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

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