bio-vcf 0.9.0 → 0.9.2

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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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+ 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
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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
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+ 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
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- OK pid=3644, processing /tmp/bio-vcf_20150816-3642-1j5rn5y/000001-bio-vcf
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- Processing /tmp/bio-vcf_20150816-3642-1j5rn5y/000001-bio-vcf
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+ bio-vcf 0.9.2 (biogem Ruby 2.2.4 with pcows) by Pjotr Prins 2015
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+ Waiting up to 180 seconds for pid=9378 to complete /tmp/bio-vcf_20160122-9376-640z88/000001-bio-vcf
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+ Processing remaining output...
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+ Trying: [[9378, 1, "/tmp/bio-vcf_20160122-9376-640z88/000001-bio-vcf"]]
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+ Set lock on [[9378, 1, "/tmp/bio-vcf_20160122-9376-640z88/000001-bio-vcf"]]
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+ 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
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+ 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
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- Waiting up to 180 seconds for pid=3632 to complete
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+ bio-vcf 0.9.2 (biogem Ruby 2.2.4 with pcows) by Pjotr Prins 2015
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+ Waiting up to 180 seconds for pid=9369 to complete /tmp/bio-vcf_20160122-9367-zhp98h/000001-bio-vcf
3
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  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
4
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  [:filter, "s.dp>100"]
5
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  [: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
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  [:filter, "s.dp>100"]
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  [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
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  [:filter, "s.dp>100"]
27
- OK pid=3632, processing /tmp/bio-vcf_20150816-3629-1g0u53a/000001-bio-vcf
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- 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
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+ 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"]]
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+ 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
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+ ##phasing=none
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+ ##reference=file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta
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+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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+ ##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
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+ ##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">
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+ ##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
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+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
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+ ##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
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+ ##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
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+ ##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality">
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+ ##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality across all reads">
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+ ##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
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+ ##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">
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+ ##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
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+ 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
+ 7 140434525 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:8,6,0,0:0,0,14,0:69:31:0:59:37:37:0:. 0/1:0/1:6:3,1,0,2:2,0,4,0:24:31:24:60,58:37:37,37:2:31
50
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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