bio-vcf 0.8.2 → 0.9.0

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 (62) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +8 -2
  3. data/Gemfile +4 -6
  4. data/README.md +92 -57
  5. data/Rakefile +3 -41
  6. data/TAGS +115 -0
  7. data/VERSION +1 -1
  8. data/bin/bio-vcf +58 -70
  9. data/bio-vcf.gemspec +23 -75
  10. data/features/cli.feature +6 -1
  11. data/features/multisample.feature +12 -0
  12. data/features/step_definitions/cli-feature.rb +2 -2
  13. data/features/step_definitions/multisample.rb +19 -0
  14. data/features/step_definitions/vcf_header.rb +1 -1
  15. data/features/support/env.rb +0 -9
  16. data/lib/bio-vcf/pcows.rb +210 -0
  17. data/lib/bio-vcf/vcfheader.rb +28 -9
  18. data/lib/bio-vcf/vcfheader_line.rb +455 -160
  19. data/lib/bio-vcf/vcfrecord.rb +30 -15
  20. data/ragel/gen_vcfheaderline_parser.rl +68 -25
  21. data/ragel/generate.sh +4 -1
  22. data/template/vcf2json.erb +16 -16
  23. data/template/vcf2json_full_header.erb +16 -17
  24. data/template/vcf2json_use_meta.erb +35 -35
  25. data/test/data/input/gatk_exome.vcf +237 -0
  26. data/test/data/input/gatk_wgs.vcf +1000 -0
  27. data/test/data/input/test.bed +632 -0
  28. data/test/data/regression/eval_once-stderr.new +1 -0
  29. data/test/data/regression/eval_once.new +1 -0
  30. data/test/data/regression/eval_once.ref +1 -0
  31. data/test/data/regression/eval_r.info.dp-stderr.new +4 -0
  32. data/test/data/regression/eval_r.info.dp.new +150 -0
  33. data/test/data/regression/ifilter_s.dp-stderr.new +28 -0
  34. data/test/data/regression/ifilter_s.dp.new +31 -0
  35. data/test/data/regression/r.info.dp-stderr.new +4 -0
  36. data/test/data/regression/r.info.dp.new +147 -0
  37. data/test/data/regression/rewrite.info.sample-stderr.new +4 -0
  38. data/test/data/regression/rewrite.info.sample.new +150 -0
  39. data/test/data/regression/s.dp-stderr.new +12 -0
  40. data/test/data/regression/s.dp.new +145 -0
  41. data/test/data/regression/seval_s.dp-stderr.new +4 -0
  42. data/test/data/regression/seval_s.dp.new +36 -0
  43. data/test/data/regression/sfilter_seval_s.dp-stderr.new +12 -0
  44. data/test/data/regression/sfilter_seval_s.dp.new +31 -0
  45. data/test/data/regression/thread4-stderr.new +4 -0
  46. data/test/data/regression/thread4.new +150 -0
  47. data/test/data/regression/thread4_4-stderr.new +15 -0
  48. data/test/data/regression/thread4_4.new +150 -0
  49. data/test/data/regression/thread4_4_failed_filter-stderr.new +5 -0
  50. data/test/data/regression/thread4_4_failed_filter-stderr.ref +5 -2
  51. data/test/data/regression/thread4_4_failed_filter.new +110 -0
  52. data/test/data/regression/vcf2json_full_header-stderr.new +4 -0
  53. data/test/data/regression/vcf2json_full_header.new +225 -0
  54. data/test/data/regression/vcf2json_full_header.ref +222 -258
  55. data/test/data/regression/vcf2json_use_meta-stderr.new +4 -0
  56. data/test/data/regression/vcf2json_use_meta.new +4697 -0
  57. data/test/data/regression/vcf2json_use_meta.ref +4697 -0
  58. data/test/performance/metrics.md +18 -1
  59. data/test/tmp/test.vcf +12469 -0
  60. metadata +38 -62
  61. data/Gemfile.lock +0 -81
  62. data/ragel/gen_vcfheaderline_parser.rb +0 -483
data/test/data/regression/thread4_4_failed_filter-stderr.new ADDED
@@ -0,0 +1,5 @@
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+ Unknown field name <t> in record, did you mean r.info.t?
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+ Unknown field name <t> in record, did you mean r.info.t?
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+ Unknown field name <t> in record, did you mean r.info.t?
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+ Unknown field name <t> in record, did you mean r.info.t?
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+ execution expired
data/test/data/regression/thread4_4_failed_filter-stderr.ref CHANGED
@@ -1,2 +1,5 @@
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- Error: Missing 'parallel' module. Install with command 'gem install parallel' if you want multiple threads
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- .Unknown field name <t> in record, did you mean r.info.t?
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+ Unknown field name <t> in record, did you mean r.info.t?
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+ Unknown field name <t> in record, did you mean r.info.t?
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+ Unknown field name <t> in record, did you mean r.info.t?
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+ Unknown field name <t> in record, did you mean r.info.t?
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+ execution expired
data/test/data/regression/thread4_4_failed_filter.new ADDED
@@ -0,0 +1,110 @@
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+ ##fileformat=VCFv4.1
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+ ##FILTER=<ID=LowQual,Description="Low quality">
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+ ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
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+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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+ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
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+ ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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+ ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
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+ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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+ ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
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+ ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
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+ ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
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+ ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
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+ ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
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+ ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
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+ ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
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+ ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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+ ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
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+ ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
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+ ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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+ ##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
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+ ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
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+ ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
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+ ##contig=<ID=1,length=249250621,assembly=b37>
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+ ##contig=<ID=2,length=243199373,assembly=b37>
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+ ##contig=<ID=3,length=198022430,assembly=b37>
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+ ##contig=<ID=4,length=191154276,assembly=b37>
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+ ##contig=<ID=5,length=180915260,assembly=b37>
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+ ##contig=<ID=6,length=171115067,assembly=b37>
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+ ##contig=<ID=9,length=141213431,assembly=b37>
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+ ##contig=<ID=12,length=133851895,assembly=b37>
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+ ##contig=<ID=13,length=115169878,assembly=b37>
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+ ##contig=<ID=14,length=107349540,assembly=b37>
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+ ##contig=<ID=15,length=102531392,assembly=b37>
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+ ##contig=<ID=16,length=90354753,assembly=b37>
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+ ##contig=<ID=17,length=81195210,assembly=b37>
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+ ##contig=<ID=18,length=78077248,assembly=b37>
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+ ##contig=<ID=19,length=59128983,assembly=b37>
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+ ##contig=<ID=20,length=63025520,assembly=b37>
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+ ##contig=<ID=21,length=48129895,assembly=b37>
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+ ##contig=<ID=22,length=51304566,assembly=b37>
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+ ##contig=<ID=X,length=155270560,assembly=b37>
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+ ##contig=<ID=Y,length=59373566,assembly=b37>
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+ ##contig=<ID=MT,length=16569,assembly=b37>
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+ ##contig=<ID=GL000207.1,length=4262,assembly=b37>
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+ ##contig=<ID=GL000235.1,length=34474,assembly=b37>
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+ ##contig=<ID=GL000201.1,length=36148,assembly=b37>
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+ ##contig=<ID=GL000247.1,length=36422,assembly=b37>
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+ ##contig=<ID=GL000245.1,length=36651,assembly=b37>
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+ ##contig=<ID=GL000197.1,length=37175,assembly=b37>
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+ ##contig=<ID=GL000203.1,length=37498,assembly=b37>
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+ ##contig=<ID=GL000246.1,length=38154,assembly=b37>
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+ ##contig=<ID=GL000196.1,length=38914,assembly=b37>
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+ ##contig=<ID=GL000248.1,length=39786,assembly=b37>
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+ ##contig=<ID=GL000244.1,length=39929,assembly=b37>
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+ ##contig=<ID=GL000238.1,length=39939,assembly=b37>
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+ ##contig=<ID=GL000234.1,length=40531,assembly=b37>
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+ ##contig=<ID=GL000243.1,length=43341,assembly=b37>
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+ ##contig=<ID=GL000242.1,length=43523,assembly=b37>
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+ ##contig=<ID=GL000230.1,length=43691,assembly=b37>
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+ ##contig=<ID=GL000233.1,length=45941,assembly=b37>
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+ ##contig=<ID=GL000198.1,length=90085,assembly=b37>
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+ ##contig=<ID=GL000208.1,length=92689,assembly=b37>
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+ ##contig=<ID=GL000191.1,length=106433,assembly=b37>
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+ ##contig=<ID=GL000227.1,length=128374,assembly=b37>
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+ ##contig=<ID=GL000228.1,length=129120,assembly=b37>
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+ ##contig=<ID=GL000214.1,length=137718,assembly=b37>
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+ ##contig=<ID=GL000221.1,length=155397,assembly=b37>
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+ ##contig=<ID=GL000209.1,length=159169,assembly=b37>
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+ ##contig=<ID=GL000218.1,length=161147,assembly=b37>
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+ ##contig=<ID=GL000220.1,length=161802,assembly=b37>
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+ ##contig=<ID=GL000213.1,length=164239,assembly=b37>
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+ ##contig=<ID=GL000211.1,length=166566,assembly=b37>
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+ ##contig=<ID=GL000199.1,length=169874,assembly=b37>
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+ ##contig=<ID=GL000217.1,length=172149,assembly=b37>
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+ ##contig=<ID=GL000216.1,length=172294,assembly=b37>
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+ ##contig=<ID=GL000215.1,length=172545,assembly=b37>
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+ ##contig=<ID=GL000205.1,length=174588,assembly=b37>
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+ ##contig=<ID=GL000219.1,length=179198,assembly=b37>
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+ ##contig=<ID=GL000224.1,length=179693,assembly=b37>
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+ ##contig=<ID=GL000223.1,length=180455,assembly=b37>
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+ ##contig=<ID=GL000195.1,length=182896,assembly=b37>
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+ ##contig=<ID=GL000212.1,length=186858,assembly=b37>
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+ ##contig=<ID=GL000222.1,length=186861,assembly=b37>
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+ ##contig=<ID=GL000200.1,length=187035,assembly=b37>
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+ ##contig=<ID=GL000193.1,length=189789,assembly=b37>
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+ ##contig=<ID=GL000194.1,length=191469,assembly=b37>
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+ ##contig=<ID=GL000225.1,length=211173,assembly=b37>
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+ ##contig=<ID=GL000192.1,length=547496,assembly=b37>
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+ ##reference=file:human_g1k_v37.fasta
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+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2
data/test/data/regression/vcf2json_full_header-stderr.new ADDED
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+ 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=3688 to complete
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+ OK pid=3688, processing /tmp/bio-vcf_20150816-3685-12epvot/000001-bio-vcf
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+ Processing /tmp/bio-vcf_20150816-3685-12epvot/000001-bio-vcf
data/test/data/regression/vcf2json_full_header.new ADDED
@@ -0,0 +1,225 @@
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+
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+ {
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+ "HEADER": {
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+ "files": [],
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+ },
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+ "COLUMNS": ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT","Original","s1t1","s2t1","s3t1","s1t2","s2t2","s3t2"],
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+ "META": {"INFO":{"AC":{"ID":"AC","Number":"A","Type":"Integer","Description":"Allele count in genotypes, for each ALT allele, in the same order as listed"},"AF":{"ID":"AF","Number":"A","Type":"Float","Description":"Allele Frequency, for each ALT allele, in the same order as listed"},"AN":{"ID":"AN","Number":"1","Type":"Integer","Description":"Total number of alleles in called genotypes"},"BaseQRankSum":{"ID":"BaseQRankSum","Number":"1","Type":"Float","Description":"Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"},"DP":{"ID":"DP","Number":"1","Type":"Integer","Description":"Approximate read depth; some reads may have been filtered"},"DS":{"ID":"DS","Number":"0","Type":"Flag","Description":"Were any of the samples downsampled?"},"Dels":{"ID":"Dels","Number":"1","Type":"Float","Description":"Fraction of Reads Containing Spanning Deletions"},"FS":{"ID":"FS","Number":"1","Type":"Float","Description":"Phred-scaled p-value using Fisher's exact test to detect strand bias"},"HaplotypeScore":{"ID":"HaplotypeScore","Number":"1","Type":"Float","Description":"Consistency of the site with at most two segregating haplotypes"},"InbreedingCoeff":{"ID":"InbreedingCoeff","Number":"1","Type":"Float","Description":"Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"},"MLEAC":{"ID":"MLEAC","Number":"A","Type":"Integer","Description":"Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same 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