@ -1,4 +1,8 @@
1
- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=3546 to complete
3
- OK pid=3546, processing /tmp/bio-vcf_20150816-3543-hoqahc/000001-bio-vcf
4
- Processing /tmp/bio-vcf_20150816-3543-hoqahc/000001-bio-vcf
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=9246 to complete /tmp/bio-vcf_20160122-9244-jah911/000001-bio-vcf
3
+ Processing remaining output...
4
+ Trying: [[9246, 1, "/tmp/bio-vcf_20160122-9244-jah911/000001-bio-vcf"]]
5
+ Set lock on [[9246, 1, "/tmp/bio-vcf_20160122-9244-jah911/000001-bio-vcf"]]
6
+ Processing output file /tmp/bio-vcf_20160122-9244-jah911/000001-bio-vcf (blocking)
7
+ Removing /tmp/bio-vcf_20160122-9244-jah911/000001-bio-vcf
8
+ Removing dir /tmp/bio-vcf_20160122-9244-jah911
data/test/data/regression/rewrite.info.sample-stderr.new CHANGED
@@ -1,4 +1,8 @@
1
- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=3668 to complete
3
- OK pid=3668, processing /tmp/bio-vcf_20150816-3666-cjkeqc/000001-bio-vcf
4
- Processing /tmp/bio-vcf_20150816-3666-cjkeqc/000001-bio-vcf
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=9405 to complete /tmp/bio-vcf_20160122-9403-3mhvpb/000001-bio-vcf
3
+ Processing remaining output...
4
+ Trying: [[9405, 1, "/tmp/bio-vcf_20160122-9403-3mhvpb/000001-bio-vcf"]]
5
+ Set lock on [[9405, 1, "/tmp/bio-vcf_20160122-9403-3mhvpb/000001-bio-vcf"]]
6
+ Processing output file /tmp/bio-vcf_20160122-9403-3mhvpb/000001-bio-vcf (blocking)
7
+ Removing /tmp/bio-vcf_20160122-9403-3mhvpb/000001-bio-vcf
8
+ Removing dir /tmp/bio-vcf_20160122-9403-3mhvpb
data/test/data/regression/s.dp-stderr.new CHANGED
@@ -1,5 +1,5 @@
1
- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=3623 to complete
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=9360 to complete /tmp/bio-vcf_20160122-9358-zf1vnp/000001-bio-vcf
3
3
  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
4
4
  [:filter, "s.dp>20"]
5
5
  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
@@ -8,5 +8,9 @@ Waiting up to 180 seconds for pid=3623 to complete
8
8
  [:filter, "s.dp>20"]
9
9
  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
10
10
  [:filter, "s.dp>20"]
11
- OK pid=3623, processing /tmp/bio-vcf_20150816-3621-12oyzp8/000001-bio-vcf
12
- Processing /tmp/bio-vcf_20150816-3621-12oyzp8/000001-bio-vcf
11
+ Processing remaining output...
12
+ Trying: [[9360, 1, "/tmp/bio-vcf_20160122-9358-zf1vnp/000001-bio-vcf"]]
13
+ Set lock on [[9360, 1, "/tmp/bio-vcf_20160122-9358-zf1vnp/000001-bio-vcf"]]
14
+ Processing output file /tmp/bio-vcf_20160122-9358-zf1vnp/000001-bio-vcf (blocking)
15
+ Removing /tmp/bio-vcf_20160122-9358-zf1vnp/000001-bio-vcf
16
+ Removing dir /tmp/bio-vcf_20160122-9358-zf1vnp
data/test/data/regression/seval_s.dp-stderr.new CHANGED
@@ -1,4 +1,8 @@
1
- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=3652 to complete
3
- OK pid=3652, processing /tmp/bio-vcf_20150816-3650-1ux3whd/000001-bio-vcf
4
- Processing /tmp/bio-vcf_20150816-3650-1ux3whd/000001-bio-vcf
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
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
data/test/data/regression/sfilter_seval_s.dp-stderr.new CHANGED
@@ -1,5 +1,5 @@
1
- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=3660 to complete
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
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, ["./."]]
@@ -8,5 +8,9 @@ Waiting up to 180 seconds for pid=3660 to complete
8
8
  [:filter, "s.dp>10"]
9
9
  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
10
10
  [:filter, "s.dp>10"]
11
- OK pid=3660, processing /tmp/bio-vcf_20150816-3658-6flwv4/000001-bio-vcf
12
- Processing /tmp/bio-vcf_20150816-3658-6flwv4/000001-bio-vcf
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
data/test/data/regression/thread4-stderr.new CHANGED
@@ -1,4 +1,8 @@
1
- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
- Waiting up to 180 seconds for pid=3555 to complete
3
- OK pid=3555, processing /tmp/bio-vcf_20150816-3553-u77v0q/000001-bio-vcf
4
- Processing /tmp/bio-vcf_20150816-3553-u77v0q/000001-bio-vcf
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
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
data/test/data/regression/thread4_4-stderr.new CHANGED
@@ -1,15 +1,44 @@
1
- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
- .Processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000001-bio-vcf
3
- .Processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000001-bio-vcf
4
- .Processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000001-bio-vcf
5
- .Processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000001-bio-vcf
6
- ..Waiting for slot (timeout=180)
7
- Processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000002-bio-vcf
8
- .Processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000003-bio-vcf
9
- Waiting up to 180 seconds for pid=3587 to complete
10
- OK pid=3587, processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000006-bio-vcf
11
- Processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000004-bio-vcf
12
- Processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000005-bio-vcf
13
- Processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000006-bio-vcf
14
- Processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000007-bio-vcf
15
- Processing /tmp/bio-vcf_20150816-3561-1a9m2vl/000008-bio-vcf
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