# -*- encoding: utf-8 -*-
# stub: bio-polymarker 1.3.2 ruby lib

Gem::Specification.new do |s|
  s.name = "bio-polymarker".freeze
  s.version = "1.3.2".freeze

  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
  s.require_paths = ["lib".freeze]
  s.authors = ["Rob Ellis".freeze]
  s.date = "2024-09-25"
  s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze
  s.email = "rob.ellis@jic.ac.uk".freeze
  s.executables = ["bfr.rb".freeze, "blast_triads.rb".freeze, "blast_triads_promoters.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, "get_longest_hsp_blastx_triads.rb".freeze, "hexaploid_primers.rb".freeze, "homokaryot_primers.rb".freeze, "mafft_triads.rb".freeze, "mafft_triads_promoters.rb".freeze, "map_markers_to_contigs.rb".freeze, "marker_to_vcf.rb".freeze, "markers_in_region.rb".freeze, "mask_triads.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "polymarker_deletions.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze, "vcfToPolyMarker.rb".freeze]
  s.extra_rdoc_files = ["README.md".freeze]
  s.files = [".travis.yml".freeze, "Gemfile".freeze, "README.md".freeze, "Rakefile".freeze, "SECURITY.md".freeze, "VERSION".freeze, "bin/bfr.rb".freeze, "bin/blast_triads.rb".freeze, "bin/blast_triads_promoters.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/get_longest_hsp_blastx_triads.rb".freeze, "bin/hexaploid_primers.rb".freeze, "bin/homokaryot_primers.rb".freeze, "bin/mafft_triads.rb".freeze, "bin/mafft_triads_promoters.rb".freeze, "bin/map_markers_to_contigs.rb".freeze, "bin/marker_to_vcf.rb".freeze, "bin/markers_in_region.rb".freeze, "bin/mask_triads.rb".freeze, "bin/polymarker.rb".freeze, "bin/polymarker_capillary.rb".freeze, "bin/polymarker_deletions.rb".freeze, "bin/snp_position_to_polymarker.rb".freeze, "bin/snps_between_bams.rb".freeze, "bin/tag_stats.rb".freeze, "bin/vcfLineToTable.rb".freeze, "bin/vcfToPolyMarker.rb".freeze, "bio-polymarker.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-polymarker.rb".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/Mask.rb".freeze, "lib/bio/PolyploidTools/NoSNPSequence.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/blast.rb".freeze, "lib/bio/db/exonerate.rb".freeze, "lib/bio/db/primer3.rb".freeze, "test/data/7B_amplicon_test.fa".freeze, "test/data/7B_amplicon_test.fa.fai".freeze, "test/data/7B_amplicon_test_reference.fa".freeze, "test/data/7B_amplicon_test_reference.fa.fai".freeze, "test/data/7B_marker_test.txt".freeze, "test/data/BS00068396_51.fa".freeze, "test/data/BS00068396_51_blast.tab".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_contigs.fa.fai".freeze, "test/data/BS00068396_51_contigs.fa.nhr".freeze, "test/data/BS00068396_51_contigs.fa.nin".freeze, "test/data/BS00068396_51_contigs.fa.nsq".freeze, "test/data/BS00068396_51_contigs.nhr".freeze, "test/data/BS00068396_51_contigs.nin".freeze, "test/data/BS00068396_51_contigs.nsq".freeze, "test/data/BS00068396_51_exonerate.tab".freeze, "test/data/BS00068396_51_for_polymarker.txt".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/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai".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_7067.fa.ndb".freeze, "test/data/PST130_7067.fa.nhr".freeze, "test/data/PST130_7067.fa.nin".freeze, "test/data/PST130_7067.fa.not".freeze, "test/data/PST130_7067.fa.nsq".freeze, "test/data/PST130_7067.fa.ntf".freeze, "test/data/PST130_7067.fa.nto".freeze, "test/data/PST130_reverse_primer.csv".freeze, "test/data/S22380157.fa".freeze, "test/data/S22380157.fa.fai".freeze, "test/data/S22380157.vcf".freeze, "test/data/S58861868/LIB1716.bam".freeze, "test/data/S58861868/LIB1716.sam".freeze, "test/data/S58861868/LIB1719.bam".freeze, "test/data/S58861868/LIB1719.sam".freeze, "test/data/S58861868/LIB1721.bam".freeze, "test/data/S58861868/LIB1721.sam".freeze, "test/data/S58861868/LIB1722.bam".freeze, "test/data/S58861868/LIB1722.sam".freeze, "test/data/S58861868/S58861868.fa".freeze, "test/data/S58861868/S58861868.fa.fai".freeze, "test/data/S58861868/S58861868.vcf".freeze, "test/data/S58861868/header.txt".freeze, "test/data/S58861868/merged.bam".freeze, "test/data/S58861868/merged_reheader.bam".freeze, "test/data/S58861868/merged_reheader.bam.bai".freeze, "test/data/Test3Aspecific.csv".freeze, "test/data/Test3Aspecific_contigs.fa".freeze, "test/data/bfr_out_test.csv".freeze, "test/data/chr1A_C1145499T/chr1A_C1145499T.csv".freeze, "test/data/chr1A_G540414846C/chr1A_G540414846C.csv".freeze, "test/data/chr1A_G540414846C/chr1A_G540414846C.fa".freeze, "test/data/chr1A_T517634750C/chr1A_T517634750C.csv".freeze, "test/data/chr2D_C112180134A/chr2D_C112180134A.csv".freeze, "test/data/chr4D_C14473543T/chr4D_C14473543T.csv".freeze, "test/data/chr4D_C14473543T/chr4D_C14473543T.fa".freeze, "test/data/headerMergeed.txt".freeze, "test/data/headerS2238015".freeze, "test/data/mergedLibs.bam".freeze, "test/data/mergedLibsReheader.bam".freeze, "test/data/mergedLibsSorted.bam".freeze, "test/data/mergedLibsSorted.bam.bai".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/some_tests/some_tests.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_blast.rb".freeze, "test/test_exon_container.rb".freeze, "test/test_exonearate.rb".freeze, "test/test_integration.rb".freeze, "test/test_snp_parsing.rb".freeze, "test/test_wrong_selection.sh".freeze]
  s.homepage = "https://github.com/cb2e6f/bio-polymarker".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, [">= 1.5.1".freeze])
  s.add_runtime_dependency(%q<bio-samtools-wrapper>.freeze, [">= 2.7.0".freeze])
  s.add_runtime_dependency(%q<descriptive_statistics>.freeze, [">= 0".freeze])
  s.add_runtime_dependency(%q<systemu>.freeze, [">= 2.5.2".freeze])
  s.add_development_dependency(%q<shoulda>.freeze, [">= 2.10".freeze])
  s.add_development_dependency(%q<test-unit>.freeze, [">= 0".freeze])
  s.add_development_dependency(%q<juwelier>.freeze, [">= 0".freeze])
  s.add_development_dependency(%q<sorted_set>.freeze, [">= 0".freeze])
end