--- !ruby/object:Gem::Specification
name: bio-polyploid-tools
version: !ruby/object:Gem::Version
  version: 0.8.1
platform: ruby
authors:
- Ricardo H.  Ramirez-Gonzalez
autorequire: 
bindir: bin
cert_chain: []
date: 2018-01-19 00:00:00.000000000 Z
dependencies:
- !ruby/object:Gem::Dependency
  name: bio
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.5.1
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.5.1
- !ruby/object:Gem::Dependency
  name: bio-samtools
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 2.6.2
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 2.6.2
- !ruby/object:Gem::Dependency
  name: systemu
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 2.5.2
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 2.5.2
- !ruby/object:Gem::Dependency
  name: shoulda
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '2.10'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '2.10'
- !ruby/object:Gem::Dependency
  name: test-unit
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: juwelier
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
description: Repository of tools developed at Crop Genetics in JIC to work with polyploid
  wheat
email: ricardo.ramirez-gonzalez@jic.ac.uk
executables:
- bfr.rb
- blast_triads.rb
- blast_triads_promoters.rb
- count_variations.rb
- filter_blat_by_target_coverage.rb
- filter_exonerate_by_identity.rb
- find_best_blat_hit.rb
- find_best_exonerate.rb
- find_homoeologue_variations.rb
- get_longest_hsp_blastx_triads.rb
- hexaploid_primers.rb
- homokaryot_primers.rb
- mafft_triads.rb
- mafft_triads_promoters.rb
- map_markers_to_contigs.rb
- markers_in_region.rb
- polymarker.rb
- polymarker_capillary.rb
- snp_position_to_polymarker.rb
- snps_between_bams.rb
- vcfLineToTable.rb
extensions: []
extra_rdoc_files:
- README
- README.md
files:
- ".travis.yml"
- Gemfile
- README
- README.md
- Rakefile
- VERSION
- bin/bfr.rb
- bin/blast_triads.rb
- bin/blast_triads_promoters.rb
- bin/count_variations.rb
- bin/filter_blat_by_target_coverage.rb
- bin/filter_exonerate_by_identity.rb
- bin/find_best_blat_hit.rb
- bin/find_best_exonerate.rb
- bin/find_homoeologue_variations.rb
- bin/get_longest_hsp_blastx_triads.rb
- bin/hexaploid_primers.rb
- bin/homokaryot_primers.rb
- bin/mafft_triads.rb
- bin/mafft_triads_promoters.rb
- bin/map_markers_to_contigs.rb
- bin/markers_in_region.rb
- bin/polymarker.rb
- bin/polymarker_capillary.rb
- bin/snp_position_to_polymarker.rb
- bin/snps_between_bams.rb
- bin/vcfLineToTable.rb
- bio-polyploid-tools.gemspec
- conf/defaults.rb
- conf/primer3_config/dangle.dh
- conf/primer3_config/dangle.ds
- conf/primer3_config/interpretations/dangle_i.dh
- conf/primer3_config/interpretations/dangle_i.ds
- conf/primer3_config/interpretations/loops_i.dh
- conf/primer3_config/interpretations/loops_i.ds
- conf/primer3_config/interpretations/stack_i.dh
- conf/primer3_config/interpretations/stack_i.ds
- conf/primer3_config/interpretations/stackmm_i_mm.dh
- conf/primer3_config/interpretations/stackmm_i_mm.ds
- conf/primer3_config/interpretations/tetraloop_i.dh
- conf/primer3_config/interpretations/tetraloop_i.ds
- conf/primer3_config/interpretations/triloop_i.dh
- conf/primer3_config/interpretations/triloop_i.ds
- conf/primer3_config/interpretations/tstack2_i.dh
- conf/primer3_config/interpretations/tstack2_i.ds
- conf/primer3_config/interpretations/tstack_i.dh
- conf/primer3_config/interpretations/tstack_i.ds
- conf/primer3_config/interpretations/tstack_tm_inf_i.dh
- conf/primer3_config/interpretations/tstack_tm_inf_i.ds
- conf/primer3_config/loops.dh
- conf/primer3_config/loops.ds
- conf/primer3_config/stack.dh
- conf/primer3_config/stack.ds
- conf/primer3_config/stackmm.dh
- conf/primer3_config/stackmm.ds
- conf/primer3_config/tetraloop.dh
- conf/primer3_config/tetraloop.ds
- conf/primer3_config/triloop.dh
- conf/primer3_config/triloop.ds
- conf/primer3_config/tstack.dh
- conf/primer3_config/tstack2.dh
- conf/primer3_config/tstack2.ds
- conf/primer3_config/tstack_tm_inf.ds
- lib/bio/BFRTools.rb
- lib/bio/BIOExtensions.rb
- lib/bio/PolyploidTools/ChromosomeArm.rb
- lib/bio/PolyploidTools/ExonContainer.rb
- lib/bio/PolyploidTools/Marker.rb
- lib/bio/PolyploidTools/NoSNPSequence.rb
- lib/bio/PolyploidTools/PrimerRegion.rb
- lib/bio/PolyploidTools/SNP.rb
- lib/bio/PolyploidTools/SNPMutant.rb
- lib/bio/PolyploidTools/SNPSequence.rb
- lib/bio/db/blast.rb
- lib/bio/db/exonerate.rb
- lib/bio/db/primer3.rb
- lib/bioruby-polyploid-tools.rb
- test/data/BS00068396_51.fa
- test/data/BS00068396_51_blast.tab
- test/data/BS00068396_51_contigs.aln
- test/data/BS00068396_51_contigs.dnd
- test/data/BS00068396_51_contigs.fa
- test/data/BS00068396_51_contigs.fa.fai
- test/data/BS00068396_51_contigs.fa.nhr
- test/data/BS00068396_51_contigs.fa.nin
- test/data/BS00068396_51_contigs.fa.nsq
- test/data/BS00068396_51_contigs.nhr
- test/data/BS00068396_51_contigs.nin
- test/data/BS00068396_51_contigs.nsq
- test/data/BS00068396_51_exonerate.tab
- test/data/BS00068396_51_for_polymarker.fa
- test/data/BS00068396_51_genes.txt
- test/data/IWGSC_CSS_1AL_scaff_1455974.fa
- test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa
- test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai
- test/data/LIB1716.bam
- test/data/LIB1716.bam.bai
- test/data/LIB1719.bam
- test/data/LIB1719.bam.bai
- test/data/LIB1721.bam
- test/data/LIB1721.bam.bai
- test/data/LIB1722.bam
- test/data/LIB1722.bam.bai
- test/data/PST130_7067.csv
- test/data/PST130_7067.fa
- test/data/PST130_7067.fa.fai
- test/data/PST130_reverse_primer.csv
- test/data/S22380157.fa
- test/data/S22380157.fa.fai
- test/data/S22380157.vcf
- test/data/S58861868/LIB1716.bam
- test/data/S58861868/LIB1716.sam
- test/data/S58861868/LIB1719.bam
- test/data/S58861868/LIB1719.sam
- test/data/S58861868/LIB1721.bam
- test/data/S58861868/LIB1721.sam
- test/data/S58861868/LIB1722.bam
- test/data/S58861868/LIB1722.sam
- test/data/S58861868/S58861868.fa
- test/data/S58861868/S58861868.fa.fai
- test/data/S58861868/S58861868.vcf
- test/data/S58861868/header.txt
- test/data/S58861868/merged.bam
- test/data/S58861868/merged_reheader.bam
- test/data/S58861868/merged_reheader.bam.bai
- test/data/Test3Aspecific.csv
- test/data/Test3Aspecific_contigs.fa
- test/data/bfr_out_test.csv
- test/data/headerMergeed.txt
- test/data/headerS2238015
- test/data/mergedLibs.bam
- test/data/mergedLibsReheader.bam
- test/data/mergedLibsSorted.bam
- test/data/mergedLibsSorted.bam.bai
- test/data/patological_cases5D.csv
- test/data/primer_3_input_header_test
- test/data/short_primer_design_test.csv
- test/data/test_from_mutant.csv
- test/data/test_iselect.csv
- test/data/test_iselect_reference.fa
- test/data/test_iselect_reference.fa.fai
- test/data/test_primer3_error.csv
- test/data/test_primer3_error_contigs.fa
- test/test_bfr.rb
- test/test_blast.rb
- test/test_exon_container.rb
- test/test_exonearate.rb
- test/test_snp_parsing.rb
- test/test_wrong_selection.sh
homepage: http://github.com/tgac/bioruby-polyploid-tools
licenses:
- MIT
metadata: {}
post_install_message: 
rdoc_options: []
require_paths:
- lib
required_ruby_version: !ruby/object:Gem::Requirement
  requirements:
  - - ">="
    - !ruby/object:Gem::Version
      version: '0'
required_rubygems_version: !ruby/object:Gem::Requirement
  requirements:
  - - ">="
    - !ruby/object:Gem::Version
      version: '0'
requirements: []
rubyforge_project: 
rubygems_version: 2.7.4
signing_key: 
specification_version: 4
summary: Tool to work with polyploids, NGS and molecular biology
test_files: []