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

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