bio-maf 0.3.2-java → 1.0.0-java

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Files changed (33) hide show
  1. data/Gemfile +3 -0
  2. data/README.md +34 -3
  3. data/bin/maf_bgzip +56 -0
  4. data/bin/maf_index +0 -6
  5. data/bio-maf.gemspec +3 -2
  6. data/features/bgzf.feature +62 -0
  7. data/features/maf-indexing.feature +10 -0
  8. data/features/maf-querying.feature +9 -0
  9. data/features/step_definitions/convert_steps.rb +1 -1
  10. data/features/support/env.rb +2 -0
  11. data/lib/bio/maf/index.rb +35 -13
  12. data/lib/bio/maf/maf.rb +3 -1
  13. data/lib/bio/maf/parser.rb +135 -39
  14. data/lib/bio/maf/writer.rb +4 -4
  15. data/man/maf_bgzip.1 +101 -0
  16. data/man/maf_bgzip.1.ronn +85 -0
  17. data/man/maf_extract.1 +5 -2
  18. data/man/maf_extract.1.ronn +4 -1
  19. data/man/maf_index.1 +3 -3
  20. data/man/maf_index.1.ronn +3 -2
  21. data/man/maf_tile.1 +5 -2
  22. data/man/maf_tile.1.ronn +4 -1
  23. data/man/maf_to_fasta.1 +1 -1
  24. data/spec/bio/maf/index_spec.rb +7 -0
  25. data/spec/bio/maf/parser_spec.rb +13 -0
  26. data/spec/spec_helper.rb +2 -0
  27. data/test/data/gap-1.kct +0 -0
  28. data/test/data/mm8.chrM.maf +2421 -0
  29. data/test/data/mm8.chrM.maf.bgz +0 -0
  30. data/test/data/mm8_chr7_tiny.kct +0 -0
  31. data/test/data/mm8_chr7_tiny.maf.gz +0 -0
  32. data/test/data/mm8_chrM_tiny.kct +0 -0
  33. metadata +30 -2
data/test/data/mm8.chrM.maf.bgz ADDED
Binary file
data/test/data/mm8_chr7_tiny.kct CHANGED
Binary file
data/test/data/mm8_chr7_tiny.maf.gz ADDED
Binary file
data/test/data/mm8_chrM_tiny.kct CHANGED
Binary file
metadata CHANGED
@@ -2,14 +2,14 @@
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  name: bio-maf
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  version: !ruby/object:Gem::Version
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  prerelease:
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- version: 0.3.2
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+ version: 1.0.0
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  platform: java
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  authors:
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  - Clayton Wheeler
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-07-26 00:00:00.000000000 Z
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+ date: 2012-08-02 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio-alignment
@@ -27,6 +27,22 @@ dependencies:
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  none: false
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  prerelease: false
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  type: :runtime
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+ - !ruby/object:Gem::Dependency
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+ name: bio-bgzf
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 0.2.0
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+ none: false
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 0.2.0
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+ none: false
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+ prerelease: false
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+ type: :runtime
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  - !ruby/object:Gem::Dependency
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  name: bio-genomic-interval
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  version_requirements: !ruby/object:Gem::Requirement
@@ -79,6 +95,7 @@ description: Multiple Alignment Format parser for BioRuby.
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  email: cswh@umich.edu
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  executables:
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  - find_overlaps
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+ - maf_bgzip
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  - maf_count
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  - maf_dump_blocks
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  - maf_extract
@@ -111,6 +128,7 @@ files:
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  - benchmarks/sort_bench
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  - benchmarks/split_bench
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  - bin/find_overlaps
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+ - bin/maf_bgzip
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  - bin/maf_count
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  - bin/maf_dump_blocks
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  - bin/maf_extract
@@ -122,6 +140,7 @@ files:
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  - bin/maf_write
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  - bin/random_ranges
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  - bio-maf.gemspec
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+ - features/bgzf.feature
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  - features/block-joining.feature
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  - features/dir-access.feature
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  - features/gap-removal.feature
@@ -159,6 +178,8 @@ files:
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  - lib/bio/ucsc/genomic-interval-bin.rb
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  - lib/bio/ucsc/ucsc_bin.rb
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  - man/.gitignore
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+ - man/maf_bgzip.1
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+ - man/maf_bgzip.1.ronn
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  - man/maf_extract.1
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  - man/maf_extract.1.ronn
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  - man/maf_index.1
@@ -185,8 +206,11 @@ files:
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  - test/data/gap-filled1.fa
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  - test/data/gap-sp1.fa
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  - test/data/gap-sp1.fa.gz
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+ - test/data/mm8.chrM.maf
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+ - test/data/mm8.chrM.maf.bgz
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  - test/data/mm8_chr7_tiny.kct
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  - test/data/mm8_chr7_tiny.maf
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+ - test/data/mm8_chr7_tiny.maf.gz
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  - test/data/mm8_chr7_tiny_slice1.maf
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  - test/data/mm8_chr7_tiny_slice2.maf
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  - test/data/mm8_chr7_tiny_slice3.maf
@@ -233,6 +257,7 @@ signing_key:
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  specification_version: 3
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  summary: MAF parser for BioRuby
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  test_files:
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+ - features/bgzf.feature
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  - features/block-joining.feature
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  - features/dir-access.feature
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  - features/gap-removal.feature
@@ -274,8 +299,11 @@ test_files:
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  - test/data/gap-filled1.fa
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  - test/data/gap-sp1.fa
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  - test/data/gap-sp1.fa.gz
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+ - test/data/mm8.chrM.maf
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+ - test/data/mm8.chrM.maf.bgz
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  - test/data/mm8_chr7_tiny.kct
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  - test/data/mm8_chr7_tiny.maf
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+ - test/data/mm8_chr7_tiny.maf.gz
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  - test/data/mm8_chr7_tiny_slice1.maf
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  - test/data/mm8_chr7_tiny_slice2.maf
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  - test/data/mm8_chr7_tiny_slice3.maf