--- !ruby/object:Gem::Specification name: bio-polyploid-tools version: !ruby/object:Gem::Version version: 0.9.8 platform: ruby authors: - Ricardo H. Ramirez-Gonzalez autorequire: bindir: bin cert_chain: [] date: 2018-11-20 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: descriptive_statistics requirement: !ruby/object:Gem::Requirement requirements: - - ">=" - !ruby/object:Gem::Version version: '0' type: :runtime prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - ">=" - !ruby/object:Gem::Version version: '0' - !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 - mask_triads.rb - polymarker.rb - polymarker_capillary.rb - snp_position_to_polymarker.rb - snps_between_bams.rb - tag_stats.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/mask_triads.rb - bin/polymarker.rb - bin/polymarker_capillary.rb - bin/snp_position_to_polymarker.rb - bin/snps_between_bams.rb - bin/tag_stats.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/Mask.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.txt - 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/chr1A_C1145499T/chr1A_C1145499T.csv - test/data/chr1A_G540414846C/chr1A_G540414846C.csv - test/data/chr1A_G540414846C/chr1A_G540414846C.fa - test/data/chr1A_T517634750C/chr1A_T517634750C.csv - test/data/chr2D_C112180134A/chr2D_C112180134A.csv - test/data/chr4D_C14473543T/chr4D_C14473543T.csv - test/data/chr4D_C14473543T/chr4D_C14473543T.fa - 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/some_tests/some_tests.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: 2.7.7 signing_key: specification_version: 4 summary: Tool to work with polyploids, NGS and molecular biology test_files: []