bio-maf 0.1.0

Sign up to get free protection for your applications and to get access to all the features.
Files changed (76) hide show
  1. data/.document +5 -0
  2. data/.simplecov +1 -0
  3. data/.travis.yml +16 -0
  4. data/.yardopts +3 -0
  5. data/DEVELOPMENT.md +40 -0
  6. data/Gemfile +23 -0
  7. data/LICENSE.txt +20 -0
  8. data/README.md +209 -0
  9. data/Rakefile +76 -0
  10. data/VERSION +1 -0
  11. data/benchmarks/dispatch_bench +53 -0
  12. data/benchmarks/iter_bench +44 -0
  13. data/benchmarks/read_bench +40 -0
  14. data/benchmarks/sort_bench +33 -0
  15. data/benchmarks/split_bench +33 -0
  16. data/bin/maf_count +82 -0
  17. data/bin/maf_dump_blocks +27 -0
  18. data/bin/maf_extract_ranges_count +44 -0
  19. data/bin/maf_index +88 -0
  20. data/bin/maf_parse_bench +94 -0
  21. data/bin/maf_to_fasta +68 -0
  22. data/bin/maf_write +84 -0
  23. data/bin/random_ranges +35 -0
  24. data/features/maf-indexing.feature +31 -0
  25. data/features/maf-output.feature +29 -0
  26. data/features/maf-parsing.feature +44 -0
  27. data/features/maf-querying.feature +75 -0
  28. data/features/maf-to-fasta.feature +50 -0
  29. data/features/step_definitions/convert_steps.rb +45 -0
  30. data/features/step_definitions/index_steps.rb +20 -0
  31. data/features/step_definitions/output_steps.rb +27 -0
  32. data/features/step_definitions/parse_steps.rb +63 -0
  33. data/features/step_definitions/query_steps.rb +31 -0
  34. data/features/step_definitions/ucsc_bin_steps.rb +14 -0
  35. data/features/support/env.rb +16 -0
  36. data/features/ucsc-bins.feature +24 -0
  37. data/lib/bio/maf/index.rb +620 -0
  38. data/lib/bio/maf/parser.rb +888 -0
  39. data/lib/bio/maf/struct.rb +63 -0
  40. data/lib/bio/maf/writer.rb +63 -0
  41. data/lib/bio/maf.rb +4 -0
  42. data/lib/bio/ucsc/genomic-interval-bin.rb +13 -0
  43. data/lib/bio/ucsc/ucsc_bin.rb +117 -0
  44. data/lib/bio/ucsc.rb +2 -0
  45. data/lib/bio-maf/maf.rb +3 -0
  46. data/lib/bio-maf.rb +12 -0
  47. data/man/.gitignore +1 -0
  48. data/man/maf_index.1 +105 -0
  49. data/man/maf_index.1.markdown +97 -0
  50. data/man/maf_index.1.ronn +83 -0
  51. data/man/maf_to_fasta.1 +53 -0
  52. data/man/maf_to_fasta.1.ronn +51 -0
  53. data/spec/bio/maf/index_spec.rb +363 -0
  54. data/spec/bio/maf/parser_spec.rb +354 -0
  55. data/spec/bio/maf/struct_spec.rb +75 -0
  56. data/spec/spec_helper.rb +14 -0
  57. data/test/data/big-block.maf +15999 -0
  58. data/test/data/chr22_ieq.maf +11 -0
  59. data/test/data/chrY-1block.maf +6 -0
  60. data/test/data/empty +0 -0
  61. data/test/data/empty.db +0 -0
  62. data/test/data/mm8_chr7_tiny.kct +0 -0
  63. data/test/data/mm8_chr7_tiny.maf +76 -0
  64. data/test/data/mm8_mod_a.maf +7 -0
  65. data/test/data/mm8_single.maf +13 -0
  66. data/test/data/mm8_subset_a.maf +23 -0
  67. data/test/data/t1-bad1.maf +15 -0
  68. data/test/data/t1.fasta +12 -0
  69. data/test/data/t1.maf +15 -0
  70. data/test/data/t1a.maf +17 -0
  71. data/test/helper.rb +18 -0
  72. data/test/test_bio-maf.rb +7 -0
  73. data/travis-ci/install_kc +13 -0
  74. data/travis-ci/install_kc_java +13 -0
  75. data/travis-ci/report_errors +4 -0
  76. metadata +181 -0

There are too many changes on this page to be displayed.

The amount of changes on this page would crash your brower.

You can still verify the content by downloading the gem file manually.