--- !ruby/object:Gem::Specification
name: bio-maf
version: !ruby/object:Gem::Version
  version: 1.0.1
  prerelease: 
platform: ruby
authors:
- Clayton Wheeler
autorequire: 
bindir: bin
cert_chain: []
date: 2012-08-08 00:00:00.000000000 Z
dependencies:
- !ruby/object:Gem::Dependency
  name: bio-alignment
  requirement: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ~>
      - !ruby/object:Gem::Version
        version: 0.0.7
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ~>
      - !ruby/object:Gem::Version
        version: 0.0.7
- !ruby/object:Gem::Dependency
  name: bio-bgzf
  requirement: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ~>
      - !ruby/object:Gem::Version
        version: 0.2.1
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ~>
      - !ruby/object:Gem::Version
        version: 0.2.1
- !ruby/object:Gem::Dependency
  name: bio-genomic-interval
  requirement: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ~>
      - !ruby/object:Gem::Version
        version: 0.1.2
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ~>
      - !ruby/object:Gem::Version
        version: 0.1.2
- !ruby/object:Gem::Dependency
  name: bio-logger
  requirement: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ~>
      - !ruby/object:Gem::Version
        version: 1.0.1
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ~>
      - !ruby/object:Gem::Version
        version: 1.0.1
- !ruby/object:Gem::Dependency
  name: kyotocabinet-ruby
  requirement: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ~>
      - !ruby/object:Gem::Version
        version: 1.27.1
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    none: false
    requirements:
    - - ~>
      - !ruby/object:Gem::Version
        version: 1.27.1
description: Multiple Alignment Format parser for BioRuby.
email: cswh@umich.edu
executables:
- find_overlaps
- maf_bgzip
- maf_count
- maf_dump_blocks
- maf_extract
- maf_extract_ranges_count
- maf_index
- maf_parse_bench
- maf_tile
- maf_to_fasta
- maf_write
- random_ranges
extensions: []
extra_rdoc_files:
- LICENSE.txt
- README.md
files:
- .document
- .gitignore
- .simplecov
- .travis.yml
- .yardopts
- DEVELOPMENT.md
- Gemfile
- LICENSE.txt
- README.md
- Rakefile
- VERSION
- benchmarks/dispatch_bench
- benchmarks/iter_bench
- benchmarks/read_bench
- benchmarks/sort_bench
- benchmarks/split_bench
- bin/find_overlaps
- bin/maf_bgzip
- bin/maf_count
- bin/maf_dump_blocks
- bin/maf_extract
- bin/maf_extract_ranges_count
- bin/maf_index
- bin/maf_parse_bench
- bin/maf_tile
- bin/maf_to_fasta
- bin/maf_write
- bin/random_ranges
- bio-maf.gemspec
- features/bgzf.feature
- features/block-joining.feature
- features/dir-access.feature
- features/gap-removal.feature
- features/maf-indexing.feature
- features/maf-output.feature
- features/maf-parsing.feature
- features/maf-querying.feature
- features/maf-to-fasta.feature
- features/slice.feature
- features/step_definitions/convert_steps.rb
- features/step_definitions/dir-access_steps.rb
- features/step_definitions/file_steps.rb
- features/step_definitions/gap_removal_steps.rb
- features/step_definitions/index_steps.rb
- features/step_definitions/output_steps.rb
- features/step_definitions/parse_steps.rb
- features/step_definitions/query_steps.rb
- features/step_definitions/slice_steps.rb
- features/step_definitions/tiling_steps.rb
- features/step_definitions/ucsc_bin_steps.rb
- features/support/aruba.rb
- features/support/env.rb
- features/tiling.feature
- features/ucsc-bins.feature
- lib/bio-maf.rb
- lib/bio-maf/maf.rb
- lib/bio/maf.rb
- lib/bio/maf/index.rb
- lib/bio/maf/jobs.rb
- lib/bio/maf/maf.rb
- lib/bio/maf/parser.rb
- lib/bio/maf/struct.rb
- lib/bio/maf/tiler.rb
- lib/bio/maf/writer.rb
- lib/bio/ucsc.rb
- lib/bio/ucsc/genomic-interval-bin.rb
- lib/bio/ucsc/ucsc_bin.rb
- man/.gitignore
- man/maf_bgzip.1
- man/maf_bgzip.1.ronn
- man/maf_extract.1
- man/maf_extract.1.ronn
- man/maf_index.1
- man/maf_index.1.markdown
- man/maf_index.1.ronn
- man/maf_tile.1
- man/maf_tile.1.ronn
- man/maf_to_fasta.1
- man/maf_to_fasta.1.ronn
- spec/bio/maf/index_spec.rb
- spec/bio/maf/maf_spec.rb
- spec/bio/maf/parser_spec.rb
- spec/bio/maf/struct_spec.rb
- spec/bio/maf/tiler_spec.rb
- spec/bio/ucsc/ucsc_bin_spec.rb
- spec/spec_helper.rb
- test/data/big-block.maf
- test/data/chr22_ieq.maf
- test/data/chr22_ieq2.maf
- test/data/chrY-1block.maf
- test/data/empty
- test/data/empty.db
- test/data/empty.maf
- test/data/ext-bin.maf
- test/data/gap-1.kct
- test/data/gap-1.maf
- test/data/gap-filled1.fa
- test/data/gap-sp1.fa
- test/data/gap-sp1.fa.gz
- test/data/mm8.chrM.maf
- test/data/mm8.chrM.maf.bgz
- test/data/mm8_chr7_tiny.kct
- test/data/mm8_chr7_tiny.maf
- test/data/mm8_chr7_tiny.maf.gz
- test/data/mm8_chr7_tiny_slice1.maf
- test/data/mm8_chr7_tiny_slice2.maf
- test/data/mm8_chr7_tiny_slice3.maf
- test/data/mm8_chrM_tiny.kct
- test/data/mm8_chrM_tiny.maf
- test/data/mm8_mod_a.maf
- test/data/mm8_single.maf
- test/data/mm8_subset_a.maf
- test/data/t1-bad1.maf
- test/data/t1.fasta
- test/data/t1.maf
- test/data/t1a.maf
- test/helper.rb
- test/test_bio-maf.rb
- travis-ci/install_kc
- travis-ci/install_kc_java
- travis-ci/report_errors
homepage: http://github.com/csw/bioruby-maf
licenses:
- MIT
post_install_message: 
rdoc_options: []
require_paths:
- lib
required_ruby_version: !ruby/object:Gem::Requirement
  none: false
  requirements:
  - - ! '>='
    - !ruby/object:Gem::Version
      version: '0'
      segments:
      - 0
      hash: -3101690621463444667
required_rubygems_version: !ruby/object:Gem::Requirement
  none: false
  requirements:
  - - ! '>='
    - !ruby/object:Gem::Version
      version: '0'
requirements: []
rubyforge_project: 
rubygems_version: 1.8.24
signing_key: 
specification_version: 3
summary: MAF parser for BioRuby
test_files:
- features/bgzf.feature
- features/block-joining.feature
- features/dir-access.feature
- features/gap-removal.feature
- features/maf-indexing.feature
- features/maf-output.feature
- features/maf-parsing.feature
- features/maf-querying.feature
- features/maf-to-fasta.feature
- features/slice.feature
- features/step_definitions/convert_steps.rb
- features/step_definitions/dir-access_steps.rb
- features/step_definitions/file_steps.rb
- features/step_definitions/gap_removal_steps.rb
- features/step_definitions/index_steps.rb
- features/step_definitions/output_steps.rb
- features/step_definitions/parse_steps.rb
- features/step_definitions/query_steps.rb
- features/step_definitions/slice_steps.rb
- features/step_definitions/tiling_steps.rb
- features/step_definitions/ucsc_bin_steps.rb
- features/support/aruba.rb
- features/support/env.rb
- features/tiling.feature
- features/ucsc-bins.feature
- spec/bio/maf/index_spec.rb
- spec/bio/maf/maf_spec.rb
- spec/bio/maf/parser_spec.rb
- spec/bio/maf/struct_spec.rb
- spec/bio/maf/tiler_spec.rb
- spec/bio/ucsc/ucsc_bin_spec.rb
- spec/spec_helper.rb
- test/data/big-block.maf
- test/data/chr22_ieq.maf
- test/data/chr22_ieq2.maf
- test/data/chrY-1block.maf
- test/data/empty
- test/data/empty.db
- test/data/empty.maf
- test/data/ext-bin.maf
- test/data/gap-1.kct
- test/data/gap-1.maf
- test/data/gap-filled1.fa
- test/data/gap-sp1.fa
- test/data/gap-sp1.fa.gz
- test/data/mm8.chrM.maf
- test/data/mm8.chrM.maf.bgz
- test/data/mm8_chr7_tiny.kct
- test/data/mm8_chr7_tiny.maf
- test/data/mm8_chr7_tiny.maf.gz
- test/data/mm8_chr7_tiny_slice1.maf
- test/data/mm8_chr7_tiny_slice2.maf
- test/data/mm8_chr7_tiny_slice3.maf
- test/data/mm8_chrM_tiny.kct
- test/data/mm8_chrM_tiny.maf
- test/data/mm8_mod_a.maf
- test/data/mm8_single.maf
- test/data/mm8_subset_a.maf
- test/data/t1-bad1.maf
- test/data/t1.fasta
- test/data/t1.maf
- test/data/t1a.maf
- test/helper.rb
- test/test_bio-maf.rb