# -*- encoding: utf-8 -*-
# stub: bio-polyploid-tools 0.7.2 ruby lib

Gem::Specification.new do |s|
  s.name = "bio-polyploid-tools".freeze
  s.version = "0.7.2".freeze

  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
  s.require_paths = ["lib".freeze]
  s.authors = ["Ricardo H.  Ramirez-Gonzalez".freeze]
  s.date = "2015-05-28"
  s.description = "Repository of tools developed in TGAC and Crop Genetics in JIC to work with polyploid wheat".freeze
  s.email = "ricardo.ramirez-gonzalez@tgac.ac.uk".freeze
  s.executables = ["bfr.rb".freeze, "count_variations.rb".freeze, "filter_blat_by_target_coverage.rb".freeze, "filter_exonerate_by_identity.rb".freeze, "find_best_blat_hit.rb".freeze, "find_best_exonerate.rb".freeze, "hexaploid_primers.rb".freeze, "homokaryot_primers.rb".freeze, "map_markers_to_contigs.rb".freeze, "markers_in_region.rb".freeze, "polymarker.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze]
  s.extra_rdoc_files = ["README".freeze, "README.md".freeze]
  s.files = ["Gemfile".freeze, "Gemfile.lock".freeze, "README".freeze, "README.md".freeze, "Rakefile".freeze, "VERSION".freeze, "bin/bfr.rb".freeze, "bin/count_variations.rb".freeze, "bin/filter_blat_by_target_coverage.rb".freeze, "bin/filter_exonerate_by_identity.rb".freeze, "bin/find_best_blat_hit.rb".freeze, "bin/find_best_exonerate.rb".freeze, "bin/hexaploid_primers.rb".freeze, "bin/homokaryot_primers.rb".freeze, "bin/map_markers_to_contigs.rb".freeze, "bin/markers_in_region.rb".freeze, "bin/polymarker.rb".freeze, "bin/snp_position_to_polymarker.rb".freeze, "bin/snps_between_bams.rb".freeze, "bio-polyploid-tools.gemspec".freeze, "conf/defaults.rb".freeze, "conf/primer3_config/dangle.dh".freeze, "conf/primer3_config/dangle.ds".freeze, "conf/primer3_config/interpretations/dangle_i.dh".freeze, "conf/primer3_config/interpretations/dangle_i.ds".freeze, "conf/primer3_config/interpretations/loops_i.dh".freeze, "conf/primer3_config/interpretations/loops_i.ds".freeze, "conf/primer3_config/interpretations/stack_i.dh".freeze, "conf/primer3_config/interpretations/stack_i.ds".freeze, "conf/primer3_config/interpretations/stackmm_i_mm.dh".freeze, "conf/primer3_config/interpretations/stackmm_i_mm.ds".freeze, "conf/primer3_config/interpretations/tetraloop_i.dh".freeze, "conf/primer3_config/interpretations/tetraloop_i.ds".freeze, "conf/primer3_config/interpretations/triloop_i.dh".freeze, "conf/primer3_config/interpretations/triloop_i.ds".freeze, "conf/primer3_config/interpretations/tstack2_i.dh".freeze, "conf/primer3_config/interpretations/tstack2_i.ds".freeze, "conf/primer3_config/interpretations/tstack_i.dh".freeze, "conf/primer3_config/interpretations/tstack_i.ds".freeze, "conf/primer3_config/interpretations/tstack_tm_inf_i.dh".freeze, "conf/primer3_config/interpretations/tstack_tm_inf_i.ds".freeze, "conf/primer3_config/loops.dh".freeze, "conf/primer3_config/loops.ds".freeze, "conf/primer3_config/stack.dh".freeze, "conf/primer3_config/stack.ds".freeze, "conf/primer3_config/stackmm.dh".freeze, "conf/primer3_config/stackmm.ds".freeze, "conf/primer3_config/tetraloop.dh".freeze, "conf/primer3_config/tetraloop.ds".freeze, "conf/primer3_config/triloop.dh".freeze, "conf/primer3_config/triloop.ds".freeze, "conf/primer3_config/tstack.dh".freeze, "conf/primer3_config/tstack2.dh".freeze, "conf/primer3_config/tstack2.ds".freeze, "conf/primer3_config/tstack_tm_inf.ds".freeze, "lib/bio/BFRTools.rb".freeze, "lib/bio/BIOExtensions.rb".freeze, "lib/bio/PolyploidTools/ChromosomeArm.rb".freeze, "lib/bio/PolyploidTools/ExonContainer.rb".freeze, "lib/bio/PolyploidTools/Marker.rb".freeze, "lib/bio/PolyploidTools/PrimerRegion.rb".freeze, "lib/bio/PolyploidTools/SNP.rb".freeze, "lib/bio/PolyploidTools/SNPMutant.rb".freeze, "lib/bio/PolyploidTools/SNPSequence.rb".freeze, "lib/bio/db/exonerate.rb".freeze, "lib/bio/db/primer3.rb".freeze, "lib/bioruby-polyploid-tools.rb".freeze, "test/data/BS00068396_51.fa".freeze, "test/data/BS00068396_51_contigs.aln".freeze, "test/data/BS00068396_51_contigs.dnd".freeze, "test/data/BS00068396_51_contigs.fa".freeze, "test/data/BS00068396_51_exonerate.tab".freeze, "test/data/BS00068396_51_genes.txt".freeze, "test/data/IWGSC_CSS_1AL_scaff_1455974.fa".freeze, "test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa".freeze, "test/data/LIB1716.bam".freeze, "test/data/LIB1716.bam.bai".freeze, "test/data/LIB1719.bam".freeze, "test/data/LIB1719.bam.bai".freeze, "test/data/LIB1721.bam".freeze, "test/data/LIB1721.bam.bai".freeze, "test/data/LIB1722.bam".freeze, "test/data/LIB1722.bam.bai".freeze, "test/data/PST130_7067.csv".freeze, "test/data/PST130_7067.fa".freeze, "test/data/PST130_7067.fa.fai".freeze, "test/data/PST130_reverse_primer.csv".freeze, "test/data/S22380157.fa".freeze, "test/data/S22380157.fa.fai".freeze, "test/data/Test3Aspecific.csv".freeze, "test/data/Test3Aspecific_contigs.fa".freeze, "test/data/bfr_out_test.csv".freeze, "test/data/patological_cases5D.csv".freeze, "test/data/primer_3_input_header_test".freeze, "test/data/short_primer_design_test.csv".freeze, "test/data/test_from_mutant.csv".freeze, "test/data/test_iselect.csv".freeze, "test/data/test_iselect_reference.fa".freeze, "test/data/test_iselect_reference.fa.fai".freeze, "test/data/test_primer3_error.csv".freeze, "test/data/test_primer3_error_contigs.fa".freeze, "test/test_bfr.rb".freeze, "test/test_exon_container.rb".freeze, "test/test_exonearate.rb".freeze, "test/test_snp_parsing.rb".freeze, "test/test_wrong_selection.sh".freeze]
  s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
  s.licenses = ["MIT".freeze]
  s.rubygems_version = "3.5.10".freeze
  s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze

  s.specification_version = 4

  s.add_runtime_dependency(%q<bio>.freeze, [">= 1.4.3".freeze])
  s.add_runtime_dependency(%q<bio-samtools>.freeze, [">= 2.0.4".freeze])
  s.add_runtime_dependency(%q<rake>.freeze, [">= 0".freeze])
  s.add_runtime_dependency(%q<jeweler>.freeze, [">= 0".freeze])
  s.add_runtime_dependency(%q<systemu>.freeze, [">= 2.5.2".freeze])
end