RubyGems - bio-polyploid-tools - Versions diffs - 0.1.0 - Mend

bio-polyploid-tools 0.1.0

Files changed (92) hide show

checksums.yaml +7 -0
data/Gemfile +16 -0
data/Gemfile.lock +67 -0
data/README +21 -0
data/Rakefile +61 -0
data/VERSION +1 -0
data/bin/bfr.rb +133 -0
data/bin/count_variations.rb +36 -0
data/bin/filter_blat_by_target_coverage.rb +15 -0
data/bin/find_best_blat_hit.rb +32 -0
data/bin/hexaploid_primers.rb +168 -0
data/bin/homokaryot_primers.rb +155 -0
data/bin/map_markers_to_contigs.rb +66 -0
data/bin/markers_in_region.rb +42 -0
data/bin/polymarker.rb +219 -0
data/bin/snps_between_bams.rb +106 -0
data/bio-polyploid-tools.gemspec +139 -0
data/conf/defaults.rb +1 -0
data/conf/primer3_config/dangle.dh +128 -0
data/conf/primer3_config/dangle.ds +128 -0
data/conf/primer3_config/interpretations/dangle_i.dh +131 -0
data/conf/primer3_config/interpretations/dangle_i.ds +131 -0
data/conf/primer3_config/interpretations/loops_i.dh +34 -0
data/conf/primer3_config/interpretations/loops_i.ds +31 -0
data/conf/primer3_config/interpretations/stack_i.dh +257 -0
data/conf/primer3_config/interpretations/stack_i.ds +256 -0
data/conf/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
data/conf/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
data/conf/primer3_config/interpretations/tetraloop_i.dh +79 -0
data/conf/primer3_config/interpretations/tetraloop_i.ds +81 -0
data/conf/primer3_config/interpretations/triloop_i.dh +21 -0
data/conf/primer3_config/interpretations/triloop_i.ds +18 -0
data/conf/primer3_config/interpretations/tstack2_i.dh +256 -0
data/conf/primer3_config/interpretations/tstack2_i.ds +256 -0
data/conf/primer3_config/interpretations/tstack_i.dh +256 -0
data/conf/primer3_config/interpretations/tstack_i.ds +256 -0
data/conf/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
data/conf/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
data/conf/primer3_config/loops.dh +30 -0
data/conf/primer3_config/loops.ds +30 -0
data/conf/primer3_config/stack.dh +256 -0
data/conf/primer3_config/stack.ds +256 -0
data/conf/primer3_config/stackmm.dh +256 -0
data/conf/primer3_config/stackmm.ds +256 -0
data/conf/primer3_config/tetraloop.dh +77 -0
data/conf/primer3_config/tetraloop.ds +77 -0
data/conf/primer3_config/triloop.dh +16 -0
data/conf/primer3_config/triloop.ds +16 -0
data/conf/primer3_config/tstack.dh +256 -0
data/conf/primer3_config/tstack2.dh +256 -0
data/conf/primer3_config/tstack2.ds +256 -0
data/conf/primer3_config/tstack_tm_inf.ds +256 -0
data/lib/bio/BFRTools.rb +698 -0
data/lib/bio/BIOExtensions.rb +186 -0
data/lib/bio/PolyploidTools/ChromosomeArm.rb +52 -0
data/lib/bio/PolyploidTools/ExonContainer.rb +194 -0
data/lib/bio/PolyploidTools/Marker.rb +175 -0
data/lib/bio/PolyploidTools/PrimerRegion.rb +22 -0
data/lib/bio/PolyploidTools/SNP.rb +681 -0
data/lib/bio/PolyploidTools/SNPSequence.rb +56 -0
data/lib/bio/SAMToolsExtensions.rb +284 -0
data/lib/bio/db/exonerate.rb +272 -0
data/lib/bio/db/fastadb.rb +164 -0
data/lib/bio/db/primer3.rb +673 -0
data/lib/bioruby-polyploid-tools.rb +25 -0
data/test/data/BS00068396_51.fa +2 -0
data/test/data/BS00068396_51_contigs.aln +1412 -0
data/test/data/BS00068396_51_contigs.dnd +7 -0
data/test/data/BS00068396_51_contigs.fa +8 -0
data/test/data/BS00068396_51_exonerate.tab +6 -0
data/test/data/BS00068396_51_genes.txt +14 -0
data/test/data/LIB1716.bam +0 -0
data/test/data/LIB1716.bam.bai +0 -0
data/test/data/LIB1719.bam +0 -0
data/test/data/LIB1719.bam.bai +0 -0
data/test/data/LIB1721.bam +0 -0
data/test/data/LIB1721.bam.bai +0 -0
data/test/data/LIB1722.bam +0 -0
data/test/data/LIB1722.bam.bai +0 -0
data/test/data/S22380157.fa +16 -0
data/test/data/S22380157.fa.fai +1 -0
data/test/data/Test3Aspecific.csv +1 -0
data/test/data/Test3Aspecific_contigs.fa +6 -0
data/test/data/patological_cases5D.csv +1 -0
data/test/data/short_primer_design_test.csv +10 -0
data/test/data/test_primer3_error.csv +4 -0
data/test/data/test_primer3_error_contigs.fa +10 -0
data/test/test_bfr.rb +51 -0
data/test/test_exon_container.rb +17 -0
data/test/test_exonearate.rb +53 -0
data/test/test_snp_parsing.rb +40 -0
metadata +201 -0

data/test/data/BS00068396_51_contigs.dnd ADDED

@@ -0,0 +1,7 @@
+(
+(
+2AS_5222932:0.20551,
+2BS_5163353:0.19641)
+:0.57378,
+2BS_5245544:0.21414,
+2DS_5334799:0.22137);

data/test/data/BS00068396_51_contigs.fa ADDED

@@ -0,0 +1,8 @@
+>2AS_5222932 6364 267569 1716390+,...,724070+
+CAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACTAAAAGATATCGGGGAGGCGGATACACAGCTTACATCACACCCCGTGCTACAAGCAACTAAAGATTGGAAAAAGAGAAGCCCGGTCGCATAGTGAGAAGTCTTCCATCTCGAAACATGTGCGAAGAAGAAGATCGCCAAGGGAAATGCCAACTGACTTGGCAACAAACTCCCCGTACGCCGACCCTGAGACACAAGAAGACGCCACACCCCCTACACCCTCACTGAAGGAGGACTTTACCCCTCGTCCTAGCTCAAAGGACGCCGCACCATTGAGCGAGGGATGTGTTCAACCTAGAACAGGAATGGTGTGGTCTTGAGGTCACAGGAGCCGAGCACATACACGCGACCCGCCACACCGCAGCGGGCAAACCATGGTGGCCATGAAGAAACGTCCGCACAATGCCTGGAACAAGAAGGGGGAACCTGTAGGAGAGGTTCACGGAAATCGAAGAAGCGGCAAGCTCAAGGCGGACAACAAGCACACAATATAAGCACAAGGAAGAAGGACCGGGTAACTACATGCCGCCACGAACAAACGTCGGGAAGGGGAACCCTTTCCCCTCCCACCCAGGTTCAAGGGTGATGAACCACCGACGAATAGGGCAGCGAATACCTCACTGAAGATAGTATACTCAACGCTTCACACAAACTGTCGCTCGAAACCCACAACAACCACAAAATTAACCACATGGCACCACACACCAGCCTCTCCTTGCCAAACGACTCCCCCAGGGAGGTAACAACACCGAGCGTCGCCGCCGCCGCATCCACAGGGATAACAGGAATTAACCTTGGGTCAAAGAAGAGGGGTAAGGAGAAGGGATCACGTCGGTGCCTCCAAGGAGGGGAGCAGCGCCAGCAGGCGGTGTCACCGACGTGGTCGGCCAAGCCACCAAAGGATTTCTCTCGAACCCAACTCACACCACCATGCCCGGCGATACAAGATCACCACCACGAGATCCGGCCGGAAGTGGACCAAATGGGAAAAAGGAGTGACCTTCAGATATGACGCCAGAAGAACCGCCGGAGCAGACCGCCGACCATGAACCGCACCTGTCGTCGCCGCACTGCCCACACGGCTGAGGACGCCGACCCTCTCGTGTGAGCATCGCCAGCCGCGAAGACGGCGTCGCCTCTCCAAGAAGGTTCGCCGCCTGGAGCCCAAAGCCCTCCGCCGAGACCGGAGCGACGAAATCCCCGTTGCCACCTTCACCGTAGGCTGCGCGGGGTTGCCCGGCAACCAGTGGCGGACCTAGAATCATAGGCTTGGGGGTGCCATAGTTCAATGTTCACATTAAACGTCATCATAATCTCAATAAATAGTCTTAAAATAGCAACAACTTGATGAATATGTAGCGTGAGGTATAGAGTAAAATTTATTTTACAACTTTGAAGGGGTGCCTGGCACCCACGGCCTCAAATTAGTTATGGCGGTGGCCAAGGTTTGATATCATCTTGGAATCGTCCACGGGAGCGATTCGGTGACCAAGGTCTTTTCTGTAAACTAAACTTATTCCCTATGCTGGCCTTATCAATTCCGAGTTAATCAAACCCATCAAAATCGAATTGAAGGAGCAAATTGATAAAATACGATTTTCTGCTTTGACACATCATCATTGTTCTCCTTTGATGGAACATCTTGACCATCAAACATCCACATTTAACCCCTTAAAAGAACACATTCTACATTTAAGCTAGCGCTTTCTTCTGTCTTGCCCCCTTGCCAAAAACACAAGATATTCCACGCTGCCAAACACACCAATCGGAAAAAGGCAATTTTCACTTTTCATCGATTAGAAGCAGCTCCGAAAAGGAAAAGAAGCAACCATCTCTCCCCACCCCACCCCGGCCCTGCTCCCCGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTGGGCGGGGGTGAGTGGCGAGCCTCCCTCGCCGCCTTGCGCTGCACAGGAACAAGGCGAGAGCGATCGGCGTCGGGATGCTGAGGCGGCGGCTGAGCTCCCTTCTCCTCCGATCCCCGTGCTCCTCCTCCGCCGTCGCTTCCTCCTACCAGCAGCAGCAGCACCTCCTCCTCCCCACCCACGCCGAGGTAACCCCCACGGTTCCCCTTTCTTTCCCTCCCGCGCATTTCGTCGAACGCCTCGCGCGCGCGCACAACGTGGCCGGACCGGATCTGGCCTGCACTCCTTTCTCGCTCCGTTTGGTTCAATGCGTGCCTGCCGTTCCTAGATGCTCATCCGCCTGACTGTTTTCCTCGCAGAAACCGCCGGCCCTGAATCTGCTCAGGCTCTTCACATCCCTAGCTGTACGTTTGTTCCCAAACCCGCATTCTTATTATTTGTGACAACTATGCAGACTGCATGTGAATAATTGGTGGTGTGTCCTCTGTTCATTCTGTAGGGAACCGATGGGGACAGGCCGTTCATCGCTTTTGTCTTGGGTAGTTTTTCCCTGCTTTTACTCCCAAAATGTAGCAGGATTGTTGTTTTCGTTCTTCGAAACGGAGGGCAAAGCTTTGCAGGGTCGGTTTTACATTTATAAAGTTCCATGCATATCTGTGTAGAGTAAACCGAGGAACCCTTGCCTCAATGATAATCAGTGCTGTTTCACATTTATAATCGCTTTCGTCTTAGGTAAAAAAATAAATCTACTAGTACTCCCCCAATATTGCAGGGTTGGTTTCACATTTACATACTCCATGCATAACCTGTGTAGAGTAAATTGAGGATCACTTCTATCAATGATAACCAGTGCTGTTTCAAGTTGGATTGTGTTGTGGCGCTCAAATTTCAGTTGTTCACACGACTAATCAAGATCCTGCATATAGGGGGACCTGGGAGTGGGAAAGGAACGCAATGTAGTAGGATCGCTTCGGATTTTGGATTTGCTCATGTGAGTGCTGGTGACCTTCTACGGAATGAAATAGCTTCTGGCACTGATCATGGGTAATTCTTCTTTCCGTTTGATCCTCTGACAGCCTTATAATGACCCACACGCACATGCATGGTTCGGTGAATTGATTTTTCAGTTTCATGGCATTTGCCAGGGAGTGGATCCTAGAGATAATAAGGGAAGGGAGGATTGTTCCATCAGAGATAACTGTTGAACTCGTCAGAAAAGCAATTGAATCAAGCTCTGCTAAAAGGGTTCTTATTGATGGTTTCCCAAGGTGTGAGGAAAACAGAATTGCCTTTGAAAAAATAGTAAGTTTTCTGTTTGGCTTGCATTACTGGTCCAGAACTTTCTATTGATTGAAATAGTATGTGATGAGATGGATAAGTCCATGCTGTTCATCAGTTTCTGTTCAATTTTTGGGAAGGCTAATAACAGGTGAATCTTCACGTTTTCTAGCGCTCTTGGCTGTAACCATTTGTGTATACACACTTGTCTTTACATTTTTACGCCAATATGCTGGCCCAAAACTGCCAGTGTACAGTATGCAATCAGCAGTTTCTTATGCATGTATTTTCTTTTAGTAGCAAATCAGTAACTATGTCCTGCTCTAGAGTGATGCACTTTTAGGATTTATGCAGTAGTCCACAGTTATGTCAGCCCCACTATGGTGGATGTATAGTTGCATCTCAACAACTACTACAAGCATTTATATCAAAGAATGTGTGTGCTGTGGTCGGGCAATTAGAAGACACTGGCATACCAACTAAGATATGTTTCATTGTTGTCCACTCAATAATTGCTAGTCAGATAGATGTAGATTGCATGATCCTGTTCTGATATGTTGACTCATAAATTTCAGACTGGAACTGAACCAGACCTTGTGCTTTTCTTTGACTGTCCTGAGGATGAGATGGTTAAACGTCTCCTAAGCCGTAACCAGGTTGGTCTTCGTATTATCTCTGGAGTAAATTGTGCTAGATATATATACACTATATGAGTACTGTACATTTCCCAATTCTTATTCGGAACTTACTCCATATGTGATTTTCTGAGATTTTATTTCCCAGCCGTTACTTTCGGCTTTGACAATTATCTTCTTATTACTCCCTCTCTTAACTAACATGAAATATAGCATTCCTAAAGGATAGTCCTTGTGGATTGCCACAAATGATTTTCTTCTTCATATGTCATTTAAATTGAAGAGAAGAAACACTAATCTAATTAGTGTAGTTCGTGCATATCAAAATGGGAGGTTGATTAATGCTCTAGCGGAGTTTCCTTTCAAAAATATCACATTAGATTGATCTCTTTATTGTTTTTGTTTTTTCGATTATCTCATGTATGCGTCTTAGGGACGAGTTGATGATAACATTGAGACAATCAAGAAGCGTCTAAAAGTATTCGAGAGTTTGAATCTTCCTGTTGTTGAGTACTACTCTTCAAGGGGAAAGGCACACAAGGTAATTAATCTATTTATTTTATGCCGAGTGTCCTGGACAGGAGCACTTCTTGTACCTTTCTTTTATGAACCGTACCTTTACCTTTTGACATGCATTTTCCTATTTCCTTCACACGGAAACAGAGCTCTACCTTCTGTTGTAGAAGTTGATCCAAAAGGCTTCTTAATGTGCAACATTAAACTATACCTGGCTTATTTTCTTGAACTTTTACAAATGCCAATATATATTTGAGAAACATCAAACATATGGGTTACCAATGTATAAATAGCAGGATAGTGTTTCCAGGGAATCATAGGACAGAGAGGCAGAGCCAGGATGCGATTCCCTCGTGTTCTGAATTCATATAACTGCAAGACCATTTTTCTATGGTGTGGGGAGGGGAGTGAGATCAGAGATCTGCGTATTTATTTGATATTAGATGAGTGTCTGCAATTCACTCATTTTGGAAGAAATTGCTAATCTCTTCAGAAGGGGTACATATCAGGGATATAACACAGTAACATATTCTGTATACCACTCATATTCAGGATCTGTAGGATGTCTTATTTATTTTTGAGACTTGACCTTTAGGGTGTCTAAGAGTACTTGTTGAACTCCATGCAGATAAATGCAACGGGAACTGAAGATGAAATCTTTGAAGCAGTTCGCAAGTTGTTTTCCTCCTTAAGGTAAATCCTGATGTTTAAGACACGAAATTCCTCTCATTTACTGTGACTATGTCCGCTCTCCTGAAGGAGATGCACATTCTTGCATCATCTGATTTCTGATTGCTTGCATATTATTTTCTAGTCCCAATTACTGTAGTTCTGAAAGCTTTTCAGTCCTCACATATTTAGCATATCCCAACCCTCAGTCCTCACATATATTGCAGCACCCACACTTTTTCAATACATTAACAAGTGATGGCATGTTCTTTATACTAAGCCTGCCATTGCAGCTAGGGCAGGCCGTCGCTATAAGCAGAAGGGTATTGCTTGTAGGTACAAAGAGCTTGCGTTCCTGAATCCTTGCCATTTGTGTTCACTGTGCACAATAAAGAAAGACAAACTGACAAGCAAAATGAACATGGTAGCATTTATCTTACTGATTGATGGATAAGGAAGAAGAGGTCCAGGATGTTGCTACGTCGCAAACTTTGTCATCTAGCTGACTCGCCGAACCCTCGCCTGTAGCTAGTTTCTCGACACGTTTGACTAAGCAACGCTAGCAACTTGCGGTTGTCCCAGCTTATGATAAAGATGCACTCCTACTTTGTTGCTACATATACACAAGGTAGTTGCAATCATTTGACCATTTCACCCTGTTTGCAGGCTATGAGGAGGCTGTCGTCTTCCGCGCGAGCGGGGGGAATTGGAATTACGCCTGGCGGAAATTCTCTCTCCCTCTTTTCTTTTACCTTTACATCTCTTAGCATAATAATTGTACATATTCTGATACACGGACCATTCCTGTGAAAACAGAGGGCCCCTGGTGAAACGCCCAGCCTGCCTGCTATGATAAACCCTGACCCTTGCGCTCTCGTCACGCGCCACGGTATACGATACTTCAGACTGCAGCAAAACTGCTACAACGATATTTTTTTTCTGCCAACACCCTACAAATATATGTCTGCCGTGTTTTTTTTACCAGGATAATATAGTTGTATGTATGTGCGCCGTGCTTGTGTTGTGACGATTTGCTGGGTATATATCTATGGAGAGATGAGGTGAGAGCTGCAGGCGTCCGATAAACTAGTGATTTGACTGGAGGAAAAAGGCCGTGTACGTTTGGATTTAGTTAATGTGAACTGCCGGCGTGTTATTGTCAGTTCTTGACCGGCCGTTTAGCAGTAGCTGATGCCATCTTCAAACGCTCGCCAAAAAAAAAAA
+>2BS_5245544 8836 99090 5145698+,...,1324530+
+CGCCACTGCCTCCAATTCACACATTCATGAAGTTCCGGATGTAGTTTTGGTCAAGTTTGAACCCATTTTTCCCTTTCAAAAGTCTTCATTACAAGTGTGAAGATCTCTGTCTATAGATTTGCCTAAAATGTACATTCATACATTCTGCTAGGTTCTACTCCCTCCGTCTCAAAATAAGTGACTCAACTTTGTACTAGCTCTAGTATAAATTTGTACTAAGCTCAAGACACTTATTCTGGGACGAAGGGACTATAATGTAATTATATATTGCGGGAGAAAATAATAGTCACATTTATGTGTGTCTTTTTTCCGCGGGGGCACATTTTATGTTTTCTTGATTGTGTGGATGTGCAAAACGCCATCTTTTTTCGGAGACAAGCACTTCAACTCCCCCTCTTTTGGGGGGATGGAAAGATATAGATGAGAAATTTTTGGCTGGCTATGACATGCCCGGTTGGAGTTTTGCTCCCCAAAAGTCTTCACATGACCTCACTCCATGGAGTCATGGCAGCTTGGTGCAGTCGATGCCGACGTTGCTCGTGACGAATCATCTTTCTCTCCATGCCTAGATTCCAACACAAATTTCAGGTTCACCTCAACCTCTTCATTCCCCGGATTATGTGCGTGCGATCGAGACAGTTTTCACATGCCCGGATTATGTACCTAGCCAAAAAAATAATAATAACGCTGCGATTTTTCCGCGTTTCGCGATCATCTATGTTGCCTTCGCGTGTGTGTTCATATCAATTTCGCGTGTTCCACTCGCAATCATGCGTGCTGCCTTTGCATATATTCCAATCGAATTCGTGTGTTCCATTCCTAGGATCCAAAGAGGCCCTCCGAGAAGTCCACCTGTCAGCGCGACGATGACGATGACGACACGCCGGCTCTGTAGCAAGTGCCAGGTGCCCGCGCTCCATGGCTTGCAAGGCGATGATGCAGGCAAGAAAAATGAGTCAATAGTAGCAGAGCTTTCTCCTCCCGTGGAGTGCACAGACAGACAATCTTTTGGAAACGGGGAGTTTTTAGATTAGACTTGGCGTGCAAGCGCCGGCGCTCCACATTTTTTTTTTCTTTCAAGATCGCATCAGCTAAACCTAAACGGCCGGTCAAGAACTGACAAAAACACGCCGGCGGTTCACACTAACTAAATCCAAACGTACACTCTCTTTTCCCTTGAGTCAAATCACTAGTTTATCGAACGCCTGCAGTTCTCACCTCGTATACAAATAGCAGATTGTCACCAGACAAGCACGGCGCACATACAACAATATCATATTCTAGTAAAAAAAACAACAACAGGGCAGGCATATACTCCCTCCGTCCAAAAATACTTGTCATCAAAATAGATAAAAGAGATGTATCTAGAACTAAAATATGTCCCATTTTGATGACAAGTATTTCCAGACGGAGGGAGTATATTGTTAGGGTGTTGGAAGAAAAATATCATTGTAGCAGTATTGCTGCCATACCAGCGTATCATGCGCTATACCGTGGCGCGCGACGGGAGCGTGAGGGTTAGGGTTTATCATAGCGGGCTGAGCGTTTCACCGGGGGCCCTCTGTTTTCACAGGCATGGACCGTGTATCAGAATATGTACAATTATTATGCCAAGACATGTAAAAGTAAATAAGGAAAGGAAGAGAATTTCCGCCAGGCGTAACTCTGATTCCCCCGGCTCCTGCGGAAGACGACGACAGCCTCCTCATAGCCTGCAAACAGGGCGAAACGGTCAAATCATTGCAACTCTCTTTTACTTATTATATTAGATAGAAGAAGATGCCGGTATTGCTTAGTCAAACGTGTCGAGAAACTAGCTACATGGAAAGGGTTCGGCGAGTCAGCTAGATGACAAAGTTAGCTACGTTGCAACCCCCTGGACCTCTTCTTCCTTATCCATCAATCAACAAGGCAGATGCTACTTTGTTCATTCATTTTGCTTGCCAGTTTGTCTTTCTTTATTGTGCACAATGAACACAAATGGCAAGGATCAGAAATTCAGTCTCTTTCTACCTACAAGCAATATCCTTTTGCTTATAGCGACGGCCTGCCCTAGCTGCAATGGCAGGCTTGGTATAAAGAACTCGTCATCACTTGTTAATGTATTGAAAAGTGTGGGTGCTGCAGCTTAGGCATTTAATTGGAAGGGTTAGGATATGCTAAATATGTGAAGACTGAAAACTTTCAGAACTAATTTGGCACTAGAAAATGATATGCAAGCAATCAGAAATCAGATGATGCAAGAATGTGCACCTCCTTCAGGAGAGCGGACATAGTCACAGTATATGAGAGGAATTCCGTGTCTTGAACATCAGGATTTACCTTAAGGTGGAAAACAACTTGCGAACTGCTTCAAAGATTTCATCTTCAGTTCCCGTTGCGTTTATCTGCATGGAGTTCAACAAGTACTCTTAGACACCCTAAAGGTCAAGTCTCGAAAATAAATAAGACATCCTACAGATCCTGAATACGAGTGATATACAGAATATGTTACTGTGTTATATCCCTGATATGTACCCCTTCTGAAGAGATTAGCAATCTCTTCCAAAATGAGTGAATTGCAGACACTCATCTAATATCAAATAAATAGGCAGATCTCTGATCTCACTCCCCTCCCCACACCATAGAAAAATGGTCTTACGGTTATATGAATTCAGAACATGAGGGAATCGCATCCTGGCTCTACCCCTCTGTCCTATGACTCCCAGGACATACTATCCTGCTATTTATACTTAGGTGACCCATATGTTTGAGGTTTCTGAAATATATATTGGCATTTGTACATGTTCAAGAGAATAAGCCAGGTATAGTTTAATGCTGCACCTTAAGAGACCTTTTTAATCAACTTCTAGAACAAAGGGTAGAGCTCTGTTTCCGTGTGAAGGAAATAAGAAAATGCATGTCAAAAAGTAAAGGTACGGTTCATAAAAGAAAGGTACAAGAAGTGCTCCTGTCCAGGACACTCTGCGTAAAATAAATAGATTAATTACCTTGTGTGCCTTTCCCCTTGAAGAGTAGTACTCAACAACAGGAAGATTCAAACTCTCGAACACTTTTAGACGCTTCTTGATTGTCTCAATGTTATCATCAACTCGTCCCTAAGACGCATACATGAGATAATCGAAAAAAACAGAAACAAATAGAGAGATCAATTTAATGTGATATATTTTATTTATTATTTTTAAAGGAAACTCCACTAGAGCATTAATGAATCTCCCATTATGATATGCACGAGCTACACTGATGAGATTAGTGTTTCTTCTCTTCAATTTAAATGACATATGAAGAAGAAAGAGCTACACTGATGAGATTAGTGTTTCTTCTCTTCAATTTAGATGACATATGAAGAAGAAAATCATTTGTGGCAATCCACAAGGAATATCCTTTAGGAATGTTAATATTTCATGTTAGTTAAGAGAGAGGGAGTAATAAGAAGATAATTGTCAAAGCCGAAAGTAACGGCTGGGAAATAAAATCTTAGAAAAACACATATCAAGTAAGTTCCGAATAAGAATTGAAAAATGTACAGTACTTATATAGTGTATAAATAGCACAATTTACTCCAGAGATAGTACAAAGACCAACCTGGTTACGGCTTAGGAGACGTTTAACCATCTCATCCTCAGGACAGTCAAAGAAAAGCACAAGGTCTGGTTCAGTTCCAGTCTGAAATTTATTAGTCAACATATCAGAACAGGACCATGCAATCTACATTTATCTGACTAACAATTATTGAGTGGACAACAATGAAACATATCTTAGTTGGTATGCCAGTGTCTTCTTATTGCCCGACCACAGAACACACATTTTCTTTGATATAAATGCTTGTATTAGTTGTTGAGATGCAACCATACATCCACCATAGTGGGGCTAACATAACTGTGGACTACTGCATAAAACCTAAAAGTGCATCACTCTAGAGCAGGACATAGTTATTGATTTGCTACTAAAAAAAATACATACATAAGAAACTGCTGATTGCATACCGTACACTGGCAGTTTTGGGCCAGCATATTGGCATAAAAAATGTAAAGACAAGTGTGTATACACAAATGTTACAGTCACAAGAGCTACAAAACTTGAAGATTCACCTGTTATCAGCCTTCCCGAAAACTGAACAGAAACTGTTGAACATCATGGACTTATCCATCTCATCACATACTATTTCAATTAATAGAAAGTTCTGGACCAGTAATGCAAGCCAAACAGAAAACTTACTATTTTTTCAAAGGCAATTCTGTTTTCCTCACACCTTGGGAAACCATCAATAAGAACCCTTTTAGCAGAGCTTGATTCAATTGCTTTTCTGACAAGCTCAACAGTTATCTCTGATGGAACAATCCTCCCTTCCCTTATTATCTCTAGGATCCACTCCCTGGCAAATGCCATGGCACTGACATATCAATTGACCGAACCATGCATGTGCGTGTGGGTCATTATAAGGCTATATCAGAGGATTGAACGGAAAGAGGTATTACCCATGATCAGTGCCCGAAGATATTTCATTGCGCAGAAGGTCACCAGCACTCACATGAGAAAATCCAAAATCCGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTACATGCAGGATCTTGATTAGATCATGTGAACATTTGAAATTTGAGCGCCACAACACAATCCAACTTGAAACAGCACTTATTGTCATGGGAGGGAAGGGATCCACAGTTTACTCTACACAGGATATGCATGGAATTTATAAATGTGAAACCAACCCTGCAACATTCTGGGAGTAAAAGCAGGGAAGAATTACCTAAGACGAAAGCGATGAACGGCCTGTCACCATCGCTTCCCTACAGAATGAACAGACGGCACATCGCCAAATTATTCACAAGAACTCTGCAAGATTTGTCACAAATAATAAGAATGCAGGCTTGGGAACGAACGTACAGCTAGGGACGTGAAGAGCCTGAGCAGATTCGGGGCCGGCGGTTTCTGCGAAGAGAACAGTCAGGCGGATGAGCATCTAGGAGCGAGAGGAACGTATTGACCCCCAATGGAGCGAGAGAGGCGAGCACGCCAGATCCGGTCCGGCCACGTTGTGCGCGCGTGCGAGGCGTTCGACGAAATGCGCAGGAGGAAAAGGAAAGGGGAACCGTGGGGTTACCTCGGCGTGGGTGGGGAGGAGGAGGTGGTGCTGCTGGTGGTGGCAGGAGGAAGCGACGGCGGAGGAGCACGGGGATCGGAGGAGAAGGGAGCTCAGCCGCCGCCTCAGCATCCCGACGCCGATCGCTCCCGCCTTGCTTGCCGTGCAGGGCAGGACAGAGGAGAAGCAAGGGGGGCTCGCCGTTCACCCCAGCCGCGGGAGGGGCCGAACGGCCGAGGTCGGCGGAGGGAGGGGCGGCGGCGAGCGGCCGTCGACTTGGCGTGGCGGGGAGCGGGGCCGGGACGGGGAGAGTTCGTCGTTTCTTTTCCTTTTCGGAGCTGCTTCTAATCGATGAAAGTGAAAAAAAAATGCCTTTTCCGCTTCGCGTGTCAGGCAGCGTGGAATATCTTGTGCTTTTAGCAAGGGGAAGCATGATGAATTGTCAAAAGCATAAATTGTTAGTATTTTTTATGGGTTGCGATAACTGCCACACGTGTGGCATGGATACGAACCCGCCCACACGCCTCGTGTGGCGTGAACAGGAACCCGCCCGCACGACCGCGTCCGGGCGCGCAATTGCACAGCCCGCACGTCCGGTGTGTGGCAACCCCGTCCGCACTGCTCCATCCGGGCCACACGACCCGCTGCCCGCACGACCCAGCCGTTCCCGTCCTCGCTCGATCGCCTCTCTCGACTGCCGCCATCGTCCCCCACCTCTCAAACACCTACCTCCGTCGCCGGCCTTCTCTGGTTGCCATGGAAACCAAAGCAGATTCGTAGGGCAAACCCACCGCAAACCACACCCCAACCCTCCCCAGCCCCAGCCCCCCACTCCAATCCAGCCCTTCAGAGACGATCAGCTAAAATCAGGTGAAAAATCTCCCGATCTCATCCTTCTCATCCTTCAGGCTGAAAATCTCCCCGATCTTGTACTGGATCCATGCTATAGGGGGCTGGCAACACCAGTAGTTCTGAGATCCAGTAGTTTTGTGATCTACGTGTTGATATTAACTTAAGTTCCTAGTTTGATTGACGCAAGTAGTTGGGTAGGCAAATGGATGAGTAGGAATCCCTGAAAAAAGGAGATGAAGGACAATTTTGGAATAAAGGGGGTGGGAAAAATTAATTGCCACTTGTGTACAACGATAGTTGCCACCTCTCGTTGTCAGTAGCTGCCACCTAGTTGACCTGTTGCTTGCCATCCCTATCTTCTCTGTGCAAGCAGCAGAAGAATACAATTCTTGTGGATTATTGATGCGTTCTTGATCATGCAGTGATTGAGAACATATTGGAAAGAAGCGAGCCACGGAAAGAATGAATCACGAAGATGGAGCTAATACTTGGGTTCTCAAAGGCCAGAAACGCCCCCTTGGGATGCATCAGAGTACAGTCAACTCATCTCTGCAGGGCCTTTGCTGCCACTACTAGAACAGTATACATGCATTGGTATGATGCGTGATAACAAAAATAAGAGAACAGTTGCCATCTTCGTAACGATGAAGATGACATTCTACTTATGTCATGCACTTTCATTTTTTCACAGGTTCTTATGACCAAAACACTCTCAGGGGCCCCCATGGCAAGTTCAGTTACAAGGCGCTAACACTAACAAATGTACGGGCAGCCAACTTCAACTAGCTAATGTGGCTAATCAAGGTAATGCATACGAAAAAAGAGCACATACTGGTGTGGACATGAAAAATGAACATGCAAAAAAATGGCAAAAGGACTCACGAGTTATCACGGGTGAAAAATGCAGAGCCTTCATGCAGCACGTGGCATCAGGCAGCACCCATGTACCTGCCATCGACGTCATACACAGGTGAGTCCATAAAAAGTGAAGTTGCGGATGCTCAATTAGCAGAAGGAACATGGTTGACAATTACACTTGCCATGACTGGACATCTACAATTGCCATGGTTAAATAACTGCAGTTGTCATCCCTGGACAAATGCTGTTGCCATCCATGGACAACTGCAGTTTCCATGGAGGAAGAACTGCAGTTGCCATGCTAGTGTAACTGCAGTTGCCATGCCATGACAACTTCAGTTGCCATGGAGGAACAACTGTAGTTGCCATACGAGTGCAACTACAGTTGCCAAGCCAGGAAAACTGCAGTTGCCACATCAGGGGCAACTAGAGTTTCCGTGCTAGCACAAACTGCATTTTCCATGAATTGACCAACCACTACTATGCTTACAGGTTATTACGGTGGTGGTAACCGGGCAAACGTCTCGTGGCAAGATTCACAAATTGCAGGTGGAGCACGTCATTTTGGTGTCACAGACCACACAAGATGGTCACATGCAGCACAACAAGGTAAAGAAAAAAACTGAACCACAAAACAGCACTACATTTGTTTTGGTGGCAAAAAAAGCACGTGCCGAAAAAAAGAATTGAAGCAGTGATGGTGGACAAGAACGAAGCATAAAACACTGAAAAAGTGGTTGCGTGCAAATGAGTCATGTATTGTCTTTGAAAAATTGCCAACTGCTAAAAGCATGTACGCATCACTAATGGTTGAACACATTTCGCCTAGTGAGATCAATCTTATAATGCAGTAGTTTTGTTGCGAGAACACAGTGGTTGCCATTTGTTGGTTGCAGTGTTTGCCATGAATGCAGGACTGCAGCTGCCATGCATATAGAACCCAAGTTTTCCTACTAAAAAAAGGAGCGTGTTGTCGTGCATTGGCAGACATTGGTTGCCATGTTTGTTGAACTGTACCTGCCATGAATGGACAGCTACATTTGCCACACATGTCCACGCGCGAACTGACATCTTGATGTTCGAATGATGTAATGCCAAATCACTCGATGTTAATGTCATCTGTTGCGATAAACATGTTATTCAAACAAAAAAATCTTACTCTCGTACCTGTTTTTTCCATTACAGGGCCTACAACTACACTGAACAGCGGCACGGGCACATCTACTGCGGGAAGCTCTGAGCGCACAGAAGACGCGTTCCCCCAGCCAGCAAACAATCATGCCGCAAATAATGCCGAGTCAGTGTCAGAAATGGCAATCATTCCAGCAATTCCCACAACCACCCCTTTGAACGCAAGCACTGGCAACATTCAAATCGATGAAACTGCTGCCGATACTGAAGTGAATGATGAAACTGACGACGAGGCACAAGGGGATGAAGATGATGGGCAACCAGATATCATGGTACCTCTGCCACCATACGTTGGGCAAAGATTTGAATCGTTTGAAGAAGCAAAGGAATTCTACCAGACATATGCAAAGTTTCATGGGTTTGCCGTCAACACCGAATACCATAGAAAAATTAAGAAAACTAATGAGTACAACAGAGGTGAGATGTGGTGCCACAAGGTACGAAGGAACAAGAAAGGGAAAGGTGTTGCGCCTGTCGTTCCGAAACGAAAGAGAGGGATCATTCTCAAGACGGGTTGCCCTGTCCGGTGTAAGCTAAACATAGATGGAACACAATATGTGGTCACTGAGTATTTTGACGAGCACAACCACAAACTCATAAAGAAGTTTGATCTGGTCAAATTTCTGACCGCCCACAGAGGGTTCACCCCAGTCGAAAGGCAATTCGTAAAGCTGCTACATGATTGTAACATCGGTCCATCAAGAATGGTCCAGATACTATCACTCATCCAGCAAAAAGGGGAAACTGAGTAGCATGCCGTACATACCAGCTGACGTCACAAACCTACAGGCCAAGTACCATAGAGAGAGCAAG
+>2BS_5163353 11974 190831 503566-,...,5145698-
+ATGTAGTGGTGGTGTGTGAGCGACATTTGAATAGTTTCTGTAATATATGTGTGGATGTGAACCTACTTAGGCGTGACAGCAGATATGTTTTTTATATTTATCATTATTACTGTGGTTTCATCGTTTGTATCACCCGTTTGCTGTTTTGAATGCATCACGATGTTTTAAAACATGGCAAATGTAGTTCATCAGACATGGTTAGCGAAAGTCATCGTCATTGTTCATTTGGACATTTTGCTTCTCCTATTTCATCACTAACTTCACCGGCTAGCATGGTAGGTTGATCATGGAGCCACAACCTTTGATGCGGTTTATGCACATTACGCTTTTTCTAACTTGTTTCCCATATATTGCACACAACACAATATGTGTCACTAAACCGCGTCGATTTTGTCATATAAATATATGCGATGCAGAGTCATTACAAATACCATGGCATATTTTCAGTACAGCTAACATGGCAGATCCAGTACAAACAACACGGCAGATCCAGCATAATTAACATGGCAGATCCAGCATAACTAACATGGCAAATCCAGTACAACTAACATGGCAGATCCAGTGCAACTAGCATTGCATATTTTTCAGTATAAAATAGTATGGCATATTTTTAGTACAAAATAGCATGGCATATTTTTAGTATAAAATAGCATGGCAGATTAACTACATATAACATGGCAGATTAAGTACCCATACCATGGCAAATTAAGTACCCATAACATGGCAGATTAAGTACCAACAATATGGCAACTACATTTACCCATTCAATGCATTCTCCTTCAACTTCTGAAGCCCCTCTAGAGTCATTATCCCAAATCAAAAAAGTTCACAGCATATAGGGTACAAAACAAATGTCCACAATGACCATGTCACAGTGCCCCAACTTTTGCTTACGGATTGCCCGTCCCTTTCTTCGTTTTCTTGTGTTTTGCTTGAATCTCCAATCCCGATTTTTACCTTATCTCTCTTGGACGACCCTTTGTGATGGAACGGGGTGGGTTCCTGACCTGGGTTTGTGTGCTTGCTGTTCCAGATCCTATCTCAGAGTTTTCAAATGATGGCCCCATGGATGAAGGCACACTTGATGTGCGGGGGAACCGGTGTAAGGCTTCCTCAGCTTTCCTCTTCTTGATCTCATCAAGCTCTCTTTTCAGGGCCTTCCTGTGTTTTTCTGCGACTCTCGTTGTCTCATCACTCTTGCACGCTTCATCAATTAGCTCAGCATAGTTCTTTGTCAACACAACATGCCTCACGGCTTCCATGGTTGCCTCAGGTCTCTCGTCATGCACAGCCAGAACTGCATTTGTTGTCTGCGGCGCAAACGCGTCGTCAGCGTCCCAAGTCCATCGCCACCTTATGAAATGGCGGGGCATGCGTGTCACAGCGTTCTCCATTACTTTCAGTATGTGACAACACACAATGTCGTCCCGTTCAAACTTGCAGCATTGGCAGTAGTATTGCCTTGTTCGATTGAGGCTTTCACGAAGTAGTTCCTTCCTTTGTCCGGGTCTTCAGGTTCTGAATCCGACATGCCCAAAATAGAACACACCTTGAACGTATGTTCGTCCGCCTGGAAAGCCGTGAACATGCTGGCACGCTTTATTTCTTCCTTGAATCTGCAAGTTTTGTGTGTTTTCTATTAAACTATCGTGTGATCTTTTTTTGTAGCATCTTATGTTGTCATGGAAATAGAAATAGATTTTTGTTTGAACATGGCAAACATAGTATACTAAACATGGCAAACATAGTGCACTAAACATGGCAAACATAGTACACTGAACATGGCAACTGCAGTAAACTATACAAGGCAACTGTATTGCATTTTCAACTGACCATTGTCATTTCCACACCAACACTCCTCACTGGAAGCCCTTTGCATAAAACATGGCAACTGAATTTTTATTGAACATGGCATCTACAGTTGAGTAAACATGGCAACTGCATTTTTCAACAAACATGGAAGTTTTGCATTTTTAGAAAACATGGCAACTGCATTTCATCAAATGTGTCTAGAATATAACGTTTTTCAGTTGACATTGGCATTTGCATACCAACATGCCCCAATGGCAGTACAGTGCATTAAACATGGCAACTGCACTTCATTAAACATGACAAACAAATTTTTCATTAAACATGGCAACTGCAATTGAGTAAGCATGGCAAACAGTATTTCATTACACATGGCAACTGCATATCATGGCAACTGCATTGCACCCTATAAGGCACCTACTGCCTTAGTGCTTTTTTTGCAAATAAGACTGTAATGCAACTGACTTACTTGTTAAAGATCTTGTTTGTGTATATCTTGCTCATTTGCCTCTCCATCGGTAAATACGTTAGCAATTTTGGCTGCTTTAGCGCGGTGGTAGCTTCTTGCTGCAGCTCAGATCCCAGAATTTTTTGTTGCAAAGCTGTGTACTGCTTGACAAACTGTAGCAATGAGTTGCCAGGGCTCACGTACCGCTTCAAAACAGCATTGAACCCCTCGCTGCACTGCGTAGTCTGCAGAAAGGGAAAGAAGCACTGCATGAAGTAGACTGGCACCCAGTACATTCGCTTCTCCCACAGGTTAGCAAGCATCTTGTTGTCTTGGACTTGATATGTTTCAATCATGGCCATCCAGCTCCTTTCAAACTCCTCCACCGTCAAGTTGTGGTCCATGCACAGCTCGAACGCCTTGTGGAGCTCTGGACGGTCAGCAAAGAACGGTCCTAGCGTCTCTTCAGCCCTCTTTATAATGTGCCACCTGCAGTGCCTGTGCACTGCCAACGGAAATACCTCCTATATGCCTGCACGCATGCTGAAATCCTGGTCTGTTATTATGTTCATCGGAGCAAGTCCATCCATGCACTCCAAGAAGGTCTTGAACAACCAAACGTACCCATCCGTGTCTTCGTTCCGAACGAGCCCGCAGCCGAACTGCAATGACTGATTGTGGTTATTTATTCCTATGAACGGAGCGCATGGCATCTTGTACATATTAGTCAGATACATCGCGTCGAATGAAATGCAATCTCGAAAATGTTTGTAGGCTCTCCTTGCAGCACCATCCACCCAATACATGTTCCTGACACGGTCCTCATCGTCCAATCTTATCCTGTAGAAGAAATCTGGATCTTCCTTCGCTTTCTCATCGAAGTAGGCCATTGTGACCTCTATGTCAGCAAGCTTGCTCTCTCTATGGTACTTGGCCTGTAGGTTTGTGACGTCAGCTGGTATGTACGGCATGCTACTCAGTTTCCCCTTTTTGCTGGATGAGTGATAGTATCTGGACCATTCTTGATGGACCGATGTTACAATCATGTAGCAGCTTTACGAATTGCCTTTCGACTGGGGTGAACCCTCTGTGGGCGGTCAGAAATTTGACCAGATCAAACTTCTTTATGAGTTTGTGGTTGTGCTCGTCAAAATACTCAGTGACCACATATTGTGTTCCATCTATGTTTAGCTTACACCGGACAGGGCAACCCGTCTTGAGAATGATCCCTCTCTTTCGTTTCGGAACGACAGGCGCAACACCTTTCCCTTTCTTGTTCCTTCGTACCTTGTGGCACCACATCTCACCTCTGTTGTACTCATTAGTTTTCTTAATTTTTCTATGGTATTCGGTGTTGACGGCAAACCCATGAAACTTTGCATATGTCTGGTAGAATTCCTTTGCTTCTGCAAACGATTCAAATCTTTGCCCAACATATGGTGGCTGAGGTACCATGATATCTGGTTGCCCATCATCTTCATCCCCTTATGCCTCGTCGTCAGTTTCATCATTCATTTCAGTATCGGCAGCAGTTTCATCGATTCAAAGGGGTGGCTGTGGGAATTGCTGGAATGATTGCCATTTCTGACACTGACTCGGCATTATTTGCGGCATGATTGTCTGCTGGCTGGGGGAACGCGTCTTCTGTGCGCTCAGAGCTTCCCGCAGTAGATGTGCCCGCGCCGCTGTTCACTGTAGTTGTAGGCCCTGTAATGGAAAAAACAGGTACGGGAGTAAGATTTTTTGTTTGAATAACATGTTTATCGCAACGGATGACATTAACGTCGAGTGATTTGGCATTACATCATTCGAATAGCAAGATGTCAGTTTGCGCGTGGACATGTGTAGCAAATGTAGCTGTCTAGTCATGGCAGTTACAGTTCAACAAACATGGCAACCACTGTTTGCCAATGCACGACAACAAGCTCCTTTTTTTAGTACGAAGACTTGGGTTCTATATGCATGGCAGCTGCAGTCCTGCATTCATGCAAACACTGCTACCAACAAATGGCAATCACTGTGTTCTAGCAACAAAACTACTGCATTATAAGATTGATCTCACTAGGCGAAATGTGTTCAACCATTAGTGATGCATACATGCTTTTAGCAGTTGGCAATTTTTCAAAGACAATACATGACTCATTTTGCACGCAACCACTTTTCAGTGTTTTATGCTTCGTTCTTGTCCACCATCACTGCTTCAATTCTTTTTTTGGCACGTGCTTTTTTTTGCCACCAAAACAAATGTAGTGCTGTTTTGTGGTTCAGTTTTTTTCCTTACCTTGTTGTGCTGCATGTGACCATCTTGTGTGGTCTGTGACACCAAAATGACGTGCTCCACCTGCAATTTGTGAATCTTGCCACGAGACGTTTGCCCGGTTACCACCACTGTAATAACGTGTAAGCATAGTAGTGGTTGGTCAATTCATGGCAAATGCAGTTTGTGCTAGCACGGGAACTGTAGTTGCCCCTGATGTGGCAACTGCAATTTTCCTGGCATGGCAACTGTAGTTGCATTGGTATGGCAACTGCAGTTGTTCCTCCATGGCAACTACAATTGTCATGGCATAACAACTGCAGTTACACTGGCATGGCAACTGCAGTTCTTCCTCCGTGGCAACTGCGGTTGTCCATAGATGGCAACAACAGTTGTCCAGGGATGACAACTGCAGTTATTTAACCATGTCAATTGTAGATGTCCAGTCATGGAAAGTGCAATTGTCAACCATGCTCCTTCTGCTAATTGAGCATCCGCAACTTCACTTTTTTATGGACTCACCTGTGTATGACGTCGATGGCAGGTACATGGGTGCTGCCTGATGCCACGTGCTGCATGAAGGCTCTGCATTTTTCACCCCTGATAACTCGTGAGTCCTTTTGCCATTTTTTTGCATGTTCATTTTTCATGTCCACACCAATATGTGCTCTTTTTTCGTATGCATTACCTTGATTAGCCATATTAGCTAGTTGAAGTTGGCTACCCGTACATTTGTCAGTGTTAGCGCCTTGTGACTGAACTTGCCACGGGGGCCCCCTGAGAGTGTTTTGGTCATAAGAACCTGCGAAAAAAATGACAATGCATGACATAAGTAGAATGTCATCTTCATCGTTACGAAGATGGCAACTGTTCTCTTCTTTTTGTTATCACGCGTCATACCAATGTCTGCATATTGTTCTAGTAGTGGCAGCAACGGCCCTGCAGAGATGAGTTGACTGTACTCTGATGCATCCCAAGGGGGCGTTTCTGGCCTTTGAGAACCCCAAGTATCAGCGCCATCTTTGTGATTCATTCTTTCCGTGTCTCACTTCTTTCCAATATGTTCTCAATCACTGCATGATCAAGAACGCATCAACAATCCACAAGAATTGTATTCTTCTGCTGCTTGCAGATAGGGATGGCAAGCAACAGGTCAACTAGGTGGCAGCTATTGACAACGAAAGGTGGCAACTGTCGTTGTACACAAGTGGCAATTAATTTTTCCCACCCCCTTTATTCCAAAATTGTCCTTCCTCTCCTTTTTTAGGGATTCCTACTCATCCATTTGCCTACCCAACTACTTGTGTCAATCAAACTAGGAACTTAAGTTAATCTCAACACGTAGATCACAAAACTACTGGATCTCAGAACTACTGGTGTTGCCACCCCCTATAGCATGGATCCAGTACAAGATCGGGGAGATTTTCAGCCTGAAGGATGAGAAGGATGAGATCGGGAGATTTTTCACCTGATTTTAGCTGATCGTCTCTGAAGGGCTGGATTGGAGTGGGGGGCTGGGGCTGGGGAGGGTTGGGGTGTGGTTTGCGGTGGGTTTGCCCTACGAATCTGCTTTGGTTTCCATGGCAACCAGAGAAGGCCGGCGACGGAGGTAGGTGTTTGAGAGGTGGGGGACGATGGCGGCAGTCGAGAGAGGCGATCGAGCGAGGACGGGAACGGCTGGGTCGTGCGGGCAGCGGGTCGTGTGGCCCGGATGGAGCAGTGCGGACGGGGTTGCCACACACCGGACGTGCGGGCTGTGCAATTGCGCGCCCGGACGCGGTCGTGCGGGCGGGTTCCTGTTCACGCCACACGAGGCGTGTGGGCGGGTTCGTATCCATGCCACACGTGTGGCAGTTATCGCAACCCATAAAAAATACTAACAATTTATGCTTTTGACAATTCATCATGCTTCCCCTTGCTAAAAGCACAAGATATTCCACGCTGCCTGACACGCGAAGCGGAAAAGGCATTTTTTTTTCACTTTCATCGATTAGAAGCAGCTCCGAAAAGGAAAAGAAACGACGAACTCTCCCCGTCCCGGCCCCGCTCCCCGCCACGCCAAGTCGACGGCCGCTCGCCGCCGCCCCTCCCTCCGCCGACCTCGGCCGTTCGGCCCCTCCCGCGGCTGGGGTGAACGGCGAGCCCCCCTTGCTTCTCCTCTGTCCTGCCCTGCACGGCAAGCAAGGCGGGAGCGATCGGCGTCGGGATGCTGAGGCGGCGGCTGAGCTCCCTTCTCCTCCGATCCCCGTGCTCCTCCGCCGTCGCTTCCTCCTGCCACCACCAGCAGCACCACCTCCTCCTCCCCACCCACGCCGAGGTAACCCCACGGTTCCCCTTTCCTTTTCCTCCTGCGCATTTCGTCGAACGCCTCGCACGCGCGCACAACGTGGCCGGACCGGATCTGGCGTGCTCGCCTCTCTCGCTCCATTGGGGGTCAATACGTTCCTCTCGCTCCTAGATGCTCATCCGCCTGACTGTTCTCTTCGCAGAAACCGCCGGCCCCGAATCTGCTCAGGCTCTTCACGTCCCTAGCTGTACGTTCGTTCCCAAGCCTGCATTCTTATTATTTGTGACAAATCTTGCAGAGTTCTTGTGAATAATTTGGCGATGTGCCGTCTGTTCATTCTGTAGGGAAGCGATGGTGACAGGCCGTTCATCGCTTTCGTCTTAGGTAATTCTTCCCTGCTTTTACTCCCAGAATGTTGCAGGGTTGGTTTCACATTTATAAATTCCATGCATATCCTGTGTAGAGTAAACTGTGGATCCCTTCCCTCCCATGACAATAAGTGCTGTTTCAAGTTGGATTGTGTTGTGGCGCTCAAATTTCAAATGTTCACATGATCTAATCAAGATCCTGCATGTAGGGGGACCTGGGAGTGGGAAAGGAACGCAATGTAGTAGGATCGCTTCGGATTTTGGATTTTCTCATGTGAGTGCTGGTGACCTTCTGCGCAATGAAATATCTTCGGGCACTGATCATGGGTAATACCTCTTTCCGTTCAATCCTCTGATATAGCCTTATAATGACCCACACGCACATGCATGGTTCGGTCAATTGATATGTCAGTGCCATGGCATTTGCCAGGGAGTGGATCCTAGAGATAATAAGGGAAGGGAGGATTGTTCCATCAGAGATAACTGTTGAGCTTGTCAGAAAAGCAATTGAATCAAGCTCTGCTAAAAGGGTTCTTATTGATGGTTTCCCAAGGTGTGAGGAAAACAGAATTGCCTTTGAAAAAATAGTAAGTTTTCTGTTTGGCTTGCATTACTGGTCCAGAACTTTCTATTAATTGAAATAGTATGTGATGAGATGGATAAGTCCATGATGTTCAACAGTTTCTGTTCAGTTTTCGGGAAGGCTGATAACAGGTGAATCTTCAAGTTTTGTAGCTCTTGTGACTGTAACATTTGTGTATACACACTTGTCTTTACATTTTTTATGCCAATATGCTGGCCCAAAACTGCCAGTGTACGGTATGCAATCAGCAGTTTCTTATGTATGTATTTTTTTTAGTAGCAAATCAATAACTATGTCCTGCTCTAGAGTGATGCACTTTTAGGTTTTATGCAGTAGTCCACAGTTATGTTAGCCCCACTATGGTGGATGTATGGTTGCATCTCAACAACTAATACAAGCATTTATATCAAAGAAAATGTGTGTTCTGTGGTCGGGCAATAAGAAGACACTGGCATACCAACTAAGATATGTTTCATTGTTGTCCACTCAATAATTGTTAGTCAGATAAATGTAGATTGCATGGTCCTGTTCTGATATGTTGACTAATAAATTTCAGACTGGAACTGAACCAGACCTTGTGCTTTTCTTTGACTGTCCTGAGGATGAGATGGTTAAACGTCTCCTAAGCCGTAACCAGGTTGGTCTTTGTACTATCTCTGGAGTAAATTGTGCTATTTATACACTATATAAGTACTGTACATTTTTCAATTCTTATTCGGAACTTACTTGATATGTGTTTTTCTAAGATTTTATTTCCCAGCCGTTACTTTCGGCTTTGACAATTATCTTCTTATTACTCCCTCTCTCTTAACTAACATGAAATATTAACATTCCTAAAGGATATTCCTTGTGGATTGCCACAAATGATTTTCTTCTTCATATGTCATCTAAATTGAAGAGAAGAAACACTAATCTCATCAGTGTAGCTCTTTCTTCTTCATATGTCATTTAAATTGAAGAGAAGAAACACTAATCTCATCAGTGTAGCTCGTGCATATCATAATGGGAGATTCATTAATGCTCTAGTGGAGTTTCCTTTAAAAATAATAAATAAAATATATCACATTAAATTGATCTCTCTATTTGTTTCTGTTTTTTTCGATTATCTCATGTATGCGTCTTAGGGACGAGTTGATGATAACATTGAGACAATCAAGAAGCGTCTAAAAGTGTTCGAGAGTTTGAATCTTCCTGTTGTTGAGTACTACTCTTCAAGGGGAAAGGCACACAAGGTAATTAATCTATTTATTTTACGCAGAGTGTCCTGGACAGGAGCACTTCTTGTACCTTTCTTTTATGAACCGTACCTTTACTTTTTGACATGCATTTTCTTATTTCCTTCACACGGAAACAGAGCTCTACCCTTTGTTCTAGAAGTTGATTAAAAAGGTCTCTTAAGGTGCAGCATTAAACTATACCTGGCTTATTCTCTTGAACATGTACAAATGCCAATATATATTTCAGAAACCTCAAACATATGGGTCACCTAAGTATAAATAGCAGGATAGTATGTCCTGGGAGTCATAGGACAGAGGGGTAGAGCCAGGATGCGATTCCCTCATGTTCTGAATTCATATAACCGTAAGACCATTTTTCTATGGTGTGGGGAGGGGAGTGAGATCAGAGATCTGCCTATTTATTTGATATTAGATGAGTGTCTGCAATTCACTCATTTTGGAAGAGATTGCTAATCTCTTCAGAAGGGGTACATATCAGGGATATAACACAGTAACATATTCTGTATATCACTCGTATTCAGGATCTGTAGGATGTCTTATTTATTTTCGAGACTTGACCTTTAGGGTGTCTAAGAGTACTTGTTGAACTCCATGCAGATAAACGCAACGGGAACTGAAGATGAAATCTTTGAAGCAGTTCGCAAGTTGTTTTCCACCTTAAGGTAAATCCTGATGTTCAAGACACGGAATTCCTCTCATATACTGTGACTATGTCCGCTCTCCTGAAGGAGGTGCACATTCTTGCATCATCTGATTTCTGATTGCTTGCATATCATTTTCTAGTGCCAAATTAGTTCTGAAAGTTTTCAGTCTTCACATATTTAGCATATCCTAACCCTTCCAATTAAATGCCTAAGCTGCAGCACCCACACTTTTCAATACATTAACAAGTGATGACGAGTTCTTTATACCAAGCCTGCCATTGCAGCTAGGGCAGGCCGTCGCTATAAGCAAAAGGATATTGCTTGTAGGTAGAAAGAGACTGAATTTCTGATCCTTGCCATTTGTGTTCATTGTGCACAATAAAGAAAGACAAACTGGCAAGCAAAATGAATGAACAAAGTAGCATCTGCCTTGTTGATTGATGGATAAGGAAGAAGAGGTCCAGGGGGTTGCAACGTAGCTAACTTTGTCATCTAGCTGACTCGCCGAACCCTTTCCATGTAGCTAGTTTCTCGACACGTTTGACTAAGCAATACCGGCATCTTCTTCTATCTAATATAATAAGTAAAAGAGAGTTGCAATGATTTGACCGTTTCGCCCTGTTTGCAGGCTATGAGGAGGCTGTCGTCGTCTTCCGCAGGAGCCGGGGGAATCAGAGTTACGCCTGGCGGAAATTCTCTTCCTTTCCTTATTTACTTTTACATGTCTTGGCATAATAATTGTACATATTCTGATACACGGTCCATGCCTGTGAAAACAGAGGGCCCCCGGTGAAACGCTCAGCCCGCTATGATAAACCCTAACCCTCACGCTCCCGTCGCGCGCCACGGTATAGCGCATGATACGCTGGTATGGCAGCAATACTGCTACAATGATATTTTTCTTCCAACACCCTAACAATATACTCCCTCCGTCTGGAAATACTTGTCATCAAAATGGGACATATTTTAGTTCTAGATACATCTCTTTTATCTATTTTGATGACAAGTATTTTTGGACGGAGGGAGTATATGCCTGCCCTGTTGTTGTTTTTTTTACTAGAATATGATATTGTTGTATGTGCGCCGTGCTTGTCTGGTGACAATCTGCTATTTGTATACGAGGTGAGAACTGCAGGCGTTCGATAAACTAGTGATTTGACTCAAGGGAAAAGAGAGTGTACGTTTGGATTTAGTTAGTGTGAACCGCCGGCGTGTTTTTGTCAGTTCTTGACCGGCCGTTTAGGTTTAGCTGATGCGATCTTGAAAGAAAAAAAAAATGTGGAGCGCCGGCGCTTGCACGCCAAGTCTAATCTAAAAACTCCCCGTTTCCAAAAGATTGTCTGTCTGTGCACTCCACGGGAGGAGAAAGCTCTGCTACTATTGACTCATTTTTCTTGCCTGCATCATCGCCTTGCAAGCCATGGAGCGCGGGCACCTGGCACTTGCTACAGAGCCGGCGTGTCGTCATCGTCATCGTCGCGCTGACAGGTGGACTTCTCGGAGGGCCTCTTTGGATCCTAGGAATGGAACACACGAATTCGATTGGAATATATGCAAAGGCAGCACGCATGATTGCGAGTGGAACACGCGAAATTGATATGAACACACACGCGAAGGCAACATAGATGATCGCGAAACGCGGAAAAATCGCAGCGTTATTATTATTTTTTTGGCTAGGTACATAATCCGGGCATGTGAAAACTGTCTCGATCGCACGCACATAATCCGGGGAATGAAGAGGTTGAGGTGAACCTGAAATTTGTGTTGGAATCTAGGCATGGAGAGAAAGATGATTCGTCACGAGCAACGTCGGCATCGACTGCACCAAGCTGCCATGACTCCATGGAGTGAGGTCATGTGAAGACTTTTGGGGAGCAAAACTCCAACCGGGCATGTCATAGCCAGCCAAAAATTTCTCATCTATATCTTTCCATCCCCCCAAAAGAGGGGGAGTTGAAGTGCTTGTCTCCGAAAAAAGATGGCGTTTTGCACATCCACACAATCAAGAAAACATAAAATGTGCCCCCGCGGAAAAAAGACACACATAAATGTGACTATTATTTTCTCCCGCAATATATAATTACATTATAGTCCCTTCGTCCCAGAATAAGTGTCTTGAGCTTAGTACAAATTTATACTAGAGCTAGTACAAAGTTGAGTCACTTATTTTGAGACGGAGGGAGTAGAACCTAGCAGAATGTATGAATGTACATTTTAGGCAAATCTATAGACAGAGATCTTCACACTTGTAATGAAGACTTTTGAAAGGGAAAAATGGGTTCAAACTTGACCAAAACTACATCCGGAACTTCATGAATGTGTGAATTGGAGGCAGTGGCG
+>2DS_5334799 7226 338754 1380402+,...,2126614-
+GCGACACCTGGACCAGCGGCGAGTTGTACCGCAGGCCGGGGCCGGGCGGCGCCTCCGTCCCCTGCTCCTGCTCCTGCGGGGACCCGGCCTCCGGCAGCTCCGTCGACACGGCCATTTCGTCACTCTGAACGGGCGGGCCGGCGGAGGGGAGTGAGGACGGCAGGTGGGTGGGTGGAGACAAATCGGCGGAGACGAAGGCGAGGTGGAAGACGATCGGCGGAGGTGGCGGTATTTATAGATGGGATCTTGGTGGCTCCTCTGTTTGATTCTGTTGCCAAGGGGGAGAAAGAGACGGCGACATTGAGGACGAGCAGAGGGCGACATTTGGAGCATCATTAGTCAGTGATGATTGCATTTAATCAGTATATTTGGGAATTTAATTACTGCCCATTTATCAGTTCAGATATGTACATCGTCTTTAATGTGGATATTTATTTGAGGGAGTAATAAGCAAAGATTGTTACAGAGTTTTTCCTTTTTTTTTTGAAATTTTCGAAAATATGTTCGACGTGGCAAAAAAAAAGACCGTAATAGCTGGCGAACGTTCGTTGTGAGGGGTGGTATTGCGAACATTTTTGCTGACAGTTTTTTCAGAGACACATGACAATTTTTTTAGATACGCATGACGGTTTCTGGAAAGAAGACTGCGGCAAAAACAAGCAGAATTAGCCATCTCCTACCACCTAAAAATGCCTTAAGAAATTGTTCGCTTGTCACCCTCCTCCCAGGAAACGTTCGCTTGTTAGTATTTTTGAAAGAAAAGGGCCCCACTCAAATTTTGGATCTTTTTGTTTCCATTCATTCGTTTTGGAGCGGTGTAGGGGAGACAGACGAATTTTGAAGATAGAATTTGTGACATTTGGTTTGGAGCATCATCATCATCGCCAATTGGAATGCACACTGAATTAAATTTTGCGAGATATGGCATTCTATTTTCATAAGTTCTTATTACAAATCATCATGATCTCCATAACACATACGCGAGTTGGAAGGAGATTTGTGCACACACGAGATGAGCCGACAGAGATGAGAAGGGGTGAAAGATAGGAGAGTCGAATATGCCGATTTGAAGAATCACCAAACTACATATAGTAAACAATTATTAATTTTCATGAGGGATATTCCGGCATTTTAACAATGGTTGCTAGGTACTAAGGATTTCTTTTCTGTGGGACTTGGCAGTCCTTCCACTCAATTTGTTCAACACACAAGTGGGTATATATATGGCAGATACGGTATAATATAAGACACAAAGGCACAGAAGAGGATTTGTGGCTCTCGGGTGCCACGCACCCCTATATGAATATAGCATTAAAAACATATTGCAAATTTTAAAAAATTCTAAAATTTTGGAATATGAACCTGGGTGCCTGTTGTACACTCGTCTTCAACTTCGTGGGGAATGAGTGCCCGTGTTCATCTCAGTAAAAAGGACAAAAAAAATCGTATGTATAGAAAAAGATAATTGGATGTAATGTATGTCAGACCGGAACTCCAGTGCCATGGATACCACGGGCAACCATTCCCAGCGAAAATGAAACAAGTGTGCAATCAATGGTCACCTAGGTTTGATATCCTAAAATATCTGATTTTTGTGAAATTTTCTGATATTTTCTTAATGCTAGTTTCATATAGGGGTACGTGACACTCGGGTGCTCCAATGCATTTCCCACAAGGGCACACGACCTTATCCCTGTCAAAAGACTCATCCTACATTGATAAATATGACTTGGCAGTGGGGCCAGCAACAGCAAGATGAGCGTCCCAACATCCCCTTGTTCTTTCTTTGGAGGATCGATGTTCCTCCATCCAACATTGCTTGGTTGATTGCCACAAGGACGCAGGGCTGAGATTCTCGGTCCTGGGATTTTGGAATTTTGCTCGCAACTTGCAGCGCAGCTGCGTCCCTGTCCTTCCTAGTGAATCACCTTCGCCCGTTGTTTGGGGCATAGGACAAATACACCCAGCTAATCATAGATTCATAGGGAGGGGGTCATAATCCTGGCTAGCTTTCACCGTTAGCGGCAGCTAGCTGGTTAATCATGCAGGCTCACACGAGGCTAGCGGCCCCCTAGTAGAGTCCAAAATGGACCTTTCCTCTGTTTTACCATCTCCGTCTGAGAAAGTGACAAGATGTGGCATCTTAGTAGTTGTTGTTAACTGCAGAATGCTCCCACCATGAAACCTTTGATTTTCATTCTAAAAGGACACCTTCGATTTTCCGAAAAAATGACATTGCGATATTTCCTCCCTTTGCGAAAGTGGGGGCGATTTGGGGATGTGTTCGTAGGATCAGCAGAGTGCGAGTGTCCTCACTACTTAGTGGACTAGGAACACCAATTACCATTCAGCATGGATGGTGGGCTATCTCAAAAACAATGAACAAAGACTAGGAACACCAATTTTTAGGAGTGTCAGCTAGCTGGTTAATCATGCAGGCCAACACGAGGTTAGGAGCTCCCTAGAGTCTAGAATAGATCATTTTCTCCGTTTCACTACCTTTATCTCACAACACAAAACATTTTTAAGAGTCGTAATGATCGGAAGACGAATGCCACACATGACACCCTTGTTTTTCCTTGCGAAATACACATGACATTCGAGCCCCCCTCCAACTCACACATTAATGAAGTTCCAGGTATAGTTTTGGTCAAGTTTGAACCCATTTTTCCCTTTCAAAAGTCTTCATTACACGTGTAAAGATCAGTATCTATAGATTGTCTAAAATATACTCGTAAAGAAATATAAGAGCGTTACAGAGGGAGCACATTCATATATTCTGTTAGGTTTTATAGTTATATATCGTGGTAGAAAGTAATAGTCACATTTATGTGTGTGTTTTTTTGTTGCGGGGGCACATTTATGTTTTCTTGATTGTGTGGATGTGCAAAACACCATCTTTTTTGGAGACAAACACTTCAACTTCCCCTCTTTTTGGGGGATGGAAAGATATAAATGAGAAATTTTTGGCTGGCTATGACATGCCCGGATGAAGGCCCCGTTGGAGTTTTGCTCCTCAAAAGTCTTCACATGACCTCACGCCATGGACTCATGGTAGCTTGGTCCAGTCGATGCCGACGTTGCTCATGATGAATCATCTTTTTCTCCATGCCTAGATTCCAACACAAATTTCAGGTTCACCTCAACCTCTTCATTCCCCGGATTATGTGCGTGCGATCGAGACAGTTTTCACAAAAAAATGTTGCGATATTTCCGCGTATTGCCTTTGCATATATTCCAATCGAATTCATGGGTTCCTTTCCTATGATCCAAGGAGGCCCTCAGGGAAGTCCACCTGTCAGCGCGACGACGACGACGATGATGCGCCGGCTCTGTAGCAAGTGCCAGGTGTCCACGCTCCATGGCTTGCAAGGCGATGATGCAGGCAAGATAAATGAATAGCACAAGTCAACAGTAGCAGAGCTTTCTCCTCCCGTGGAGTGCATAGACAAACAATCTTTTGGAGATGGTGAGTTTTCAGATTAGACTTCGCGTGCAAGCGCCGGCGCTCCACACTTTTGTTTCAAGATCGCATCAGCTACTAAACGGCCGGTCAACAACTGACAAAAACACGCCGGCAGTTCACATTAACTAAATCCAAACGTACACTGCTTTTTTCCTTCAGTCAAATCACTAGTTTATCGGACGCCTGCAGTTCTCACCTCTTATCTGAGAATAGATATATACAAATAGCAAATCGTCACCAGGCAAGCACGGCGCACATACAATTATATCATATTCTGGTAAGAAAAATATCGTCGTAGCAGTTTTGCTGCTGCCATACCAGCGTGTCATGGGTTATACCGTGGCGCACGACGAGAGCGTGAGGGTAAGGGTTTATCATAGCAGGCTGGGCGTTTCACCAGTGGCCCTCTGTTTTCACAGGCATAGACCGTGTATCAGAATATGTACAATTATTGTGCTAAGAGATGTAAAAGTAAAAGGAAAGAAAAGAGTATTTCCGCCAGGCGCAATTCTAATTCCCTCAGGCTCCTGCGGAAGACGACGACAGCCTCCTCATAGCCTGCAAACAGGGCGAAACGGTCAAATGATTGCAACTCTCTTTTGTACAGGTAGTGCATCTTCATTAGAAGAAGATGCTGGTATTGCTTAGTCAAACGTGTCAAGAAACTAGCTACAGGCGAGGGTTCGGCGACTCAGCAAGATGACAAAGTTCGCAACGTAGCATCCTCCCGGACCTCTTCTCCCTTATCCATCAATCAACAAGACAAATGCTACTCTGCTCATTTTGCTTGTCAGTTTGTCTTTCTTTATTGTGCGCAGTGAACACAAATGGCGAAGATTCAGAAATTCAATCCCTTGCCACCTACGTACAAGCAATACCCTTTTGCTTATAAATGTCCTACCCTGGCTGCAACGGCAGGCTTAGTATAAAAGAACTTGCCGTCACTTGTTAATGTATTGAAAAGTGTGGGTGCTGCAACTTGGGCATTTAATTGGAAGGGTTGGGATATGCTAAATATGTGAGGACTGAAAAGCTTTCAGAACTTCAGTAATTGGGACTAGAAAATGATATGCAAGCAATCAGAAATCAGATAATGCAAGAATGTGCACCTCCTTCAGGAGAGCGGACATAGTCACAGAATATGAGAGGAGTCTCGTGTCTTAAGCATCAGGATTTACCTTAAGGAGGAAAACAACTTGCGAACTGCTTCAAAGATTTCATCTTCAGTTCCCGTTGCGTTTATCTGCATGGAGATCAACAAGTAGTCTTAGACACCCTAAAGGTCAAGTCTCGAAAATAAATAAGACATCCTACAGATCCTGAATATGAGTGATATACAGAATATGTTACTATGTTATATCCCTGATATGTACCCCTTCTGAAGAGATTAGCAATCTCTTCCAAGATGAGTGAATTACAGACACTCATCTAATATCAAATAAATAGGCAGATCTCTGATCTCACTCCCCTCCCCACAACATAGAAAAATGGTCTTACGGTTATATGAATTCAGAACACGAGGGAATCGCATCCTGGCTCTGCCTCTCTGTCCTATGATTCCCTGGAAACACTATCCTGCTATTTATACATTGGTAACCCATATGTTTGATGTTTCTGAAATATATATTGGCATTTGTAAAAGTTCAAGAAAATAAGCCAGGTATAGTTTAATGCTGCACATTAAGAAGCCTTTTAAATCAACTTCTAGAATAAAGGGTAGAGCTCTGTTTCCGTGTAAAGGAAATAGGAAAATGCACGTCAAAAAAGTAAAGGTACGGTTCATAAAAGAAAGGTACAAGAAGTGCTCCTGTCCAGGACACTCTGCGTAAAATAAATAGATTAATTACCTTGTGTGCCTTTCCCCTTGAAGAGTAGTACTCAACAACAGGAAGATTCAAACTCTCGAACACTTTTAGACGCTTCTTGATTGTCTCAATGTTATCATCAACTCGTCCCTAAGACGCATGCATGAGATAATCGAAAAAACAGAAACAAATAGAGAGATCAATTTAATGTGATATATTTTATTATTATTTTTAAAGGAAACTCCACTAGAGCATTAATCAACCTCCCATTATGATATGCACGAACTACACTGATGAGATTAGTGTTTCTTCTCTTCAATTTAAATGACATATGAAGAAGAAAATCATTTGTGGCAAACCACAAGGACTATCCTTTAGGAATGCTATATTTCATGTTAGTTAAGAGAGAGGGAGTAATAAGAAGATGATTGTCAAAGCCGAAAGTAACGGCTGGGAAATTAAGTCTTAGAAAAACACATATCGAGTAAGTTTCGAATAAGCATTGGGAAATGTACAATACTTATATAGTGTATATATATCTAGCACAATTTACTCCAGAGATAGTACAACGACCAACCTGGTTACGGCTTAGGAGACGTTTAACCATCTCATCCTCAGGACAGTCAAAGAAAAGCACAAGGTCTGGTTCAGTTCCAGTCTGAAATTTATTCATCAACATATCAGAACAGGACCATGCAATCTACATTTATCTGACTAGCAATTATTGAGCGGACAACAATGAAACATATCTTAGTTGGTATGCCAGTGTCTTCTTATTGCTTGACCACAGCACACACATTTTCTTTGATATAAATGCTTGTAGTAGTTGTTGAGTTGCAACCATACATCCACCATAGTGGGGCTAACATTAACTGTGGACTACTGCATAAAACCTAAAAGTGCATCACTCTAGAGCAGGACATAGTTATTGATTTGCTACTAAAAAAATACATGCATAAGAAACTGCTGATTGCATACTGTACACTGCCAGTTTTGGGCCAGCATATCGACGTAAAAAAAAAGTAAAGACAAGTGTGCATACACAAATGGTTACAGCCAAGAGCGCTACAAAACTTCAAGATTCGCCTGTTATTAGCCTTCCAAAAATTGAACAGAAACTGGTGAACATCATGGACTTATCCATCTCATCACATACCATTTCAATTAATAGAAAGTTCTGGACCAGTAATGCAAGCCAAACAGAGAACTTACTATTTTTTCAAAGGCGATTCTGTTTTCCTCACACCTTGGAAAACCATCGATAAGAACCCGTTTAGCAGTGCTTGATTCAATTGCTTTTCTGACCAGTTCAACGGTTATCTCTGATGGAACAATCCTCCCTTCCCTTATTATCTCCAGGATCCACTCCCTGGCAAATGCCATGAAACTGACAAATCAACTCACCGAACCATGCATGTGCGTGCGCGTCATTATAAGGTTATCAGAGGATTGAACGGAAAGAAGTATTACCCTTGATCAGTGCCAGCAGATATTTCATTCCGCAGAAGGTCACCAGCACTCACATGAGAAAATCCAAAATCCGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTACATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAACACAATCCAACTTGAAACAGCACTGATTATCATTGATAGAAGTGATCCTCAATTTACTCTACACAGGTTATGCATGGAGTATGTAAATGTGAAACCAACCCTGCATTATTGGGGGAGTGCAGGTAGATTTTTTTTTTACCTAAGACGAAAGCGATTATAAATGTGAAACAGCACTGATTATCATTGAGGCAAGGGTTCCTCAGTTTACTCTACACAGATATGCATGGAATTTATAAATGCAAAACCAATGCTGCAAAATTACCTAAGACAAAAGCGATGAACGGCCTGTCACCATCGGTTCCCTACAGAATGA

data/test/data/BS00068396_51_exonerate.tab ADDED

@@ -0,0 +1,6 @@
+Command line: [exonerate --showalignment no --bestn 10 --showvulgar no --model affine:local --ryo RESULT:\t%S\t%pi\t%ql\t%tl\t%g\t%V\n /Users/ramirezr/Dropbox/code/bioruby-polyploid-tools/test/data/BS00068396_51.fa /Users/ramirezr/Dropbox/code/bioruby-polyploid-tools/test/data/BS00068396_51_contigs.fa]
+Hostname: [n87398.nbi.ac.uk]
+RESULT:	BS00068396_51 0 101 + 2AS_5222932 3015 2914 - 501	99.01	101	6364	.	M 101 101
+RESULT:	BS00068396_51 0 101 + 2DS_5334799 6812 6913 + 501	99.01	101	7226	.	M 101 101
+RESULT:	BS00068396_51 0 101 + 2BS_5245544 4549 4651 + 462	96.04	101	8836	.	M 69 69 G 0 1 M 32 32
+RESULT:	BS00068396_51 0 101 + 2BS_5163353 7425 7323 - 462	96.04	101	11974	.	M 69 69 G 0 1 M 32 32

data/test/data/BS00068396_51_genes.txt ADDED

@@ -0,0 +1,14 @@
+2AS_5222932
+2BS_5245544
+2BS_5163353
+2DS_5334799
+for g in  2AS_5222932 2BS_5245544 2BS_5163353 2DS_5334799;
+ grep -A1 2AS_5222932 /Users/ramirezr/Documents/PHD/201305_Databases/iwgcs/2A*.fa >> contigs_2.fa
+ grep -A1 2BS_5245544 /Users/ramirezr/Documents/PHD/201305_Databases/iwgcs/2B*.fa >> contigs_2.fa
+ grep -A1 2BS_5163353 /Users/ramirezr/Documents/PHD/201305_Databases/iwgcs/2B*.fa >> contigs_2.fa
+ grep -A1 2DS_5334799 /Users/ramirezr/Documents/PHD/201305_Databases/iwgcs/2D*.fa >> contigs_2.fa
+ grep -A1 2DS_5334799 /Users/ramirezr/Documents/PHD/201305_Databases/iwgcs/2D*.fa >> contigs_2.fa

data/test/data/LIB1716.bam ADDED

Binary file

data/test/data/LIB1716.bam.bai ADDED

Binary file

data/test/data/LIB1719.bam ADDED

Binary file

data/test/data/LIB1719.bam.bai ADDED

Binary file

data/test/data/LIB1721.bam ADDED

Binary file

data/test/data/LIB1721.bam.bai ADDED

Binary file

data/test/data/LIB1722.bam ADDED

Binary file

data/test/data/LIB1722.bam.bai ADDED

Binary file

data/test/data/S22380157.fa ADDED

@@ -0,0 +1,16 @@
+>gnl|UG|Ta#S22380157 FGAS065873 Triticum aestivum FGAS: Library 2 Gate 3 Triticum aestivum cDNA, mRNA sequence /gb=CV771480 /gi=55676420 /ug=Ta.5437 /len=859
+acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcagg
+ctggtaccggtccggaattcccgggatatcgtcgacCCACGCGTCCGCGTCCGACCAGCA
+CAAACAAGACTGTACTCTGGGCTCCTCTGACTCCGTGTCTTGCTAAAATATCTTTGGTCG
+ACTCGTTGCGAGGTTGATCAGATGGCGGAGGAAGCGAAGCAGGATGTGGCGCCACCCGCG
+CCGGAGCCGACCGAGGACGTCGCGGACGAGAAGGTGGCGGTTCCGTCGCCGGAGGAGTCT
+AAGGCCCTCGTTGTCGCCGAGAATGACGCTGAGAAGCCTGCAGCTACAGGGGGCTCACAC
+GAACGAGATGCTCTGCTCACGAGGGTCGCGACCGAGAAGAGGATTTCGCTGATCAAGGCA
+TGGGAGGAGAACGAGAAGGCCAAAGCCGAGAACAAGGCCGTGAAGTTGCTGGCGGACATC
+ACCTCGTGGGAGAACTCCAAGGCCGCGGAACTGGAAGCCGAGCTCAAGAAGATGCAAGAG
+CAGCTGGAGAAGAAGAAGGCGCGCTGCGTGGAGAAGCTCAAGAACAGCGCCGCGACGGTG
+CACAAAGAGGCGGAANGAGAAGCGTGCCGCGGCggaagcgcggcacggcgaggagatcgt
+cgcggcggaggagaccGCCGCCAAGTACCGCGCCAAGGGTGAAGCGCCGAAGAAGCTGCT
+CTTCGGCAGAAGATAGATATCGCTTCATCTTCAGCTTCTCTCTGTTTGACCGNTTGCATG
+TCTCCTGCCCATGGCATCACTTGTGTATTTATCTTTGGGGGNGATCTTAGTTTGTATGGT
+ATCATCAAATGCGTCGTGA

data/test/data/S22380157.fa.fai ADDED

	@@ -0,0 +1 @@
1	+ gnl\|UG\|Ta#S22380157 859 158 60 61

data/test/data/Test3Aspecific.csv ADDED

	@@ -0,0 +1 @@
1	+ BS00183592,3A,TTGATCTCATAGAAGATGTAACAGCTCAGTTGCCTCCCAGCAAGGTGCCCCGTCTTCACTGTTTGGTGTGGCGAAAGTTATCATCTGTTGATTTTCTAGC[A/C]AAGTGTCCTGCTGTTGAGCCTTCACCAAGTCTCCTAAAAGGCATCCGGCAATCTTTGGTCTCACATCTCACTCTGGTATTAGGGAAAGATGACCTGGCAG

data/test/data/Test3Aspecific_contigs.fa ADDED

@@ -0,0 +1,6 @@
+>IWGSC_CSS_3AS_scaff_3293289
+atagttatgtcataaaaatattaaatacataatatgaatgtatttcaaaatttatgtaatctcactttatatgcaaagttccaaaaaaagctatgacagatgattaatgaaccgtgggtgcacttcacacgggtcacannnnnnnnnnnnnnnnnnnnnnnnnnnnnctttttaccgcttaccttgtataagaaaaggttgtcttcttcttcgccgcttccatccatccatcctcgggagtcagggcctgagctaacctcttggagcttttactccccgagctgccctcccccgttccaagagcaaatcagccgcagaggggagcggccgcagagcgagtcaaccaggtgagctgctccgcgattcccctgagagaatatctactactagctgatttgctccgccctgcccggttgggttggaccccccatgttcatcctgcatctaccgagcgacgctcgattcgagcagcatccgctgcacgtttttggatctcgtcgggccttgttctggcgtggggacggaagattgttctggcggtgccacaagaacgagtcttgctgaatctggtgctcattgactttctaggaattggggttagcaagagggattttccgtgcattctagccttctgaattctgatgcacaccttcatagctgttgggacatctccctgttttgtgctctgggtccccaaattaactgtccggcaaacttgtgagcaggcatggcggtggcgagctcgacgaggacgtcgaggaggcttgcgtttgtgctactcgtgctggccttttcggccgcgctcgcagagagcagagatgcatatatgaggagcgcagatcgatatgcctgcatactgagtaagctgtggattcattgcaagattgaatgctcgtattggttgttcttgtttgatatgcaggagtttctgttcatgtctcaatggtatccatgctgataatgttaggtaggtcgaccgaatgcagcagttgtgtgccaccaatccacttttctggaaaatacttgctagaaaaccatctgaaacatgtgatgcttgctactgtataatatactgtatgtatgaagaactgccacttaatttttgaccaaaatactaatggagtactatctttcaatttggttttgtgctgattccagaaataattctgcgtctatttttctacttcatctgggttgcacagacacatacaagtatgaattgtgttgttgatgcctgtgttgtacaaactatgaattgcgtacttgctgcttatcagatatctttagtttagcagtagtcacaattatggcatgttattctgcttccattcactgattctgaaagtccgaattatcacttatggtttctcttctcataaagaaaactcagatccagatgtgataaattatgctcaccacatcttcagctaaacaaccctctacttgcaaaaattgaagttccacctgtttttgagtgttcgccttatgataagactgcaacttaatttttgaccagacgactgtctttttattttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttctgctttgatctaagttgcaaagacacataatagtatgaatcatgttgctgatgcctgtattgtaagaaactaagaattgctttacttgctgcctgttagatatatttagctggaagtagtcacaattagggcatgtaaattctgcttccatttactaatcctgtaagtctgaactctcacttatagctactcataaagataactgtgatcctgctgtgacaaattatgctgaccacatcttcagctaaacacccctctccttgtaaaaactcaagttccacagcgttgagtgctgagcttatgagttatgatcaaactgctttgctgtatccatttcagcccaggaaaacttccctcctgcaagcagagggtcaggattaacttcggcaaacggaaagctatgtgtactatgtgagcaatactcaaccgaagctctggtctacctgcgacaaaacgaaacccaaaccgagattctcagtgtcctccaccacacgtgtgcaagcctgggtcctctaagacagcaggtatggctaaatggcaatgcctgccatgcatagcataattgtaatctcagtaaactgattggctttcatcttctcgcagtgcatcacgctggtcgactactacattcccgctttcttcttggaggtttctgtggttaaacctgaagagctctgtgagtcggcgcacctgtgcccaaagggggcggcgactctgtcgtccacacgaggggatgcctgtggtctatgccatcatgttcttgttgaagttcttatgatgcttaaggatcccaacaccaaggtaactgtcatgttctcaatcgcatttaccgatcttctgtgcaatggttggcttgtactttgcacatggctaatgctttcttgtgcatgtcgcgattttttgcagctggagatagtcgggcttcttttcaaaacatgcagcaaggcgaagaactatgaaccgcaggtgagttaagttcggaaacagtcgtagttaccggaacacagacgaatctgcctgcagttaaatgatagcatatcacaggatcacctagttctcatggtcttttgtacaacagaaataactgggaaaccctgacctgttctaatgcttctgaaagttagctgttcaatactacagtgcttttctccaatacaccagctccagtaatatacagtatataccagttcaggatcattagaactttagatgttgctaactatttgtgtaattggctaactttgtaacaactgaatggtacgcataaaccttttggcgtttttgacgctttgcaaggtatctagtttcttgttaaaaaaacggtatctagttttgttctgctcacgaatctgcttttctttttatctctcagtgcaagaggcttgtccttgactacatcccactgattctgctgaagacccaggagttccttgagacgacggacatctgctttgcgacacatgcctgtaaaacaggcatgcaagcaaccattcctctctccgccgctttgtgaagaacaaatatgtaggaatcatacaggggcaaagaagcctgtaaatgttcctcctgtattttgctcaagcactgccaagctatgaaacttggttgtgcgagggtttgtacaatttgagctctgctctctgaagtttatgcaacaagccagcagctgtactatcattcatttgctcagcacataatcgtctcagagcagcatactgcgcaattgtgaaaagttacatcacattgtatctactggctatatatccagtcatgatggtactattattcagtgttcatgtcttgctttggcattagcaagtgaagcaatttttattgggaaggtaatcctggattttgatatgaaaagattgatgagattgggttgttaacatacttggttccagaaatacacatttcaattcacattaaattctccagagttagaagtgaactgaagaaactgaaagtgttagatttaataatccattcaagggcagaatagcaccagctgcccttaattctccagagttgggagtaactaccgaatgttagatttagttgtccattcaaggccagacagaatgtagctaccagagaacatttcacaaaaacacaggcttaacttgataattgagttgtcaaatgacactcacaggaaggatcacaaacaatggtgcagatccaagtcttgatgatttagaccctagtagaaggaaatatacacatcacagcaagccattactacaactagagtttcacacatccatgtgcttatgacactgtcttctcattgcatcctctcctttctgagcctctcaagctccttcaccatctgccagtgctccagggaaaggctcttctcaccaaagcttgaggctgttatctgagccattgtcagccatctgcacatcagcgcaaaaaaagttagtcggatggaggttcataaactaccatgttatcgcaaacgcaacatgttagacgcccaagattacctgctaagttcagtgcaacccaagctcctgtcgttgcgcatggcactgaccatttcatcttggatcgtctacagttaagatgcaaacattgagcaaactcagtacatgtttaaacataatctgaaattctgaatctgctaaataagtggagtgagggatagttacctggtaaatctcaggttcagaagactgagggagagacctcactgtggccaagtaccacctccagctctcaagctcctcagaagttgcattcaccgcagaaacagtggatggacgaaaaggcactaccaagtctgaaggcaggatgtttgattttccctcagaaagagtaagtagctgcacatcggtcgccatctccagcttgtagtactcaaaatcatactcaacctgtaagtacaacagacaaaaattgtaaatgaaaaattacccagcaatgataatttggaggttcatgcttgaagtatcatgccatcactaattaactttagatgtgcacagttggttacacctaagtgcttgtgaattttgattcaaattttcattcacttttggatcatgtagtcactgacctaaaatggttgatactgacatgtatgctgacaaaagacttacacaccactctaatgggatgagcatagaatcttaaagaaatataatgcaatacattcttatatgtatgatgtcttaaag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+>IWGSC_CSS_3DS_scaff_2586804
+atggatgtaagctcttgtcatgtttgttacaataaagcattctcttaaaagtttcagtgtccagtaaccagcattggcatctgatgcattgcttgctacaggtctcagaaaatggaaatggcgagagttcttcatgcagcaagaaaccagtaagaaccaaacttagttttctaccatatagctttgtcatttccccatacgaaatggtcccataatctagtgtgtttctgtttcctgtttgaagttcatctagcttctgatagcctaaattacttgcctggatatagattagcataatcataaaataggatgagtaagcgtatcaattgattagtaacatgttttagttaattaaaatgtcccatttcatgctaatccgaagtcatgtagaatgaagggtttggttgtctgacataaagtgcatttgctttttctcagaaggaagatgacgtccagatcccatctagttcagccgagatgccagcaagtgaaaatgtgccacagatgaatgggaatgatcatcatattcctggaagctctttttcatgtctagtgaaggtggggcacctcaacttttttgtatgaaatgtacattagctaatttatttgccgtgcttcctgttcttgcaagtcctattgttacagacttttatgcactgcagatctatgatatgcctgaaagtcaagtcaaactaaatgatgttgctgagttcataggggtatacacatttgacccagaacttgctgctcccaatgataattcggatgatataatgtttgatctcatagaagatgtaacagctcagttgcctcccagcaaggtatgcctattgtagggtgcatagtgcttgatttcatgcgtgacatagaaacttgaatttctatgcatattttaatatttgccctaacctctagccttgaaactgtttgtataggtgccccgtcttcactgtttggtgtggcgaaaattatcatctgttgattttctagcaaagcatcctgctgttgaggtgaatttatgaccttgaactgaaaaatgggcctgttggtttaaccaatgtattcatttcctcctagtaacatacagaactcttaaccactgttttttttatcatgcagcctttgccaagtctactaaaaggcatccggcaatctttgctctcacatctcactctggtattagggaaagatgacctggcagctaactgtttactgctgcatcttctatccagagtatgtcttatcactgcacattgctttctttttgtgctttttgccagatattttgtatgttggtttaatgatttcattgccttttcaatatctctacagctacgaactagggtggatgtggtcaccgttggcaggctctccttgaatttcactggatttaacagagaaagtgtttccatttttggaaaacagctaaatactttgatccagggactaatgccatattcacaagctattcctctgtcaattgagtatctcaacacagccacacttcaacctagaaaggacaacaagtcaggaaggtaagtcctgttcagtttctttttgtttgttcaatcaaattccataagtatgcaactccttgcctttattgggagctaacctataaactgtgctcttcataaaatttggtgtaggttggttacaggagttctgcagctacctcaaggcgctcacttgacatttgatgaaactctcttgcaatctggatctttggcatctaaaggtgttgagaatactgtgctgcttaagaacttgatggagtcacagatggtaataattctccctgaatttgtatttaagacatgatacatataagaatgtattgcattatatttctacaagattctatgctcatcccatttgagtggtgtgtaagtcttttgtcagcatatgtatcagtatcaaccattttaggtcaatgactacatgatccaacagtgaatgaaaatttgaactcaaaattcacaagcacttaggtgtaaccaactgcgcacatctaaagtgaattagcgatggcatgatacttcaagcatgaacctctaaattatcattgctgggtaatttttcatttataaattttgtctgttgcacttacaggttgagtatgattttgagtactacaagctggagatggcgaccgatgtgcagctacttactctttccgagggaaaatccaacatcctgccttcagacctggtagtgccttttcgtccatccactgtttctgcggtgaatgcaacttctgaggaacttgagagctggaggtggtacttggccacagtgaggtctcttcctcagtcatctgaacctgagatttaccaggtaacgaacaaatccctccttccatttattatctactccctccgttcctaaatacttgtccgcattttaacaaatgactacatacagagtaaaatgagtgaatctacactctaaaatatgtctacata
+>IWGSC_CSS_3B_scaff_10398983
+cccccnnnnnnnnnacttctgttttggcttaccatgcatgcctgtggtgctgttgtaaaagtggatctcactccaaatggcagatctacctttgttgaagctaagatacaaaattgcaaattctgggcaggggatctcttgtattatttttcgcatgttcagctcccgatccgcggttgtaactttggtcgcaagacataaatatcaacacgtagtttacattctttttttgtacaagtgtccactgcatgatctgtggtgatctttttacctttcagtttgtggtataagatgcatttttctctctcttgggtctcatatgccagttgctaaagacaagacttgtttaggctaatcattgttgaagaaatgcatgccagtttttgtatcaaaatgatacgcacaaactttgcgagccaattttgttcgatcatgatgcctgacataaaataataaatatgattatgcttcttatcctacgataatggatggtgggaagctttctttttcattatctaaaacaaacaaattctttttgacaaagggtggattttattgacttaaaatgaagcatcaagttgatacaaacacgatgagaacacacccggcctctgcataactaagatgcacataggcagcaccaacacacacaataacccgctggcaaatagcaaagtcatataagaccaaatctatgcctaagcgaacaaatccgcgatcgacaaactacaacaatggctatatccataccaaccatctcatgacaccataaggacaacggggttcttcaacaacaacgccttcatgaagggagcgatgctcgagagaatctaaaacaaacaaatatatgttcttttcaagagaatctaagacaactgtttattgtttcttgtctcacaaaaccgaaatgttagnnnnnnnnnctggaggggtaaccgaaatgttagtcgtaaaaaacttggtacattaacaaaatgggcctcgggtcccatcaatggcaaaattgggcctgggtcggcccagtacacgcacccagcccacaaaaattggcgggaactggagggagaaacggcgggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccgcacaacctccccgccattgctcctgcnnnnnnnnnnnnnnnnnnnncaactccccaagaagagagagcgagatccactgccggagaaaggcagagaggatggtgggcccgcagtacgacctcgtcggcaaccccctgggcgcggtgcgcgccaccttcgagagggcgtcggcggcggagtccgggggccgcgacccggtggcggcgttccggtccaaggactggggcgccagcgaggtcttccgctccttcctcttcgagcagggcggcctcgacaaggtatcgacccctcgccgtctctgttcttgcctttatttccctctcgcatgccagtacgccgcacgtgattaggttatccactcgcggtctggtttggcgtctgccggtttcctttgcgtcagtctatcatgttatagattaatcggcctcatcatagatagataaatcatcaaattttgataatcttatgtacgcagtccgcactctgcactgtaaaaggggaaaagtgattagcaacaaaatgaatagaatgtagaagaatgcttgagacttgagagcaaatgcgtttacggatttatggcggggagtagggatttatttttgtatgtattaggagtagattctactgcactgttaggagatttcaaattgtctttcaccagatgaaacgagatttcttacactgtgtttgtcctttccaggttccattgttggatgcatcaaatctcggattgatcaaacccaacaccctcgtccggttccgggggatggttcaggacatgctcgggaacgagttctatgccggggctttcaaggtactactgacatgactctgctgatatgccgccgtcaagcttcggctagtgccttcttatgcttacctgtatgaacactgtttttgaaggatgggtctacctggaggacgaacaagttcacagatttctcgccatttgcgatgccgcacccgtgtgactcgcacctctgggagcgccatctcttccattgcgtgccggtatgttactgaatctcagagcatttgtttcccattttctgatcagttctagaaattatttgtacaaagggttggttagtgggattcacctgaatagtttgattggcttctttcaggtgcctggacagaattcgtggacactggagtcttcccctgggtctgacctgcgccaaatggcaagctgcttgtcacctgaacaaagggagaaaaggaagagggatggagatgatgatgccatggatgtaagctcttgtcatgtttgttacaataatgcactctcttgacaatttcagtgtccagtaaccagcattggcatctgatgcattgcttgctacaggtctcagaaaatggaaatggcgagagttcttcatgcagcaagaaaccagtaagaaccaaacttagtttcccataatctagtgtgtatctgtttctggttttaagttcatctagcatttgatagcctaagttacttgtctggatatagattagcataatcatagaatagaatgagtaagcatatcaattgattagtaacatgttttagttaattaaaatgccccatttcatgctaatccgaagtcatatagaatgaagggtttggttatctgacataacgtgcatttgctttttctcagaaggaagatgacgtccagatcccatctagttcagcagaaatgccagcaagtgaaaacctgccacagatgaatgggaatgatcatcatattcctggaagctccttttcatgtctagtgaaggtggggcgcctgaacttttttgtatgaaatgtacattagctaatttatttgctgtgcttcctgttcttgcaagtcctattgcttacagactttcatgcactgcagatctatgatatgcctgaaagtcaagtgaaactaaatgatgttgctgagttcataggggtatatacattcgacccagaacttgctgctcccaatgataattcggatgatataatgtttgatctcattgaagatgtaacagctcagttgcctcccagcaaggtatgcctattatagggtgcatagtgcttgatttcatgcgtgacacaggaacttgaatttctatgcatatattaatatttgccctaacctctagccttgaaactgtttgtataggtgccccgtcttcactgtttggtgtggcgaaaattatcatctgttgattttctagcaaagcatcctgctgttgaggtgaatttatgaccttgaactggaaaaacggcttgttggtttaaccaatgtattcatttcctcctagtaacatacagaacacttaaccactgnnnnnnnnatcatgcagccttcgccaagtctactaaaaggcatccggcaatctttgctctcacatctcactctggtattagggaaagatgacctggctgctaactgtttactgctgcatcttctatccagagtatgtcttatcacttcgcattgctttcttttcgtgctttttgctagacattttgtatgttggtttactgatttcattgccttttcaatatctctacagctacgaactagggtggatgtggtcactgttggcaggctctccttgaatttcactggatttaacagagaaagtgtttccatttttggaaaacagctaaatactttgatccagggactaatgccatattcacaagctattcctctgtcaattgagtatctcaacacagccacacttcaacctagaaaggataacaagtcaggaaggtatgtcctgttcagtttctttttgcttgtccaatcaaattccataagtatgtaactccttgcctttattgggagctagcctataaactgtgctcttcataaaatttggtgtaggctggttacaggagttctgcagctacctcaaggctctcacttgacatttgatgaaactctcttgcaatctggatctttggcatctaaaggtgttgagaatacggtgctgcttaagaacttgatggagtcacagatggtaataattgtccctgaatttgtatttaagacatgatacatataagatccaacagtgaatgaaaatgaaaatttgaatcaaaattcacaagcacttaggtgtaaccaactgcgcacatctaaagtgaattaatgatggcatgatacttcaagcatgaacctccaaattatcattgctgggtaattttcatttattaattttgtctgttgtacttacaggttgagtatgattttgagtactacaagctggagatggcgaccgatgtgcagctacttactctttctgagggaaaatcaaacattctgccttcagacttggtagtgccttttcgtccatcaactgtttctgcggtgaatgccacttcggaggaacttgagagctggaggtggtacttggccacagtgaggtctcttcctcagtcttctgaacctgagatttaccaggtaacaacaatcccttgttccactatctagcagattcagagctttcagatgtttgcgtgcatggtttacactgtactgagttgctcaatgtttgcatcttaactgtagacaatccaagatgaaatggtcagcgccatgcgcaacgacaggagcttgggttgcactgaacttagcaggtaatcttgggcgtctaacatgttgtgtttgcgataacattgaagtttatgaacctccatcccgctaactttctttgtgctgatgtgcagatggctgacaatggctcagattacagcctcaagctttggtgagaagagcctttccctggagcactggcagatggtgaaggagcttgagaggcttagaaaggagaggatgcaatgagaagacgtgtcatcagcacatggatgtgtgaaactctagttgtagtaatggcctgctgtgatgtgtatatttccttctactagggtctaaatcatcaaagacttggatctgcaccgttgtttgtgatccttcctgtgggtgtcatttgacaactcaattatcaagttaagcctctgtttttgtgaaatgtgctctggtaactatattctgtctggctttgaatggacaactaaatctagcattcgtagttactctggagaattaaggtcatctggtgctattctacccttgaatgactactaaatctagcacttgtagtttcttcagttcacttctaactatggagaatttaatgtgaattgaaatgtgtatttctggtaccaagaagtatgttagcaatccagtctcatcaatcttttcatatcaaaattcaggcttaccttccccataaaaatggcttcacttgctaatgccaaagcaagatatgaacactgaataataataccatcatgattggatacatagcagtagatacaatgtgatgttaactttcacaattctctgagacgattgtgcgctgagcaaatttatgatagtacagctgcaggcttgctgcataaacttcagagggcagagctcaaattgtacagacaaagcatcacacgacccgaagtttcatagcttggtagtgcttgagctaaacataggaagaacatttacaggcttctttgccgcgtatgattcctacacatttgttcttcacaaagcggcggatagaggaatggttgcttgcatgcctgttttacaggcatgtgtcgcaaagcagacatccgtcgtctcaaggaagttctgggtcttcaccagaatcagtgggatgtagtcaaggacaagcctcttgcactgagaaataaaaacaaaagcagactcgtgagcagaacaaaactagatagcctttttttaacaagaaactagatacttgcaaagcgtcaaaaacatcaaaaggtttatgtgttacattcagttgtcacaaagttagccaattacagaaatagttagcaacatctaaagttctaatgatcctgaactggtatatatatcactggaactggcatgctagagaaaagcactagtattgaaccgctaactttcagaagcattagaacaggtcagcgcttctcagttatttctgttgtatgaaagaccatgagaactaggtgatcctgtgatatgctatcgtttaattacaggcagattcgtctgtgttccggtatctacgactgtttctgaacttaactcacctgcggttcatagttctttgccttgctgcatgttttgaaaagaagcccgactatctccagctgcaaaaaaccgcgacacccacaaaaacacattagccatgtgcaaagtagaagccaaccattgcacaaaagatcgatgacggcgatcgagaagatggcagttaccttggtgttgggatccttaagcatggtaagaacttcaacaagaacatgatggcatagaccacaggcctcccctcgcgtggacgaccgagtcgccgccccctttgggcagaggtgcgctgactcacagagctcttcaggtttaaccacagaaacctccaagaagaaagcgggaatgtagtagtcaaccagcgtgatgcactgcaagaagatgaaagccagtcagtttagtgagattacaattatgctatgcatggcaggcattgccatttagccatacctgctgtcttagaggaccaagacttgcacacgtgtggtggagggcactgagaatctcggtctgggtttcgttttgtcgcaggtagaccagagcttcggttgagtactgctcacatagtacacacagctttccgtttgccgaagttaatcctgcccctctgcttgcaagagggaagctttcctgggctgaaatggatacagcagagcagtttgagcacaactcataaggtcagcactcaacactgtggaacttgagtttttacaaggagaggggtgtttagctgaagatgtggtgagcataatttgtcacagcaggatcacagttatctttatcactttatgagtagctataagtgagagttcagacttacagaatcagtaaatggaagcagaatttacatgccctaattgtgactacttccagctaaatgtatctaacaggcagcaagtaaagcaattcttagtttcttacaatacaggcatcagcaacgtgattcatactaccatgtgtcttttctacttagatcaaagcagaaaagtagatcacccgcnnnnnnnnngcagaaaagtagatgcaggattatttatggacagccttctggtaagtagatgcaggattatttagggacagtcttctgctcaaaaataaaaagacagtcttctggtcaaaaattaagttgcagttcttatcataaggtgaacactcaaaaacagtgggactttaattttcgcaaggagaggggtgtttggctgaagatgtggtgaacataatttatcacatttggatctgagttttctttgtgagaaaccataagtgataattcagactttcagaatcagtgaaaggaagcagaataacatgccctaattgtgactactgctagctaaagatatctaataagcagtgggtacacaattcatagtttgtacaacacaggcatcaacaacacaattcatacttctatgtgtctgtgcaactcagatgaaacagaaaaatagacgcagaattatttctggaatcagaacaaaaccaaatctaaagacagtagtatttcggtcaaaaattaagtggcagttcttcgtacatatattatagcaaagatcacagctttcagatggttttctagcaactattttccagaaaagtggaccggtggcacacaattgctgcacccggtcgatctacctagcattatcagcatggataccactgagacatgaacagaaactcttgcataagaaacaagaataaccaataccagcattcgatcttgtaatgaattcacaacttactcagtatgcaggcatatcgatttgcgctcctcatatatgcatctctgctctctgcgagcgcggccgaaaaggccagcacgagtagcacaaacgcaagcctcctcgtcgagctcgccatcgccatgcctgctcacaagtttgccagaacacagttaatttggagactcatgacacaaaacagggagatgtcccaacatcagaaggctagaatgcacgcagcagctaaccccaattcctaaaaagtcaacacatgcatatctgcatacacacgttctgagctccagattcagctagaattgttcttgtggcaccgccagagcaagcttccgtccccacgccggaacaaggcccgacgcgatccaaaaacgtgcagcggatgctgcttgaatcgagcctcgctcggtagatgcaggatgaacatgggggtccaacccagccgggccgggcagagcaaatcaacaagtagtaaaatattctctcaggggaatcgcggagcagctcacccggttgactcgctctgcggccgctcccctcggcgtctgatttgctcttggaacgggggagggcagctcggggagtaaaagctccaagaggttagctcaggcccctgactcctgaggatggatggatggaagcggcgaagaagaagacaaccttttctttacaaggtaggagtaagctgtaaaaagactgaactgaactgtgtggtttgttcatttgttgtagtgtagcagcctgtcctttttcatgtttttttaatcaaactagcaaaatggtgtccattaatcatctgtcataatatttttttggaactttgcatataaagtgagattacataaattttaaagtacatttggattaattatctattatttttatgacataactcttagtaaaagaaaatcctatcccaaagaatgaatattaatgcaaatatagcagttgcagcctaattaaaacaatatttcgttaaaatttaatggtattatacgctttaatgtcatttagcagggtaaattcactcgannnnnnnnatacttcacatacacgtcaaactgttacgtcaatgggtcttaaagtttggttgatattaatttcattttatcttaaccagnnnnnnnnnnnnnnnnngaattagacttctactgtttgtctatctttaaaacaactattttgtcgggaacgtcttttctatgtatttttctaaataataataaagttaaaatttctagtaaattaaattatgtatgttaatgattggttttcgttcataaatatgacataannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngattagttttgctttcgtaaagataagatatttatgacgtcttagattgattatatatcaggaagatgcatagtatgcattctattttaatcattgtcacacctaacacatcctatctagtacaccacatcttgaatgaagaagtatgagtcaaccactcctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngctgagcatagcaacaccacccctagcactactgccctgaagagatgaagctacatatgacgaaccatgcgctccaaggcaacaccttcaggaagggtacgacaccagagcatcgccattgcccgatccaagaatcagagtttcccctggagccgcatgacaggcaatgagagccgcgannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccaacattcaccaccaccgaacgccacaccccggcaaccacaccgctcacacagccatggtgaccgggcatcaccagggcacgggctctgcccaagagcaccgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccccaacgaaagagacgagcagaaaggtcccaccttttacgcccctgggcgactcccagcatcgagacccaataggtcggccagaactggcatccaccgacccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggtgtaccgtagctgggagaggaccagcccattgatgggagtagcgcccgggagacgaggagatggggtgaaggacgagacaacccaaacgcagacgaaccgacaccggagaagccggccgctgccgcgggcagatccgtcgagccatcatgaagccaccacgaaaccggtaggccgccaccgagacctccccatgccgccgcccacggctgg

data/test/data/patological_cases5D.csv ADDED

	@@ -0,0 +1 @@
1	+ BS00119198,5D,ATGCGGCTTGGTGCTCTATATATCAGACAGGATTCGGGCACAATAAATTG[A/G]CCCTCCTTCTGTGAGCTGTACTGAACTCGATATAATTCAGATATGTCAGA

data/test/data/short_primer_design_test.csv ADDED

@@ -0,0 +1,10 @@
+BS00167765,3D,CTTGGAGGCTTCCGAAGTGAATACAACATAGTCTTGCAGGATAGTACAAA[T/C]GCAGTCTGATTATATGCCATGGAATGCTTTTCACCAAGAGGTGTATTAAC
+BS00068396_51,2AS,CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTA[T/C]ATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA
+Excalibur_c25234_143,2BS,GTGGTGATGAAGATGGATGTGGAGGGGACTGAGTTTGACTTGATCCCGAG[A/G]CTCTTCGACACGGGCGCAATCTGCTTGGTCGACGAGGTGTTCCTCGAGTG
+BS00183592,3B,TTGATCTCATAGAAGATGTAACAGCTCAGTTGCCTCCCAGCAAGGTGCCCCGTCTTCACTGTTTGGTGTGGCGAAAGTTATCATCTGTTGATTTTCTAGC[A/C]AAGTGTCCTGCTGTTGAGCCTTCACCAAGTCTCCTAAAAGGCATCCGGCAATCTTTGGTCTCACATCTCACTCTGGTATTAGGGAAAGATGACCTGGCAG
+BS00183592,3A,TTGATCTCATAGAAGATGTAACAGCTCAGTTGCCTCCCAGCAAGGTGCCCCGTCTTCACTGTTTGGTGTGGCGAAAGTTATCATCTGTTGATTTTCTAGC[A/C]AAGTGTCCTGCTGTTGAGCCTTCACCAAGTCTCCTAAAAGGCATCCGGCAATCTTTGGTCTCACATCTCACTCTGGTATTAGGGAAAGATGACCTGGCAG
+BobWhite_c10578_272,2BS,CAAGACGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCTCC[A/G]CTGGAATCATATGCGGACATTGGTGGGTTGGATGCTCAGATTCAAGAAAT
+D_comp3873_c0_seq1:967,2DS,TTACGTCAAGAGATTGAAGACCTAGAGAAGGACACTGGATATAAGTTGAGAGTTCTCGCACAAAATTATCCAGATACACCAGGATTGGCTATCAAGGATTTTTGGCAAGTTGATGACAGAACTATTGTCTTTGTTGCAGATCCTACCTTCGGTAACATTATAAATTTCAACATTGGTTCGTTGATTGATCTAGACATTCCTCAGAGCTTCTGGAGTCGTGTTGCAGGGAAGTATGGGAACATGTTCTATTGGAAAGAAAAGGGAGAGGATGCGTCAATTGAAGGCGCTGTGATGGCAATATCGCGCTGCCTGAGAGAGCCCACAGGGGCAAGTAATTGTTCCGAGGTGTTTTAGAGGTGGAAGTTCATCGCGGAAGGACTGAGACATGAGGAACATAAGACCAGCGAATACTATATGTACATAATCGAAATGCCAGTTACATTAACTGAACATATTTTCGCCTTAATTTTTTAAAGTCAAAGGACATTCTTTTATCCTCG[G/C]TAGAATGCTGCAAAGATACAAAATCATCACCACCTGGCATCTGATAATCTGGGCAGAGTCAGACAGGACCAAGAAATAGCCCCTTGCAGTTGCCACAGCCATGGGAACCGGCCAGTTTCAGCCGGTTTTTATAGCCAGTGTAGACCAAGATATGCTATCTGAACCGGCTATCAGCACTGCTGATTCAACATTGATTCCAATCATCGTTTTGGCTGGTTCGATCGACTCTGGTCAGTTTGCACCTATTTTCATGTTAATTTCCAGTTGGAAGATACTA
+BobWhite_c11739_325,2BS,GGATCAAGACTTTCAATGCGATTCGTAGCTAGAATAACTTTAACATCTCC[A/G]CGTGAGTCAAAACCATCTAGCTGGTTCAGCAACTCCAACATAGTTCTTTG
+BobWhite_c10287_421,1BL,CTCGTGGCAGCTCTGAAGGTGTCCGGTTTCCCTGAGTTGCTCTTCACCAA[T/C]gcagggaagatactgcaccgagagaaagctgtccggtcggccgaggtgtt
+BobWhite_c23388_471,6AS,AGGGTARCCGTCCTTGTCCTGGGCAGCGGGTAGGCTACAACTTCCATCTC[A/G]CCGTCCTCAACCACTTTCCTCATGACCACCGCGCCCATGACGACGAGCAG

data/test/data/test_primer3_error.csv ADDED

@@ -0,0 +1,4 @@
+Excalibur_c93405_296,6AL,gtacttcagccctagcatatcgaacctgaacctgtctttttagtgtggcc[A/G]CGGGTGGAGACGGAGGCTGGTAGCGGCTCCCCAGGAAGAAGACCTTCTTC
+Excalibur_c97559_331,5BL,CGCTGCAGCCTCCACGCCTGCCTGTGCACCACCGCCGGCGCCAAACGCGA[T/C]GTTTGGGACACTCATGAAATCCCGTGACGCCACTGGAAAGACGTAACTGT
+Excalibur_c9760_365,5AL,aagttctgattctttaatcgagataaaggagatgaggctgatcttccact[T/C]GAATCAGGACGCTGTGAGGCAGTACATCGCCCGCACCCCGAAGCTCCAGT
+Excalibur_c9761_475,4AL,ACATTTGATGAGCTGAAAGATGGCTTGAAAAGGGTGGGCTCAGAGCTAAC[A/C]gaacatgaaatccaggctttaatggatgcggcggacatcgacaacagcgg

data/test/data/test_primer3_error_contigs.fa ADDED

@@ -0,0 +1,10 @@
+>IWGSC_CSS_3AL_scaff_4441924
+catgaatttagnnnnnnnnnnnnnnnnnnngagagagagagagggagggatcatagtatgcatcgtccttcgcttatctagtgcgaggaactacagatagaaaggagaaatatgcttggcactgatggatatagaatgcagtgcatcataaccaaatatggacaaagcggcaatggctgtaaaagcaaccacgtgatgaaaatttgcaaatgggaacatggaacaaaaatagcaagagtttccatctcatgtacagtagtaaaggaaccctgaaaatggctgtaaaagcaatcacgtgaccgataacatactccctgtcgtaaaggaaccctgacatataaagttgtactatttcatcagataccttattagcgcagtagtacgtctttctagatgcctagaccccgcggccgataacatactccctgtcgttgcagaagaatggaaactgcacaggcaaggcaagcagtgaaggcaaaacttatatagtttgtaatgctttccagaaatattgccagggatatcacgcagatagtggcaaagcagtactacagcgggcattctagaatgaaacaaagtgaccaattttttaatcctaagctatagtatagtatcttgtatgtctaaacactgaataactgaaccaaatttcattgcaatcaatatcacaaatctacatatctcgtcaacaatccaaaaacagtacaataattgatataattttgaaaagttcagacaccgttgctcttgaattgtaaggctatgtctgaatcaactttgaaagactacacacacaaaattcttcagttatgcagtcgctcaactaaaaaactaactaagaaggcttcatgcatacctcgggatctcttctccaggcctggcaccgcatcgtcggcaatgtgtgttccatcatgtgtaggccgggccgccgtccttctcttcgacgaccctccctgcatcaagtccatgtgctcactgaaattgttgctccggcgccacagaagccgcctttgctctacacgatttacaatcaaatcaggcgaccacaacacgcacacacaggccgcaccctctgcctgtagccgccggctcgcgtgcaccctcaagcacaaacctgcatgcacctctgccgactggcctctgacgcatacgctctgcaatacactgagtttgaggggatgattacataattctgaaaaggttcaagaattgtatatcttttaaaagcataaacaacatatttcagaatctactagtgcaaaacttacacattcacaactttccctttagtagttttttaaatgcataaagaacatcatatttctcatgggcggcctgctggttgcacaaatactccaggagaaccatagctgattagtttcacttctttctagatttccattttgcgctagtccaccaagtcctccaccaatatccgtgataaccccgtggcacggtaagtgaaggatacatcacaaatactctgaaaaaggatgaaaaataaacataattgtcaaatgaagatattattatgtaaatggaacagccggagaggcttacgttcaagctgaaagagccatgatcccacaggtcctaatccgtcccttcgtgtaaataacaatggaattgatacagtgctttaatatagcatttgacaaacaataagcaagaagaggattgatgcttcattctctaatacatgtctttagttcctgcatacacactggacggatttaattcagatgaagataaggaaaaacgggtgcacccttcctatgcacatggcatatccattagagaattagtggcagtggttaacctaaagagtctggaattacattacacaaaaagagaacagggaaatgtgtagacatcatatcatacagctagaatgctaaatgttgctcctaactgaactgaactaagatggcagccaaatctgaacttgaactcaactaaatggctacttgagctaatataattggtccaaaaaggtcattttaaaactgtatcggagataaccatggaaataatttatagaacataaaaaagaaaaacaacatttagcttcttgtaaccgtacaagtggcaggaatatacaaacagaattatctttgggtgcccaaaacaacttcacttcaattactcactatacaatttggttctgtagaatggtagatcagaagtttctttctggttgatacaataactatgcatgaggtgctagctccagtaaagtagtatatgttagttctaccagattgcaataatatcggataagcctccaaataggtgcatgttgacaagaaaatatgactggtatactaagtattcactataacatgcatgctttcttaatggtaatatttgttgatttccatattctgcaaatacgaacgactgatgctttcccaccacgaatacattttgtactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncaatagcaccgtacctacagagtctctcgaggtctttctttaactcaggagcgtacttcagccctagcatatcgaacctgaacctgaaaacaacgattgtcggtttaatagatagtgcatatgcacaaccaagtgatagtttaactggacatcaaaatcccgttgtccacaggcgtaatttaaaccctgccgggcatgaagatcatgacacacaccattctaagaaaactaagaaattttatttgtcgtggatgtggtggtgagaacacaaaacagcaggggcacaccaagcagacgtgcacagcagcagcaaccagcaacatccacacatgcacattagcaagcaagtattgagatctgccaaggccgtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncttgaccatacgtgcagtagggaatatgtcgagggcgcggcggcgtacctgtctttttagtgtggccgcgggtggagacggaggctgg
+>IWGSC_CSS_7AL_scaff_549424
+ttttgtgttctcaccaccacatccacgacaaataaaatttcttagttttcttaggatcatgtgtgccatgatcttcatgcctggcagggtttacatgacgcttgtggacaacaggattttgatgtccagttaaactatcatatggttgtgcatatgcactatctattaaactgacaatccttgtttttcaggttcaggttcgatatgttcagggctgaagtacgctcctgagttaaagaaagaccttgagaaactcttagtgtgttgttgtcagtactactccaatactttggtgtggggttgcatagtactccaataatttagtgtggggtagtaaaaaatgtgttcgtggtgggaaagcatcagtggttcgtatttgcagaatagggaaatcaataaatattaccattaagaaagcatgcatggtatagtgaatacttagtataacagtcatatcttcttgtcaacatgcacctatttggaggcttattcgatattattgcaatctggtagaactgtgttactactaagaattgaatatttttagttggaatactattttaatgatcaatcacaatgttggacgcgaccacctatttattcccaagactttaagtcttgggtggcttaagcacaatatgccaggcatatgttctacatctgtggcatgtaatgaccctactggcatttcaagaggtcttgtaaatacaaaaataagtgttcactgcgtgagatttattaaatgttttagatatctcgcttgtggatgctcacccgtagctaatatcctgagtatattgataacaggtttaggtctggacggttattgagcctgcattgatgaaatagttgacaaagaagcaactgaaatgaggttattgagcctgcattgaagaatcttggttgatgagctgatatctgaccaaaaactcaagaactagaagcaagcctgacatcctttttttgtaatcggtatgttctcggtagcaagcctgtcatccttttctatccacatgaggcttactattttttacttgttgtcaccaatcaataaaacattgtgtattcattgcatatggtgaatggccttctagatttgtaagttcataggtagttatacaacagcagagccatgttctaaaaacagattcgagcctttccttggtttggagttgggccccgacgaaacgtccgagcgcatgaaatcagttcttttcaagaatgcaactgctttttttctctcatagtttccacccgtaacatatcacaagtatctttagtctaagaaagtaagaaaagtgaacttacatgatttttttaaattactaaataacttacaagataatgtatatttccgtttgagcattccaaaaactgaatgacactccattaagttgtaggatgcataaggtaagggaaatataggaagccaagacatctgtagtaataccagaagtggaagaacaagggcaagaaaacatttaaaagggccaatgataggcggaaaaagattcacgtggttaatagtcatgttttacaccaaggaagaacagaggaatggaaccaaagagaaatgagtgagcatacacctttgctagattttatgaactggactaatgtacaaaaacacacattgtcatcttggtgcatgtagatatttaatttaacaaattgaattccacatgaagcatactatactggacttctttgggctttacatgtgctcatattccataattcggatcagaaatgaagcctatgtgtatgtataaagcatttgcattatactaatattgtgtgtgttgtttttaatgccaaaggtaaatctgaacctgctcagaccacggggaggatttctctggtggactatcgctggcaaggttggcatgggagtaggcccgtaccatgggttcgtgcagctggagaaccgtggctagtgttgcgattgcctaatgtccatgtggagcataactcggcatgaggtgatatccttttatgataacctagctgtacacaatttcttcaaagaaaattaagattgatatcaaacttgagatcttcaatgtatttaaattagttcttaaattgctccaaagctactgaaatctcccttattatatttttctgtagatactgattgttctaattaaactcaccacttaaattccatagaaatgagaggctcaaggaagcaacaagtaggatgaaggagttaacgggcagaagcatagatcacagaaaaacaagaatatgttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngctttgtatctcagtatgttcagagtggcttcaatctacaatttaaaaaggtgaatattggttggatcatgacacaagtgatgtggcttcagtcatgtttcttaagctaccgtggttatatcatcactaggccatatagcttaccaataaccttcttaagtacttccactgaaccatcatgattgccgactaatttttgtgttcatggttatatttcagagaaccggttcaaagaaatgtgaacactggttgggggttctaagaaggatgaccctaaatgggagcatgacagacaccgtggtccaggaaataagggggaatctcgtggtgtctactatgctttcagaaatcctatgcagtcaaggagattccttcagatttttgcatgatgagcaggtagttgtaaagggtcgtggtgtctactatgcttatcagaaaagtgagtgcatttgtgaagcttcctgcagagtttcacatgatgagtaggtaaatgtgttgcttgtgcatttaccaagtagttatataggagagcacacaagcaacagaccacacatcttgtgctaatttccatgataagttttagcacatatgaacaagttatagtgccagttaagttatgaatagaaattgagttgcttatcattgagtaaaagacgttcctttagagtatttatagttttatactaatactttatcaaggtgatatgctgaagatttgtgattatcatagtatggcctttacattgcttctgtatgatctgacctgttgagctcatcacaaagaccataaaaattggctctatccctgatgtacaataaaaaaggggaactatagcctcagatcaaaaaattttcttttcctatgtgattttgcagcgggacttgcttatggagacattcgctctgggtcaaagcttaagaggactgatgcttttgaccatttaattagtgtttaggtatgccctcctctcctttcccttcagctggaatctctgataaggttgtaatttgctggtgcagtgctgctctgcttttatttgtggatttctttgggatctaattttgaactgtcaaaactggtttgttgggtgccggttggtttaacatgatgctataatgccgtagagagagatatgtttttccagtagaagtggccggttagttaatttgagatttgtgccttttgttcttcaggcctgaagcttttggtttcaggccgacagttaaaagttgcattggcttgtaaaaaacttcatgtgactggaccagtagggggaggatagcttcatatggaaaataattctccatggtgggaaaatttgttatttgacatgattatatacagagatacaactagcagtgtttaaatatgggttcatctcaacctatgattcctatgtatataatttttggggctagaact
+>IWGSC_CSS_6AL_scaff_5756048
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+>IWGSC_CSS_3AL_scaff_4451587
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caagatgtccggagcctctcttgtgaatcacattgcttacaatgatttcatgattgagatgttgggatttgaacaagatgcatcttttaaaggtgtgactgtagaagtttagctaaataaacagaatatatctactgcaagttgatatatagaaaagtggatttttgcataggttttgtatnnnnnnnnnnnnnngttaagtcggtacttccttttctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccgttgatttaatcaccgttgtctgtgatagacgttcacagatctggatgcctttgcttgccaaataaaatatgaacaataattatgttaggaagttacactagctttgacgatccgatcattcatggaatgttttccggcattgccaacatattgagtacttcagttgtaagtctgtaagcagttctctttgaaagagaaaaatgcatacatgcttcagtgaatggccacccccttctattttagtaacactgcacttcttagtagtacttgctaatcagtatggttattggtctgtaatcttattgtttctacattaattctttgtacgtaggccggatcaagcgcatcgccgatgccacgatcgccggtctgccgtgttactcctctcatgtgcgccctcgatgctgacgccgtcctattttccgcagccaccgccgtcgggctccgcgtccacgtgcgccttcaaacctactggatgcaatctcgcattgcgctgtcatccgcactatctggcaccacctatggacacagaacgacggatcaaggtttaatgactttgatcaggcaagatacattctgcccgctcatctccccgtgttgccgttggtaagtatggtagtattctcgatgcttcttttagtgcttctctctaaattcgttgggatccaattttgttcctgcaaaagttgcttgtgttctgtataggtgtacagttttcatgttaactggaaagtaccaaagttatctatcctagcggcatcaaactacaattttcttgttttattaataatttaatatgagatatacaagaaagtgcagcgggcatggcttgtactcatgcttgaggatatttggcttaggctcctggactgtgtcatggccacactgaagacgggacacttgtggttatcttcatgtgtcattggtggtcagagaaaccaaacaaagctggagtgaaaggtctatgagtttcaatacagaacaaagggtctacgagtttcaatacattgtcgaaaaattgtgccaaacattaaggttgatttcagttccttcatccttctagagcataagaaaaatatggttctttgcttgaaaaaattatggcttaattctggaaagcattaagtttccatgcatgctcatactgatcaatccataactctaaaaacatgataccctctttcacatgcttcatataagttatgcacatgccatctcgctaagcactgataacatgtttcgtttaacagatcatctaagatttgcataattgttttgagaatgagcagaacagcatcgacatcggcctcgatcggtgtcggggcaatggtgaaccaatgaagaagcttaaggcggctcaggtagggtggcacacgatattgacatcgaccacgaccagcgtcggaggatgggtcattgggacggaaggaggaagacaaagaggaggaagaagacgatgatcacaaaattttagcactgataaaaaacatgcggtcgatgcatagttgctcttgtagtatctgctaaagaaattcataaaatatgatatatattcgtaggacttcactc
+>IWGSC_CSS_5BL_scaff_10844348
+gtgttagtgcctacatgcagttttgaacattactacatgcctagctatttggtttgcaggatttgtaaaatgcactaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaacattcagaaatcgtactacattgtcattgtaaacttggaaaaaggtgtcacaaattgaactcccttatggttaacatttaacaggaaaggaacatcacctcgacatatagcttctccaggcatggaaagcatctcaggaaactgacaacttgctccaggtcgggcccgacagattctacttccaagaccttcactgtgcgcagtttcagggtcaagcttgtcggaatcattttctgaatgacagacgaacaaacatctttaaaattagaaataatgttaatttgtagaaggagaggtagaaggcggttgttgtacctgaacgggtgtggatccaataacaggttcagagtatttgtcagacgagtagctcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatcggaaaatgccaatgacggccgagccacaggtaggccggtatctgggccgtcctgccaccatggggatgtgcgctgttagagtatatgtcttgtatttgatttatttttgaactgtattgagtcaggtaggtcccaggcacatgcaaaggcatctaggcttctcacacgcctctgacatttatggcgatctggtgcatgtccatgccgtacgtcctggtgcatgcatggcctggcctggagcatgtgtgtccaacggagaccaccaattcaccgagtgcggacgtggagcatgggtgaccagcgaacagataagtttggtcaccattagccatcattcattagtcaaatcatgttaatgtgatcactcaggccgaactaacaaaacgagtcaggggtagatagtatgtgtgctaacatgtgaatggattttatctgttttacagactaaaaaatcgcacagattaggtacagactcgctaacaagtatgtgatggaggcatggagctaatagtttcaaaatcacacgtttcgtgttgacttaacacaccaatgcgacattagtgatgtcactttacgcgggcgcgcgcagtgtatctatgcagatttcttgtcgcccaactgccggcgttgcgcggcaggaaagcagcaccatcatttctaggagaaaagtttttgggagcagggcttccatcagttgtcacctcgtactaccagcggctaaatttcgtgttttgacttttttcgtaacttattcgaaatctgactctagttcgtaaaaaattcgagatctgacccttttctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgnnnnnnnnctaagtatggaacacagtgcacgctcgcacctaccgccggacaccttggcggtagggttgtacagcctaccgccagcctgtttggcggtaggggtctttcttaacgccaggggccttggcggtaggctgttataccctaccgccaagggctttggcgataagaaagggttagatcccaaaatttttatgaatcggggtcagacctcgaataggtttcagaaaagggtcaaaacatgaaatttagccactaccagcacatgcactcatcgagcacgcacactacttagccgtgacagaccaggcggtgtggtgcacgagcaaactagacgagaaacgcacaacacaatgtgttaacacccgccaaaaactgacacggaatacttattagcacggagtactattaatttcttttcgctcgtaggtcgaaacgtcaaaaattcaggtaaaacatcgttcacttttcgggtgattagcaactcgttggcgaagagcatataactgaagcccaacagaaacaaaatgcaggcatgtgtagttaacaacagccacaacaacatttgaattgagttcctgcctaccaaagctaagtagtggcatgatatcaacgccacagttttgaactagcggttacgtaaactaacagccccatgatttaacatgcagtttacatagtagaccaaacaacaattcagggaagggcataaaagatagttctggttgtgcccaacaacaccacgtttgataaacttcggcgctgttttcacaactggaccatcacccttctctgcataagcacgcacagaccattgtagcgatgttttcctgttgggattcatctccctctcctcaggagccctgccgatccttatcctgaacaattgggttagcaacatatcaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatagatgcaagttatttttttgctcatggcaaacatatgcactcccaacagttacctataactaaattcagcacaaagaataaaacacctataccatcagcttggtcgcacgttccgctgagccacaaacaaataatcttactacttttggctgtgtcaaaaacacagatataagaccatccacaatccagaattacaactacctaggtctatagctgcacattgacagtatcttcatgccaccaaataatccagtcctctttctgagaacaccagcatctaaatccaaatacagataatcaactgtttgttcctttcaatgcatacacatcaccggtgcattattacaactgaatccacaccttcagtacatctgaacccagtaattacaacatccactcgagcatataaaccgcaaagatctatcaaggataataacagtttttccatctaacaccaccaacagaatgcatcatcccagtgctcccctaaaaattaatcatgtacacaaatccaaccaccatactataaaatccaaccacatgtgcaaaaatcttcaatctccaaacacctgtggagttttcaaatctcgagttatgcaaagaatccaactaccccactattaatcaaagagccactaggttagtgctaacatcagtggcgctgcaattccaacaatctatattaatcaaagagctctacattttcatacccagaactctttttttcgaaaatgatccacggcatgtacaactagcacactaccggaacagtacaaatatgtgcagaacatactatgaatcgccgcagaaacccaaaatcaactcttctgcacactagcaacataaacatgattcagatctaacttcgcacggcactccaaagaagaattgtggcagagcatcagcacactgacctccgttgtccagccactggtggcttcagagcacacctcgcccgctgcagcctccacgcctgcctgtgcaccaccgccggcgccaaacgcgatgtttgggacactcatgaaatcccgtgacgccactggaaagacgtaactgttccacggcgagggcgcagcacacatcctgcatgaatcgaagccgagccaaatcggttagaaatccccaaaatctgcggcggtaaacagacacctagatcaagagagggttggccggagggggagcatacatacccgttgagctgaggccattggtggaaatctcgccggagcagcacaggcgccgccgttcgccagatggggatgggggtggaggagccgacccgctgcgtggctctggtttattccacgcagacacaggccgcagtatcgtcgtggggacgcgggtgactagggcaagattctctcgcctgtgctgtttcgaacgataagtcatgggccgcacacaataggccagtactaggcgccggtccgccggcgctaggttcggccggtcagaccccagccgttcgatctggtacagtacagccgtccaaaaaaatcattcgtcccgatctagccttcccttccgtcttcttcctcccaacgaatcccaaataaaatcccacgccgctgtccccgcggctccgccttcgtgtgcagctcggcgaggggaacgactgccggccgccgcgcgcttgcacctctattccttgtagcccctctgctgctcgccggagaaccttctcgctagttaattttcagttacaagctccacctcagagttgcaactcccccgtcaacgctccatggttgtggcacccaatgtgtcgcctccgccactcgtcgtcgaccctcgctgcgactgacgaccaccattaaacgacattgagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtcaccgtcatcgcgggggcgcaggtccgccatgatgaatgtagcaaaatcgtttgccggttgcagctttttgagccgctgcttccagctttttgcatcaatggttccaacattggcagcgacggcgtggttgcagctcgcggaccgccgaccattgattagccgatgtgcaggttacagcttgccgaccaccggatgtagcaccgcctgatgccggttgtagcgccgcagccgtggggaggcaagagctgcgcgagcaccgcatcagcaaagtcgctcctcgggaaagattgacgtgcttgaccaccatggcttgcagtctggaggaaggggatttgggaggaaagagatgggaaaaaacaagtggacgctgttgtcttggggaagataagacaaagaaggaagcggtgcgtgtggggccggagtgacgtgttgcatgctcgatggcgcaaagcgcgttagcgagcgaggcgtccggcccagtttcggccggttcgccgattacaaacgtttacccacacaatacgcctacacattccctagccgtatcgcaggctgtatttcactacatagacctgccacccactgacggattgcacatcccaaggctcaaatggacgcccatgataccggcctacatgtggctcggcctctgaaaattcgcactagcgttacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnng

data/test/test_bfr.rb ADDED

@@ -0,0 +1,51 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
+#puts path
+require path
+require "test/unit"
+class TestPolyploidTools < Test::Unit::TestCase
+  #Set up the paths
+  def setupre
+    data_path= File.expand_path(File.dirname(__FILE__)   + '/data/' )
+    @ref=data_path + '/S22380157.fa'
+    @a=data_path + "/LIB1721.bam"
+    @b=data_path + "/LIB1722.bam"
+    @f2_a=data_path + "/LIB1716.bam"
+    @f2_b=data_path + "/LIB1719.bam"
+    @fasta_db = Bio::DB::Fasta::FastaFile.new(@ref)
+    @fasta_db.load_fai_entries
+    @bam_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@a})
+    @bam_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@b})
+    @bam_f2_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_a})
+    @bam_f2_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_b})
+    puts "SETUP"
+  end
+  def teardown
+  end
+  def test_snp_between_consensus
+    setupre
+    reg="gnl|UG|Ta#S22380157"
+    region = @fasta_db.index.region_for_entry(reg).to_region.to_s
+    min_cov=2
+    puts region.to_s
+    cons_1 = @bam_a.consensus_with_ambiguities({:region=>region, :case=>true, :min_cov=>min_cov})
+    cons_2 = @bam_b.consensus_with_ambiguities({:region=>region, :case=>true, :min_cov=>min_cov})
+    puts cons_2
+    puts cons_1
+  end
+end

data/test/test_exon_container.rb ADDED

@@ -0,0 +1,17 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
+#puts path
+require path
+require "test/unit"
+class TestExonContainer < Test::Unit::TestCase
+  Query=File.dirname(__FILE__) + '/data/'+"BS00068396_51.fa"
+  Target=File.dirname(__FILE__) + '/data/'+"BS00068396_51_contigs.fa"
+   def test_simple_container_test
+   end
+end

data/test/test_exonearate.rb ADDED

@@ -0,0 +1,53 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
+#puts path
+require path
+require "test/unit"
+class TestPolyploidTools < Test::Unit::TestCase
+  Query=File.dirname(__FILE__) + '/data/'+"BS00068396_51.fa"
+  Target=File.dirname(__FILE__) + '/data/'+"BS00068396_51_contigs.fa"
+  #Set up the paths
+  def setup
+    File.expand_path(File.dirname(__FILE__) + '/data/')
+  end
+  def teardown
+  end
+  def test_simple_align_array
+ #   puts $LOAD_PATH
+    alignments = Bio::DB::Exonerate.align({:query=>Query, :target=>Target})
+    assert(alignments.size == 4, "The count of alignments should be 4, it was #{alignments.size}")
+  end
+  def test_parse_alingn_line
+    line="RESULT:\tBS00068396_51 0 101 + 2BS_5163353 7425 7323 - 462\t96.04\t101\t11974\t.\tM 69 69 G 0 1 M 32 32"
+    aln =  Bio::DB::Exonerate::Alignment.parse_custom(line)
+    assert(aln.query_id == "BS00068396_51")
+    assert(aln.query_start==0)
+    assert(aln.query_end==101)
+    assert(aln.query_strand==:forward)
+    assert(aln.target_id=="2BS_5163353")
+    assert(aln.target_start==7425)
+    assert(aln.target_end==7323)
+    assert(aln.target_strand==:reverse)
+    assert(aln.score==462.0)
+    assert(aln.pi==96.04)
+    assert(aln.ql==101)
+    assert(aln.tl==11974)
+    assert(aln.g==".")
+    assert(aln.vulgar_block.join(',')=="M	69	69	0	69	7425	7356,G	0	1	69	69	7356	7355,M	32	32	69	101	7355	7323" )
+    assert(aln.line==line)
+    #puts aln.vulgar_block.inspect
+    #puts aln.inspect
+  end
+end

data/test/test_snp_parsing.rb ADDED

@@ -0,0 +1,40 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
+#puts path
+require path
+require "test/unit"
+class TestPolyploidTools < Test::Unit::TestCase
+  #Set up the paths
+  def setup
+  end
+  def teardown
+  end
+  def test_default
+ #   puts $LOAD_PATH
+    assert(true, "Unit test test")
+  end
+  def test_snp_sequence
+    snp = Bio::PolyploidTools::SNPSequence.parse("BS00068396_51,2A,CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTA[T/C]ATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA")
+    assert(snp.gene == "BS00068396_51" )
+    assert(snp.chromosome == "2A")
+    assert(snp.sequence_original == "CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTA[T/C]ATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA")
+    assert_equal(snp.position ,  51, "Position isnt parsed #{snp.position}")
+    assert_equal(snp.original , "T", "ORiginal base not parsed, is #{snp.original}")
+    assert_equal(snp.snp , "C")
+    assert(snp.template_sequence == "CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA", "#{snp.template_sequence}!=CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA")
+    #true
+  end
+end

metadata ADDED

@@ -0,0 +1,201 @@
+--- !ruby/object:Gem::Specification
+name: bio-polyploid-tools
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Ricardo H.  Ramirez-Gonzalez
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2014-03-31 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: bio-samtools
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.6.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.6.2
+- !ruby/object:Gem::Dependency
+  name: rake
+  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: jeweler
+  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'
+description: Repository of tools developed in TGAC and Crop Genetics in JIC to work
+  with polyploid wheat
+email: ricardo.ramirez-gonzalez@tgac.ac.uk
+executables:
+- bfr.rb
+- count_variations.rb
+- filter_blat_by_target_coverage.rb
+- find_best_blat_hit.rb
+- hexaploid_primers.rb
+- homokaryot_primers.rb
+- map_markers_to_contigs.rb
+- markers_in_region.rb
+- polymarker.rb
+- snps_between_bams.rb
+extensions: []
+extra_rdoc_files:
+- README
+files:
+- Gemfile
+- Gemfile.lock
+- README
+- Rakefile
+- VERSION
+- bin/bfr.rb
+- bin/count_variations.rb
+- bin/filter_blat_by_target_coverage.rb
+- bin/find_best_blat_hit.rb
+- bin/hexaploid_primers.rb
+- bin/homokaryot_primers.rb
+- bin/map_markers_to_contigs.rb
+- bin/markers_in_region.rb
+- bin/polymarker.rb
+- bin/snps_between_bams.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/PrimerRegion.rb
+- lib/bio/PolyploidTools/SNP.rb
+- lib/bio/PolyploidTools/SNPSequence.rb
+- lib/bio/SAMToolsExtensions.rb
+- lib/bio/db/exonerate.rb
+- lib/bio/db/fastadb.rb
+- lib/bio/db/primer3.rb
+- lib/bioruby-polyploid-tools.rb
+- test/data/BS00068396_51.fa
+- test/data/BS00068396_51_contigs.aln
+- test/data/BS00068396_51_contigs.dnd
+- test/data/BS00068396_51_contigs.fa
+- test/data/BS00068396_51_exonerate.tab
+- test/data/BS00068396_51_genes.txt
+- 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/S22380157.fa
+- test/data/S22380157.fa.fai
+- test/data/Test3Aspecific.csv
+- test/data/Test3Aspecific_contigs.fa
+- test/data/patological_cases5D.csv
+- test/data/short_primer_design_test.csv
+- test/data/test_primer3_error.csv
+- test/data/test_primer3_error_contigs.fa
+- test/test_bfr.rb
+- test/test_exon_container.rb
+- test/test_exonearate.rb
+- test/test_snp_parsing.rb
+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: 2.2.1
+signing_key:
+specification_version: 4
+summary: Tool to work with polyploids, NGS and molecular biology
+test_files: []