bio-vcf 0.8.2 → 0.9.0

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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
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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=7,length=159138663,assembly=b37>
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+ ##contig=<ID=8,length=146364022,assembly=b37>
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+ ##contig=<ID=9,length=141213431,assembly=b37>
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+ ##contig=<ID=10,length=135534747,assembly=b37>
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+ ##contig=<ID=11,length=135006516,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=GL000226.1,length=15008,assembly=b37>
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+ ##contig=<ID=GL000229.1,length=19913,assembly=b37>
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+ ##contig=<ID=GL000231.1,length=27386,assembly=b37>
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+ ##contig=<ID=GL000210.1,length=27682,assembly=b37>
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+ ##contig=<ID=GL000239.1,length=33824,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=GL000249.1,length=38502,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=GL000202.1,length=40103,assembly=b37>
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+ ##contig=<ID=GL000234.1,length=40531,assembly=b37>
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+ ##contig=<ID=GL000232.1,length=40652,assembly=b37>
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+ ##contig=<ID=GL000206.1,length=41001,assembly=b37>
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+ ##contig=<ID=GL000240.1,length=41933,assembly=b37>
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+ ##contig=<ID=GL000236.1,length=41934,assembly=b37>
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+ ##contig=<ID=GL000241.1,length=42152,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=GL000237.1,length=45867,assembly=b37>
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+ ##contig=<ID=GL000233.1,length=45941,assembly=b37>
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+ ##contig=<ID=GL000204.1,length=81310,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
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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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