bio-vcf 0.8.0 → 0.9.4

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Files changed (85) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +1 -11
  3. data/Gemfile +4 -5
  4. data/Gemfile.lock +28 -65
  5. data/LICENSE.txt +1 -1
  6. data/README.md +387 -107
  7. data/RELEASE_NOTES.md +20 -0
  8. data/RELEASE_NOTES.md~ +11 -0
  9. data/Rakefile +3 -40
  10. data/TAGS +115 -0
  11. data/VERSION +1 -1
  12. data/bin/bio-vcf +176 -109
  13. data/bio-vcf.gemspec +14 -70
  14. data/features/cli.feature +22 -4
  15. data/features/diff_count.feature +0 -1
  16. data/features/filter.feature +12 -0
  17. data/features/multisample.feature +25 -0
  18. data/features/somaticsniper.feature +2 -0
  19. data/features/step_definitions/cli-feature.rb +15 -6
  20. data/features/step_definitions/diff_count.rb +1 -1
  21. data/features/step_definitions/multisample.rb +19 -0
  22. data/features/step_definitions/somaticsniper.rb +9 -1
  23. data/features/step_definitions/vcf_header.rb +48 -0
  24. data/features/support/env.rb +0 -9
  25. data/features/vcf_header.feature +35 -0
  26. data/lib/bio-vcf.rb +2 -0
  27. data/lib/bio-vcf/bedfilter.rb +43 -0
  28. data/lib/bio-vcf/pcows.rb +303 -0
  29. data/lib/bio-vcf/template.rb +75 -0
  30. data/lib/bio-vcf/vcffile.rb +46 -0
  31. data/lib/bio-vcf/vcfgenotypefield.rb +25 -20
  32. data/lib/bio-vcf/vcfheader.rb +146 -6
  33. data/lib/bio-vcf/vcfheader_line.rb +778 -0
  34. data/lib/bio-vcf/vcfrecord.rb +56 -18
  35. data/lib/bio-vcf/vcfsample.rb +27 -3
  36. data/ragel/gen_vcfheaderline_parser.rl +165 -0
  37. data/ragel/generate.sh +8 -0
  38. data/template/vcf2json.erb +19 -7
  39. data/template/vcf2json_full_header.erb +22 -0
  40. data/template/vcf2json_use_meta.erb +41 -0
  41. data/template/vcf2rdf_header.erb +24 -0
  42. data/test/data/input/empty.vcf +2 -0
  43. data/test/data/input/gatk_exome.vcf +237 -0
  44. data/test/data/input/gatk_wgs.vcf +1000 -0
  45. data/test/data/input/test.bed +632 -0
  46. data/test/data/regression/empty-stderr.new +12 -0
  47. data/test/data/regression/empty.new +2 -0
  48. data/test/data/regression/empty.ref +2 -0
  49. data/test/data/regression/eval_once-stderr.new +2 -0
  50. data/test/data/regression/eval_once.new +1 -0
  51. data/test/data/regression/eval_once.ref +1 -0
  52. data/test/data/regression/eval_r.info.dp-stderr.new +10 -0
  53. data/test/data/regression/eval_r.info.dp.new +150 -0
  54. data/test/data/regression/ifilter_s.dp-stderr.new +34 -0
  55. data/test/data/regression/ifilter_s.dp.new +31 -0
  56. data/test/data/regression/pass1-stderr.new +10 -0
  57. data/test/data/regression/pass1.new +88 -0
  58. data/test/data/regression/pass1.ref +88 -0
  59. data/test/data/regression/r.info.dp-stderr.new +4 -0
  60. data/test/data/regression/r.info.dp.new +114 -0
  61. data/test/data/regression/rewrite.info.sample-stderr.new +10 -0
  62. data/test/data/regression/rewrite.info.sample.new +150 -0
  63. data/test/data/regression/s.dp-stderr.new +18 -0
  64. data/test/data/regression/s.dp.new +145 -0
  65. data/test/data/regression/seval_s.dp-stderr.new +10 -0
  66. data/test/data/regression/seval_s.dp.new +36 -0
  67. data/test/data/regression/sfilter_seval_s.dp-stderr.new +18 -0
  68. data/test/data/regression/sfilter_seval_s.dp.new +31 -0
  69. data/test/data/regression/thread4-stderr.new +10 -0
  70. data/test/data/regression/thread4.new +150 -0
  71. data/test/data/regression/thread4_4-stderr.new +25 -0
  72. data/test/data/regression/thread4_4.new +130 -0
  73. data/test/data/regression/thread4_4_failed_filter-stderr.new +5 -0
  74. data/test/data/regression/thread4_4_failed_filter-stderr.ref +5 -1
  75. data/test/data/regression/thread4_4_failed_filter.new +110 -0
  76. data/test/data/regression/vcf2json_full_header-stderr.new +10 -0
  77. data/test/data/regression/vcf2json_full_header.new +225 -0
  78. data/test/data/regression/vcf2json_full_header.ref +225 -0
  79. data/test/data/regression/vcf2json_use_meta-stderr.new +10 -0
  80. data/test/data/regression/vcf2json_use_meta.new +4697 -0
  81. data/test/data/regression/vcf2json_use_meta.ref +4697 -0
  82. data/test/performance/metrics.md +18 -1
  83. data/test/stress/stress_test.sh +15 -0
  84. data/test/tmp/test.vcf +12469 -0
  85. metadata +65 -64
data/test/data/regression/vcf2json_full_header-stderr.new ADDED
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+ bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
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+ Waiting up to 180 seconds for pid=30682 to complete /tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf
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+ Processing remaining output...
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+ Trying: [[30682, 1, "/tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf"]]
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+ Set lock on [[30682, 1, "/tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf"]]
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+ Processing output file /tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf (blocking)
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+ Checking for output_lock on existing /tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf
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+ Trying to remove /tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf.keep
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+ Removing /tmp/bio-vcf_20201222-30680-iio5eo/000001-bio-vcf.keep
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+ Removing dir /tmp/bio-vcf_20201222-30680-iio5eo
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 as the AC), for each ALT allele, in the same order as listed"},"MLEAF":{"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"},"MQ":{"ID":"MQ","Number":"1","Type":"Float","Description":"RMS Mapping Quality"},"MQ0":{"ID":"MQ0","Number":"1","Type":"Integer","Description":"Total Mapping Quality Zero Reads"},"MQRankSum":{"ID":"MQRankSum","Number":"1","Type":"Float","Description":"Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"},"QD":{"ID":"QD","Number":"1","Type":"Float","Description":"Variant Confidence/Quality by Depth"},"RPA":{"ID":"RPA","Number":".","Type":"Integer","Description":"Number of times tandem repeat unit is repeated, for each allele (including reference)"},"RU":{"ID":"RU","Number":"1","Type":"String","Description":"Tandem repeat unit (bases)"},"ReadPosRankSum":{"ID":"ReadPosRankSum","Number":"1","Type":"Float","Description":"Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"},"STR":{"ID":"STR","Number":"0","Type":"Flag","Description":"Variant is a short tandem repeat"}},"FORMAT":{"AD":{"ID":"AD","Number":".","Type":"Integer","Description":"Allelic depths for the ref and alt alleles in the order listed"},"DP":{"ID":"DP","Number":"1","Type":"Integer","Description":"Approximate read depth (reads with MQ=255 or with bad mates are filtered)"},"GQ":{"ID":"GQ","Number":"1","Type":"Integer","Description":"Genotype Quality"},"GT":{"ID":"GT","Number":"1","Type":"String","Description":"Genotype"},"PL":{"ID":"PL","Number":"G","Type":"Integer","Description":"Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"}},"FILTER":{"LowQual":{"ID":"LowQual","Description":"Low quality"}},"contig":{"1":{"ID":"1","length":249250621,"assembly":"b37"},"2":{"ID":"2","length":243199373,"assembly":"b37"},"3":{"ID":"3","length":198022430,"assembly":"b37"},"4":{"ID":"4","length":191154276,"assembly":"b37"},"5":{"ID":"5","length":180915260,"assembly":"b37"},"6":{"ID":"6","length":171115067,"assembly":"b37"},"7":{"ID":"7","length":159138663,"assembly":"b37"},"8":{"ID":"8","length":146364022,"assembly":"b37"},"9":{"ID":"9","length":141213431,"assembly":"b37"},"10":{"ID":"10","length":135534747,"assembly":"b37"},"11":{"ID":"11","length":135006516,"assembly":"b37"},"12":{"ID":"12","length":133851895,"assembly":"b37"},"13":{"ID":"13","length":115169878,"assembly":"b37"},"14":{"ID":"14","length":107349540,"assembly":"b37"},"15":{"ID":"15","length":102531392,"assembly":"b37"},"16":{"ID":"16","length":90354753,"assembly":"b37"},"17":{"ID":"17","length":81195210,"assembly":"b37"},"18":{"ID":"18","length":78077248,"assembly":"b37"},"19":{"ID":"19","length":59128983,"assembly":"b37"},"20":{"ID":"20","length":63025520,"assembly":"b37"},"21":{"ID":"21","length":48129895,"assembly":"b37"},"22":{"ID":"22","length":51304566,"assembly":"b37"},"X":{"ID":"X","length":155270560,"assembly":"b37"},"Y":{"ID":"Y","length":59373566,"assembly":"b37"},"MT":{"ID":"MT","length":16569,"assembly":"b37"},"GL000207.1":{"ID":"GL000207.1","length":4262,"assembly":"b37"},"GL000226.1":{"ID":"GL000226.1","length":15008,"assembly":"b37"},"GL000229.1":{"ID":"GL000229.1","length":19913,"assembly":"b37"},"GL000231.1":{"ID":"GL000231.1","length":27386,"assembly":"b37"},"GL000210.1":{"ID":"GL000210.1","length":27682,"assembly":"b37"},"GL000239.1":{"ID":"GL000239.1","length":33824,"assembly":"b37"},"GL000235.1":{"ID":"GL000235.1","length":34474,"assembly":"b37"},"GL000201.1":{"ID":"GL000201.1","length":36148,"assembly":"b37"},"GL000247.1":{"ID":"GL000247.1","length":36422,"assembly":"b37"},"GL000245.1":{"ID":"GL000245.1","length":36651,"assembly":"b37"},"GL000197.1":{"ID":"GL000197.1","length":37175,"assembly":"b37"},"GL000203.1":{"ID":"GL000203.1","length":37498,"assembly":"b37"},"GL000246.1":{"ID":"GL000246.1","length":38154,"assembly":"b37"},"GL000249.1":{"ID":"GL000249.1","length":38502,"assembly":"b37"},"GL000196.1":{"ID":"GL000196.1","length":38914,"assembly":"b37"},"GL000248.1":{"ID":"GL000248.1","length":39786,"assembly":"b37"},"GL000244.1":{"ID":"GL000244.1","length":39929,"assembly":"b37"},"GL000238.1":{"ID":"GL000238.1","length":39939,"assembly":"b37"},"GL000202.1":{"ID":"GL000202.1","length":40103,"assembly":"b37"},"GL000234.1":{"ID":"GL000234.1","length":40531,"assembly":"b37"},"GL000232.1":{"ID":"GL000232.1","length":40652,"assembly":"b37"},"GL000206.1":{"ID":"GL000206.1","length":41001,"assembly":"b37"},"GL000240.1":{"ID":"GL000240.1","length":41933,"assembly":"b37"},"GL000236.1":{"ID":"GL000236.1","length":41934,"assembly":"b37"},"GL000241.1":{"ID":"GL000241.1","length":42152,"assembly":"b37"},"GL000243.1":{"ID":"GL000243.1","length":43341,"assembly":"b37"},"GL000242.1":{"ID":"GL000242.1","length":43523,"assembly":"b37"},"GL000230.1":{"ID":"GL000230.1","length":43691,"assembly":"b37"},"GL000237.1":{"ID":"GL000237.1","length":45867,"assembly":"b37"},"GL000233.1":{"ID":"GL000233.1","length":45941,"assembly":"b37"},"GL000204.1":{"ID":"GL000204.1","length":81310,"assembly":"b37"},"GL000198.1":{"ID":"GL000198.1","length":90085,"assembly":"b37"},"GL000208.1":{"ID":"GL000208.1","length":92689,"assembly":"b37"},"GL000191.1":{"ID":"GL000191.1","length":106433,"assembly":"b37"},"GL000227.1":{"ID":"GL000227.1","length":128374,"assembly":"b37"},"GL000228.1":{"ID":"GL000228.1","length":129120,"assembly":"b37"},"GL000214.1":{"ID":"GL000214.1","length":137718,"assembly":"b37"},"GL000221.1":{"ID":"GL000221.1","length":155397,"assembly":"b37"},"GL000209.1":{"ID":"GL000209.1","length":159169,"assembly":"b37"},"GL000218.1":{"ID":"GL000218.1","length":161147,"assembly":"b37"},"GL000220.1":{"ID":"GL000220.1","length":161802,"assembly":"b37"},"GL000213.1":{"ID":"GL000213.1","length":164239,"assembly":"b37"},"GL000211.1":{"ID":"GL000211.1","length":166566,"assembly":"b37"},"GL000199.1":{"ID":"GL000199.1","length":169874,"assembly":"b37"},"GL000217.1":{"ID":"GL000217.1","length":172149,"assembly":"b37"},"GL000216.1":{"ID":"GL000216.1","length":172294,"assembly":"b37"},"GL000215.1":{"ID":"GL000215.1","length":172545,"assembly":"b37"},"GL000205.1":{"ID":"GL000205.1","length":174588,"assembly":"b37"},"GL000219.1":{"ID":"GL000219.1","length":179198,"assembly":"b37"},"GL000224.1":{"ID":"GL000224.1","length":179693,"assembly":"b37"},"GL000223.1":{"ID":"GL000223.1","length":180455,"assembly":"b37"},"GL000195.1":{"ID":"GL000195.1","length":182896,"assembly":"b37"},"GL000212.1":{"ID":"GL000212.1","length":186858,"assembly":"b37"},"GL000222.1":{"ID":"GL000222.1","length":186861,"assembly":"b37"},"GL000200.1":{"ID":"GL000200.1","length":187035,"assembly":"b37"},"GL000193.1":{"ID":"GL000193.1","length":189789,"assembly":"b37"},"GL000194.1":{"ID":"GL0001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Jan 25 10:33:56 CET 2014","Epoch":1390642436187,"CommandLineOptions":"analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"}},"fileformat":"VCFv4.1","reference":"file:human_g1k_v37.fasta"},
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