bio-polyploid-tools 0.9.5 → 0.9.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 104e83c6297886d6ab29a59691abf89708756dec7047b343193098f4438faa1f
+  metadata.gz: a4e070d13bafaa5f717b6f0104e4c57f6c59989cf5065879bcc05819b1028f94
+  data.tar.gz: cd2b12efae0f78de859f1ac87e3e286642878f4787103e7508dfb8e410994cb7
 SHA512:
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+  data.tar.gz: 0e83d23c9dc229924a1fe3ff029fd7f1bead31aaa1f8d86da44abce0a817c60782e704be588c93027254837b839c47248058437bd64ad3a59c38f8260543a09d

data/VERSION

@@ -1 +1 @@
-0.9.5
+0.9.6

data/bio-polyploid-tools.gemspec

@@ -2,11 +2,11 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.9.5 ruby lib
+# stub: bio-polyploid-tools 0.9.6 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.9.5"
+  s.version = "0.9.6"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
@@ -151,6 +151,7 @@ Gem::Specification.new do |s|
     "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",
@@ -166,6 +167,7 @@ Gem::Specification.new do |s|
     "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",

data/lib/bio/PolyploidTools/SNP.rb

@@ -19,6 +19,7 @@ module Bio::PolyploidTools
     attr_accessor :errors
     attr_accessor :repetitive
     attr_accessor :hit_count
+    attr_accessor :snp_type
 
     #Format: 
     #Gene_name,Original,SNP_Pos,pos,chromosome
@@ -356,24 +357,24 @@ module Bio::PolyploidTools
       rev_pos = seq_snp.size - position
 
       if pr.homoeologous
-        snp_type = "homoeologous"
+        @snp_type = "homoeologous"
       else
-        snp_type = "non-homoeologous"
+        @snp_type = "non-homoeologous"
       end
 
       pr.chromosome_specific.each do |pos|
 
-        args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_specific exon #{snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
+        args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_specific exon #{@snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
         primer_3_propertes << return_primer_3_string(args)
-        args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_specific exon #{snp_type} #{chromosome}"
+        args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_specific exon #{@snp_type} #{chromosome}"
         args[:sequence] = seq_snp
         primer_3_propertes << return_primer_3_string(args)
       end
 
       pr.almost_chromosome_specific.each do |pos|
-        args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_semispecific exon #{snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
+        args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_semispecific exon #{@snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
         primer_3_propertes << return_primer_3_string(args)
-        args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_semispecific exon #{snp_type} #{chromosome}"
+        args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_semispecific exon #{@snp_type} #{chromosome}"
         args[:sequence] = seq_snp
         primer_3_propertes << return_primer_3_string(args)
 
@@ -381,26 +382,26 @@ module Bio::PolyploidTools
 
       pr.crhomosome_specific_intron.each do |pos|
 
-        args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_specific intron #{snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
+        args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_specific intron #{@snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
         primer_3_propertes << return_primer_3_string(args)
-        args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_specific exon #{snp_type} #{chromosome}"
+        args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_specific exon #{@snp_type} #{chromosome}"
         args[:sequence] = seq_snp
         primer_3_propertes << return_primer_3_string(args)
       end
 
       pr.almost_crhomosome_specific_intron.each do |pos|
-        args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_semispecific intron #{snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
+        args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_semispecific intron #{@snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
         primer_3_propertes << return_primer_3_string(args)
-        args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_semispecific exon #{snp_type} #{chromosome}"
+        args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_semispecific exon #{@snp_type} #{chromosome}"
         args[:sequence] = seq_snp
         primer_3_propertes << return_primer_3_string(args)
 
       end
 
 
-      args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_nonspecific all #{snp_type} #{chromosome}", :left_pos => pr.snp_pos, :sequence=>seq_original}
+      args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_nonspecific all #{@snp_type} #{chromosome}", :left_pos => pr.snp_pos, :sequence=>seq_original}
       primer_3_propertes << return_primer_3_string(args)
-      args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_nonspecific all #{snp_type} #{chromosome}"
+      args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_nonspecific all #{@snp_type} #{chromosome}"
       args[:sequence] = seq_snp
       primer_3_propertes << return_primer_3_string(args)
 

data/lib/bio/db/primer3.rb

@@ -61,6 +61,7 @@ module Bio::DB::Primer3
     attr_accessor :primer3_errors
     attr_accessor :repetitive
     attr_accessor :hit_count
+    attr_accessor :snp_type
     
     def line_1_name
       "#{gene}:#{position}#{original}>#{snp} #{line_1}}"
@@ -125,9 +126,8 @@ module Bio::DB::Primer3
       @values << snp_from.chromosome
       @values << regions.size
       @values << regions.join("|")
+      @values << snp_type
       if primer3_line_1 and primer3_line_2
-        @values <<  primer3_line_1.polymorphism
-
         #Block that searches both if both pairs have a TM
         primer_2 = primer3_line_2.left_primer_with_coordinates(primer3_line_1.left_coordinates, primer3_line_1.orientation)
         primer_2_tm = find_left_primer_temp(primer_2)
@@ -213,7 +213,6 @@ module Bio::DB::Primer3
         end
 
       elsif primer3_line_1 
-        @values << primer3_line_1.polymorphism
         @values << primer3_line_1.left_primer
         @values << primer3_line_1.left_primer_snp(self) 
         @values << primer3_line_1.right_primer 
@@ -226,7 +225,6 @@ module Bio::DB::Primer3
         @values << "first+"
         @values << primer3_line_1.best_pair.product_size
       elsif primer3_line_2 
-        @values << primer3_line_2.polymorphism
         @values << primer3_line_2.left_primer_snp(self) 
         @values << primer3_line_2.left_primer
         @values << primer3_line_2.right_primer
@@ -769,6 +767,7 @@ module Bio::DB::Primer3
       snp.repetitive = snp_in.repetitive
       #puts snp_in.inspect
       snp.hit_count = snp_in.hit_count
+      snp.snp_type  = snp_in.snp_type
       snp.line_1 = @line_1
       snp.line_2 = @line_2 
       snp.snp_from = snp_in

data/test/data/chr1A_C1145499T/chr1A_C1145499T.csv

@@ -0,0 +1 @@
+chr1A_C1145499T,1A,cgggccaacaaggtgtccttctccaaccacaagaccaagaagcagcaatttgtgaacctgcagtacaagaagctgtggtgggaggccggcaagcgctacg[C/T]caagctccgcctctccaccaaggccctcaagaccatcgagaagcacggcctcgacgccgtcgccaagaaggcagggatcgacctcaacaagaaatgaaat

data/test/data/some_tests/some_tests.csv

@@ -0,0 +1,201 @@
+chr1A_C1145499T,1A,cgggccaacaaggtgtccttctccaaccacaagaccaagaagcagcaatttgtgaacctgcagtacaagaagctgtggtgggaggccggcaagcgctacg[C/T]caagctccgcctctccaccaaggccctcaagaccatcgagaagcacggcctcgacgccgtcgccaagaaggcagggatcgacctcaacaagaaatgaaat
+chr1A_G540414846C,1A,TTCGCCTTTGCTGCCTACCTATATGTACACATGCACGCCGATGCCAGTTGTGGATGCATCCATACGTAAACTATTGGATAGGTCAATCTTCTATACTTAG[G/C]GCATCTCCAACAGGCGCCGAACGCGCCGCGCGCAAAAAACAGCTTATAGCGCGCGCCCATCGTCTGGTTTGGCGCGGCGCGCAGCGCTGGCTCCAGCAGC
+chr2D_C112180134A,2D,aaacataaaggaatgagcaaaagggtcccggcctttctgtgggcggaagtactactgcgagaaaacgcccataaaaacgctcgctatgcgaactctttgc[C/A]tgtactgttgtgtgtatagcgtctaggttcacgcccgcaaccaaatgcggcatgcatgccatgtcacgtgggcggtgaaaatcacgcccaaatattacaa
+Chr4D_C14473543T,4D,AACCAGTGTAAACCTTGTGTCCCTTGTTCTTCGGGCTCGACGCGCTAAGCCTTGAGATCGCGGTTTGGGCGTGAGTTAGGGAAGAGAGAGATCTTCGTGC[C/T]CACCCCAGAGTTCGAACCTTAAGGGTTTTGCCGAAACCCGAAATCCGACAATTGTGATGAAAGTTGAGCTCCTCGGTAGCCTTGACTCCGGGAACAAGCT
+BS00068396_51,2A,CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTA[T/C]ATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA
+RAC875_c8174_1034,3A,CTGATGACTTCTCCGCCTGTGTATCCTTTGGTAAGTATCAACTTTCCACC[A/G]TACCATATGGCTAAGCCATAGCTAGAGAAGAATATGAAGAAAACAGAACC
+RAC875_c8183_201,1B,GTCAACCAGTCTCTACATCTTTGAAGAAGAAGAAGAAGAGAAATGCTCCA[T/C]TGACATGGCCCACTGGAGATCATTTCCTGGCTACTCCTTTGTTCCCAGCC
+RAC875_c8197_810,2B,cggtccaaccagaattttgctgcaaatgtgactgtattgtgctgttgctg[T/C]TGGCCAGCTGAATGAGCTTGTTGGCTATGCGTGTAATATGACCAACAAAT
+RAC875_c82073_306,5D,ACTGCCAACTGCCTTTTCGTTCATATGTTCGTGAGTGACACGATGGATCT[A/G]TGCTTGGAGGGGTGGACCAATGTATATGTCGCGCAAGAGACCAACTGATC
+RAC875_c8221_649,7B,CGTACAATTTACCTGCAGAGGTTGAGAATGTCCTTTCTAGCTGCTTTGAG[T/C]ACGACTTTCGGGATCGCCCCTTGATGTCAGATATCTTACAAGCATTTGAA
+RAC875_c8221_711,7B,gatcgccccttgatgtcagatatcttacaagcatttgaaagtgctaaaga[T/C]GTGGATTATGACAACAATGGCTGGGATAGTTCTGAAAACCCAAGGGCAGT
+RAC875_c8234_293,4D,GGCTGTGGTCGGCGCGGACGCCTCGGGCCTCCTGTGCTCCCCTACACAGA[T/C]GAGATGAGCGGAAGAGGCTAGTCGTTAGAGCTCCCCTATATTCTTTCTAG
+RAC875_c8254_1203,6B,ttcatattgctggtgatgaaggctgtgtcggttgggaggcggaaattcag[T/C]GCCGAGTTCCAGCTCGTGTTCCGGCTGCTCAAGGGGCTCATCTTCATCGT
+RAC875_c8254_594,6B,TTTGTGCTCATGCAGCTTCAGTTAGCGTCCGTCTTCTTCACATTCTCCCT[T/C]GGAACCAAGACTCACTACTACGGAAAGACGCTGCTCCACGGAGGAGCCGA
+RAC875_c8254_657,6B,CACTACTACGGAAAGACGCTGCTCCACGGAGGAGCCGAGTACAGAGCCAC[T/C]ggacgtggattcgtggtgttccatgccaaattcgctgagaactaccgcct
+RAC875_c8254_795,6B,ATGATCCTGCTTATCGTGTTTGAGATCTTCGGGCAGTCGTACCGAGGAGC[T/C]ATCGCGTACATCTTCATCACCTTCTCCATGTGGTTCATGGTTGTCACCTG
+RAC875_c8256_464,3B,AAAAAGGTGAGTGCTCCAAGACTGAAGCCAGCACCACAGGCCAAGGCCTC[A/G]TCCCTGCGCCTCTTCCTGTGTTTCTCTACAATCTTGTCCAGTGCCCGGCG
+RAC875_c82649_146,1B,ATTGGGGCTCAATGCGTCAGAGTTGCGTCGGTCTTGGATGCCATTTACCA[A/G]GCTCTGTTTGCTCTTATTCTGAACTGAACCTGTGGATTCCTCTCCTCCTC
+RAC875_c8271_1352,1B,TGGCCAATCCTACCATGCTGACTATTGGATTTAACATTAATCTTAACCTG[T/C]GATATCCTGCCTCTAGGATCAGATCCAGAATGTGCACCATTTATCTGCTG
+RAC875_c8271_1469,1B,GACTTAACCTTCACACCATGACCAACTTGAGGCTTCCTGCTCCTGTAATC[A/G]CCTTCAGGCTGCCCTCTCTGCCAGTCACTTAAGAGATCAGCATGGCTACC
+RAC875_c8271_887,1B,CTGGCCAGCCTATCACTCTCTGGTGACCTCAGTGATTCATTGGCTTTCTC[A/G]TTGCTATCATGCAATTCAGAGTTGTCATAACCATGCATGTCCAGGTTTGC
+RAC875_c8282_644,1B,TCGAAGGAAGACTTCCAACGGTGTGCAAATGCTCAGATGGCTGTGTATCG[A/G]AAAGCCACATTTGGATGGGCTTACTGGTCGTACAAGCATGTTAGCAACCA
+RAC875_c8286_432,2D,CCGACAGCTGCCCTGATGTCTGCCATTTACGAGGAGAACAAGGACGAGGA[T/C]GGCTTCCTCTACATGACCTACAGCGGCGAGAACACCTTCGGATTGCTCTA
+RAC875_c8286_574,2A,GTAAATAAGGCGTGCCAATCAACTGTGTATATATTCCGGTTTGCCTCGTC[A/G]TAGGATCTTTAAATTGCACAACCAAGAAAACCTATTCTTATCCTGACTTA
+RAC875_c82888_83,1D,TCCCGATGGGCGTGTTTGGCTCCGTGGCCCCGGTGCTCACCCTGGGATCC[A/G]TCTCCAAGAGATGGGTGGTGCCTGGATGGCGGCTTGGATGGATCGTGACC
+RAC875_c829_1971,2B,CCTGACGTTGAAGGACAAAGACGGTGAATATATGACGAAAGAGGTGCAGC[A/G]CGAGGTGGAGACATCAGTGAAGAGGAGGACCGATGGCAAGGCGCCCAAGA
+RAC875_c83182_90,3D,GGCTATGGAGCTTACGGGCCACCTCCTGGGATGGGCGTGCAAGGCATGTA[T/C]GACGGCGGCTACAATACCTACACAGACAGGCGCTAYRGTACGGGTGCTGG
+RAC875_c83211_30,5A,GACGTGCACCGGTTCAGCTACATATCGCG[A/G]AAGGGCCTCGAGACCTTCCGAGAGCGGCTGAAACATGGTGTCATTGATCT
+RAC875_c83414_707,6B,TTCAGCGGCGACACGGACTCGGTTGTCCCGGTGACAGCGACGAGGTTTTC[A/G]CTCAGCCACCTTGGTCTCAAGACTAAGATCCGCTGGTACCCATGGTACTC
+RAC875_c83712_84,2B,GCATCTACTTGGAGGTGCCAGGTTTCGTTGGCCCCGTGGAACTGGAACGC[A/G]TCCCGGACGGCCATGGAGTCGGCGAGGTGGAACCACGAGCCTCCCTGGTC
+RAC875_c84224_177,7D,TCCATGGGTGGAAGCCACAAGTTACATGCCATGATCCAACTGATATATCT[A/G]AGGATAATGGCATGGCATGGGCAATTGATATCCCATGCATCCCTCAGACC
+RAC875_c8452_1646,5D,CGGATTGATGCCATTGATGGGGCATTGCGTAGACCTGGCCGTTTTGATCG[T/C]GAGTTCTATTTTCCTTTACCTGGCTATGAGGCACGAGCTGAAATACTGGA
+RAC875_c84527_446,7A,ACGGGAGAAAAAACTTATGACATGCCCATCCACTACCTATCTTACATCGA[T/C]CATAACTTACATGAAAACAAACGTTGCCCACTATGAACACCACAACATCC
+RAC875_c8459_1233,3B,AGGAAGAACTACCCTGCTGGCACTCCTAGGACAAGTCCTAGGTTTGAACC[A/G]AAGCGTGAATGTCATAACGGGTCTGTGGAAGAAATGCCAGCCAAGGTTCT
+RAC875_c8459_1291,3B,AATGTCATAACGGGTCTGTGGAAGAAATGCCAGCCAAGGTTCTGACCTCT[A/G]AAGGTGGTGATGCTGAGCTGGTGAGAGGGGAAGTGAAACATTCTAGGAAG
+RAC875_c8472_1174,4A,ATTGTACTGGAACAGTGAAGATGCTGACAATATCATTGGAGCATCGAGGC[A/G]TGATCAGTTGGATTGGTTTACTCTGGACCCAAGGGTGGCACAAGATCAGC
+RAC875_c8481_2685,6A,caacggacctgcaccaatttagttgcttgagttgctccacattaactaga[T/G]CTCCCATATATTTGGTGCTTGGTTTAGTGTTTGATGTCGGGCAGAGGAAT
+RAC875_c8503_644,1D,TTTCCAGTATCGACATGACCAAGGATGCAACAGATTGGTGAACGGAGGTC[A/G]CTAGCATTGTCAGCATCATCATCTTTAGAAGATCCTTTCTTCCCTTTCTT
+RAC875_c85031_525,1A,CCTGCGCCCACCAGCAGGAACTGTGGAATCAGCATGAACACGCTGATCGG[T/C]AGCGCGGTCCCATTCGTGGCCGTGGAGGCGACGGTGAGACGCTTCTTCTC
+RAC875_c85261_84,2B,gagcgcatctcaggaagtgctggtgatgtgctagaagacaatcctgtggg[A/G]AAGTTAAAGGTTTTCATATATGACTTGCCAAGAAAGTATAACAAGAAGAT
+RAC875_c85778_184,1A,GTGCTACCGTGGGCGTCTTCGCCAACATCTCACGCCGGTGAACGTGTCCT[A/G]CCGGTGGTTCCTCCTGCCGTCATAACGTAAACCAGCAAAGCATGTGCGCA
+RAC875_c85927_269,2B,GCAAAACGTGCCATGAATGTATATGATGAAGCTGTAAGGGCTGTTCCCAA[T/C]ACTGAAAAGATGAGTATGTATGAAATATACATTGCACGTGCTGCTGAACT
+RAC875_c8624_539,6A,AACCAGTCACCCTAATGTGCATAGAAAAGATTGAAGGGTGATGCCACAAG[A/G]accgatgaggaaatcaaactgagggtatctacggttatcctattgagatc
+RAC875_c8624_825,5B,CACAGGGAATGACAGGATGACCACCATCACAACCAACTGGACAGAGTTCC[A/G]CTGTCATGCAAACATGCATGAGGGTGACATCTGCGTCTTCTACTTCAGAC
+RAC875_c86296_278,6B,CAGACAAAGCTAAGCTTCCTAGCATCAACTAGTGTCACTGATAGCTCTCC[A/G]ACAAAGTCCTTGTTTCCATCTTGAACATCTTGAACTAAGTCACTTGCAAC
+RAC875_c864_88,1B,CTCAGGAATTGGCTTAAAGAGATTGGAGCTTGATATATTTGATGATGACC[A/G]TACCTTGCCTTATATCGACAGTTGGCTCCAGTTTGCTGTCACACCAGGGA
+RAC875_c8642_231,5A,TGGCAATGTCGACGAGGCGAAGATGATGCTCCAGAGGCTGCGTGGCACGA[T/C]GGGGGTTCAGAAAGAGCTCGACGATCTGGTCACTGCCAGCAACATATCCA
+RAC875_c86537_84,7D,GGAAGGACGAACAGAGTTCTACCGGTGATCCGTGTTGTCGCTGACGGTGT[A/C]ATAGGATCTGCGGTGCACGTGGACAAGGCGATGGGGCTGCCAACCTACCT
+RAC875_c8662_140,3D,AGGGAAGCACCGCATAAGTCGCCAGTACTATGAGGAACCACGAGGATTTC[A/G]TGATGGTCCTCCTCCTCGACTTGCACGAGAAAGGTCTATCTCACCACGTT
+RAC875_c8662_762,1B,gctgagattgagaagagaaagccacctagtttcagcggccatggagctta[T/C]GGACCACCTATGACAACTCTTGGGATGGGCTTGCAAGACATCTACAACAG
+RAC875_c8662_917,1B,CTATCCGCACCCATGATTTGGGCTTTTGATCCTTGTCAGAGTTCATCACC[A/G]TCAGTACTTGTGACAAAGTTCCTATCTTAGCAGTGAAACTTGTGGTGACT
+RAC875_c8684_1668,2D,TTCTCCTCCAGGGACAGAATCTGGCCCTTCAGCTTCAAGATGGTGACCGC[A/G]CTGTCGTACCGGAACTGCTGAGCCTGGTAGAACAGCACGGCCATGTCC
+RAC875_c87052_193,2B,CACCGATGTTCACAATGAATGCTCCGGGTGTGGGCGTGACATCTACCCAA[T/C]GGTCCTCGTTGAAGATCTGTAGTCCGCCGACTTCATCTTGGAGGAGTACG
+RAC875_c871_1345,7B,CCAGATCAAGTGATCTGATCATCTCCTGCGGACAGAATCGCCCTACGCTC[A/G]GTGTAAGTTCCCGGCCGTGCACGAACCTGTGACCGCTAGAGCAGTGGCAT
+RAC875_c8714_653,4A,GAAAGTGAACATTGAAACCATTTTTGGAGTGCCATGGATTTGCTTTCAGA[T/C]GATGACAAAAAGCTTCCCCAGGTTTCAAATATGCTTCCCTTATTGAAACG
+RAC875_c8721_212,6A,AGACCTGATTATTGCCTGGGGCCTCATTTGCGGCAAATGCTATCTTATGG[A/C]TGTACCCGCTTAGAAATTGGTGTTCAGAGTACATATGAGGATGTTGCACG
+RAC875_c8751_378,6B,CAGGAGATGTCCCTCATGGCCAGCCTCAGCAACCCCTACATCGTCGAGTA[T/C]aaggacggatgggtcgacgaggggacctccgtttgcatcgtcacaagtta
+RAC875_c8752_1079,7B,AAAACAATCAAATTGCCAAATATCAGGAGACCCAAAGAATCTGGAGCTCA[A/G]cctgcatgatcttcatcccgcctcttggtactgcgttgcgtggtatccca
+RAC875_c8752_705,7B,TGTTATGGCTTGGAAGTGAAGGCACAGGATCTCCGTAGATCGAAAGGCTT[A/C]TGGAATAGTCGTTATCAGTTTAATGCCTACTTTGTGCCATATCTATCTGC
+RAC875_c8754_346,7D,ATGAGACTCGACCTTGTTTTACCTTAATTATCATGGTGTGCCTTTTTTTA[T/G]AATAGCTCACCATTTTGTTAGTGGCAATAAAATGCATCTTTAGGCACACC
+RAC875_c8784_503,7A,GCTGCTCATCTGTGGAGGAACCGTGGAAAGTGCCCTCTAACACCAAGTGA[A/G]ACAGCATTTATCCTCCAAGCACTAGGTATTCCTACAGAGACAAACATTTA
+RAC875_c87890_234,1B,agtcgctccaggcatggggcgtccaccacagcgatttcctcaaagaagga[T/C]AGGATGATCTTCACGCACCGGATGCTTTGGCTGACAAGGCGAAGGCCAAG
+RAC875_c8878_232,1B,AATTACTATTACATTCATGACCTGATGCATGACCTGGCAGAGAGTGTCTC[A/G]CGAGTTGACTGTGCAAGAGTTGAGAGTGCTGAGGAGAAGCAGATACCTCG
+RAC875_c8888_802,1B,TGGGACAGCATAACCATTGCATACTTGTCAATTTTCTGCAGCTGCTGTGT[T/G]TTCGGGTGGAACGTGCAGAGGCTTGGATTCGGCAACATGTACGTCCACAT
+RAC875_c8898_382,5B,TGCGGCAGGCACCTCGACCACGGTGTCCTTCTCGTCGGCTACGGGGCGTC[T/C]GGCTTCGCGCCTTCCCGCTTCAAGGAGAAGCCCTACTGGATCATCAAGAA
+RAC875_c8907_453,6B,TGTCAAACCAGCCCAAACTCCGGCCAGGCCAAACACACGTGGAGCATATA[A/G]caagaccaacgatgatatcaccccaaccacaatcgtagcttgagcgacat
+RAC875_c89201_221,5A,TCTTCAGAAGGGATAATAGATGACAGTGAAAGGAAAAGGAACAAACCAGA[T/C]GAAATTTGAAGTCACCTAGACCGAGCCAAGCACATCTTTTTGTACATGTA
+RAC875_c8927_1434,5B,GGTTGGGCAGACATTGAGGAGGAGGGAGTCTGGAAGGGGGAGGGAGGAAA[T/G]CAGGTCAGGAGACATAAACGCCGGCAGCCCCTTGCGTGTGGACAAAAGCA
+RAC875_c89312_129,7B,ATGACATTCTCCACATACCACTTGTATGTCTCGACAAGCCCCTCCTTGAG[A/G]GGAACCTTGGGCTTCCACCCCATCCCATGTATCTTGGAGCTATCCATGAG
+RAC875_c89312_61,7B,TCATATCAAGATACAAACTTTAAGAGGCAAAGGAGAACATGATACCACCC[T/C]GTTACTTCTTGTCGGCGATGACATTCTCCACATACCACTTGTATGTCTCG
+RAC875_c89709_124,5A,tctcaaaggcatgcaactccgagaatcggtggaaatggcagccatcgatg[A/C]GGACGACGATCCAGTTGGAGGCCGGGAGGTGGCGGTGGAACTCGAACTCC
+RAC875_c899_1326,5B,TGACCAAGTAGGAGTGGGAGTCAAAATGGCGAGGGTATTGGAGAACGATG[A/C]TGTCAACTCAGCTAATGAATCAGGGAATATGATGGCATGCTTATTACCTC
+RAC875_c89978_107,3D,ATGGCCGTGTGGAATGCGGCGTGGAGAGCGTCGAGGCGGTGCTTGAGCAC[A/G]TTGGGGAACCGGAGGATCATCGGAAACTGGATGTCCTTCCTCTTCTGCTT
+RAC875_c89978_152,3D,AGCACGTTGGGGAACCGGAGGATCATCGGAAACTGGATGTCCTTCCTCTT[T/C]TGCTTTGCAGCTTGAATGACGTGCAGCACGTCCATCTCCTGCCCTGCCTT
+RAC875_c90425_234,4B,TGCCCGACTCCGGTTACAGCTGAATGACTGCTTGTTTATCTGCTTTGAAA[A/C]CCTCGACTCATATGTGGTGTCCCTTTTTACCGCAAAACCCACACGCCGGG
+RAC875_c90426_136,2D,atggctcatcatgcgacggacgtccatcagtggctctccgccacgggtgc[A/G]CTCCTGGATGAAGACACTTCGCTATGGCTGTCGCCGGGAGATAACCCGGC
+RAC875_c90426_151,2D,acggacgtccatcagtggctctccgccacgggtgcgctcctggatgaaga[T/C]ACTTCGCTATGGCTGTCGCCGGGAGATAACCCGGCTGATGGTGGATTGCT
+RAC875_c90431_188,1B,ATGAGGACGACGAACTCCTGGAACTGGATACCCTTGCGGCTGTCGACGTC[A/G]CAGTAGCGGTGCACGTCGTCGGCCTCCTTCTCCGACATCCGCACCTCGAG
+RAC875_c90431_275,1B,ATCCGCACCTCGAGCTTGCTCAGGCAGCTCCGCAGCTCCTCGTTGTCGAT[A/C]gtcccgttggagtccgtgtcgtagtggtcgaagacgtcccggatgtcctt
+RAC875_c906_657,7B,GTAGTAGTACTACAACCACCCTCACTACGTGAGCATCTCCACAACGAGTG[T/C]GTGCGTGCTTCACTTGTGTCCTGCTAGCTTCAGTTAGCTGCAGTATAGAT
+RAC875_c90778_632,4D,ATGACACCGGCAATGCGTCGTGGTCCAGCTGGTCCAAGGACTTTGTGCAA[T/C]GCTTGTGGACTGATGTGGGCCAACAAGGTACAATCTCATCCTTAACATGC
+RAC875_c9122_395,2B,CTTACTATAGCTAAGAACTGCCCAAATTTCACGCGATTCAGACTCTGTAT[T/C]CTTGAGCCTGGGAAGCCTGATGCCATGACAAACCAACCATTAGATGAAGG
+RAC875_c9130_154,5A,CCAAGGAGCTACTACAAATGTACTCACCAGGGCTGTTCGGTGCGCAAGCA[T/C]GTGGAGAGAGCGTCGCACGATCTGAAATCCGTGATCACGACGTACGAGGG
+RAC875_c9140_470,3D,GGCGGTGGTAATGTGTTCCAACTTGGACGGCGTTGCCCCCATTCTGGTGT[A/G]CGGAGCTAGAGATGTGTAGTGCTATGGATGAAAGTCATGTGCAGCTTAGG
+RAC875_c91464_170,5A,CTGCTGATTTAATATGTTCTTTCTTAACAACCCCATCGCCTATTGACACA[T/C]GACCATGAGGAATGCCACCTGATGCTTCATACAACAGCTCACCGTCCAAC
+RAC875_c91986_410,5B,ctatgcccggctgaatcacttaatttcacagagaacttgtatccatcagg[T/C]GGGGCAGCAGCATTCGTCAGAATCTCCGCAGGAGCATCAACAACTATCTG
+RAC875_c92239_415,6B,AGGTTGAGATGAACAACAGCAAGAAGGAAGAAGAGATTCAGATTGGTGGC[A/G]TGAGGTGCAGCAAGGGACTCGTGGTAGTTATGGTGGATGGGTCGCGGTGC
+RAC875_c92348_127,6B,ACATCCTTTCTTGCTCACCCAACACACGGCATTCCTGTAAGCCTCATACT[A/G]TCGAGTTGTTTGACGAGATGTGCATCAATAATTTCAGTTAATCCGTGTGC
+RAC875_c92464_53,1B,GTATAATGTACGCACATGATCAATCTATGTCCATATCGTCAACATTATAA[A/G]CATTAGTGGACCGTATATGCATTTGCATGACTGAGCCATCTCAGCTAAGC
+RAC875_c9309_145,7A,GGCAGGGCAAAGCAATTACCAAATGATTAACCACATGTCACCAATAGGCC[A/G]tataaagttgttcagtgaggaggactacaagattggcaccagcaacaacc
+RAC875_c93097_105,5B,GGTTGGTTGAGAGGTGATGGTTGTATATCTCCAGATGTTGTTAAGATGTT[T/C]GGGCTTGCGGTTTCACTGGCTTCTATGCTGTCATCTCTAGGTGATCTAGT
+RAC875_c9318_401,4A,AGAAACTCCCTGAATGACTCTGGTAACTTCTTATCAGAAGTGGATTCCTC[A/G]TTGTTAACTTGATCAAAAATCCTATACAGGTCTTGCACCAGTCTCGTAGA
+RAC875_c9386_358,1A,TTTGTTGTATAGAATTCTTGGCTTCGGTTAAAGATCATTCTGATCTTGAG[T/C]GCCTATAGACATGCTGTTGTACATAGTATATACTACCGATCGCTTCTGTA
+RAC875_c9412_75,6B,TCCTTGAACATTGATGATCTTGCACTATCAGCTTGACTGCGGAGCAAGTC[A/C]tgtgcctccttgctggacttcaatgcactttccagctctatctgaagccg
+RAC875_c94439_63,3D,GCTTACAGCTACGGGCTGGAGGCAGGCTCCAAGCCGGAGTTGCTCATCGC[A/G]ATGAGCTGCCTCACAAAGGAGGCTAATTCCAGAGCCTTCCTGGTTTGCAA
+RAC875_c94519_419,4B,ctctgttrgagytggcacctgcgcctgccgccgccatgctgattcttctg[A/C]GGCCTTTGCTTAATAGCTACTTTGGTGGCCACAGCGCTGCTCTCTTCTTG
+RAC875_c9457_457,1B,GGAGTCAATGTAAGTCGTCCCCGCAGCTCCAAAGAAGCCGATGATCCGGG[T/C]GGAAACTAGCGGGACGTTGAAAGAACCCCCAGAGCCGGCAGTGCCGCCAT
+RAC875_c9457_788,1B,ACTAGTGCGAAAGGAGTGTATTCGATGTCGCGAGGTTCGCCTCCATCGCC[A/G]ccccatggcccgatcttcacaggcttgctcatcttgaacctagctagcaa
+RAC875_c947_383,3A,GRCATAGATATGATTCCGACGAGGATAATGTTGATCAGCTGCTTGAACTG[A/G]GAACTTTCACTGGGAAGAGGGCTATTGAATCACAATGTGGAAGCTGGTAC
+RAC875_c9476_916,5D,TGGATACAGGCTGGCTCAATGCACACGGGTTGTACACAATAAGCTTGATT[A/G]CCCTTTTGGTTAGGATCTACACCAGGGTTGGAAGATTTAAGAAGTGTAGG
+RAC875_c9494_651,7B,GTAACTTCTCTGGAGCGAATCCTTCCAAAGCGCTGCCGACAACATCGTCC[A/C]TGTGGCGCTGCTCCTTCCTTTTCGTGCCTTTTGCTTCATTGACCTCCTTC
+RAC875_c9500_1796,2B,TTGCCCATGACACAGCTAGATTCTGTCACCTCAATCTTTGTAATCTCATC[A/G]TCTTAGGACATGCCACATCTTGCAATGTTGTGAGTAGATGACAGATAAGA
+RAC875_c95103_67,7A,GTGTGCATGTTGGATGGTCACATTCTAGTGTACTAGCTAGCTAGTAAGCT[T/G]GTTTTGCTACCGGATGATTGAATGTCATCTCAGTTTGTACCTCATCTAGC
+RAC875_c9523_328,2A,TCGGCGTGTTGATCCTGGAGATCGTGTGTGGCCGTAGGAACAGCTCCCTC[A/G]ttgatcacgaatggtcaatgaaccttgtgggccacgcatggacgctgtgg
+RAC875_c9542_235,7A,TATTTCATCCGAGCAGGGAGAAATGCCAGTAGTTCAATATTGCCAGATGG[T/G]CAACTGTCTTATTAGGATGGAATCCCGTCCGTATAAGATTGGTGGTTCCT
+RAC875_c9543_99,7B,CGGAGTAAATATATGAAACACAACGGGGAACTTGTGTTTGCTAAAATGAT[T/G]GAGCGACTACTCTGCTTTGAATATATGCAGGGCGGAAGCCTTGAGAAATA
+RAC875_c95993_265,3B,GCGGCTCCATGGAAGCCGCCATCATGTTGTCCGACTAAATGTGGAGTTAC[T/C]TGTGCAAGTTCCACCATCAACAAACACAAAGTTCTGCATGCTATCATCGC
+RAC875_c9601_1680,1D,CTGATGAACCAGAATGCCCATTCCTTATGAAGCGTGGGTACTGTAAACTT[A/C]gggcacaatgtaagttttatcacccagaggcttcgagcccaacagatgca
+RAC875_c9617_395,5A,TCCACTTCCAGCACCCAGCCCTCCCAGATATCGAAACTATGGCTTGCAAA[T/C]acaaactccatcttcctattgatctgcaacaattttgccaccagcaacaa
+RAC875_c9643_641,4B,GACTCATGGTTGAAGGTCCACTTGGAGCCCGACCACATAAAGATCCCACC[A/G]TTCTTTGAGTCTGTGTCCATATTCAAACGCATACTGGAAAATAGGCCTTG
+RAC875_c9677_131,7A,TCCCCCTACAGCGACTACGTCCGCGACATGCGCAAGCTTTTCATCGTCGA[A/G]CTGCTCAGCCGCCGCCGCGTGCAGGCCGCTTGCTACGCTCGCGATACCCA
+RAC875_c96815_366,7B,AGGAGTGCCGCGAGGCCATGGACGCCATCAAGGCTCAGCGCGACCACGAC[T/G]AGAGGGTCCTCGCCGACTTCAAGCGCGACGGCTACGCCTACGTCCAGGTT
+RAC875_c9691_870,2A,ATGTACGGAAAGGCAGCCGAATTCTGGGCGGACTTGCGCCTTGAGCTCCT[A/G]TCAGCAGGTGAAATCTCTGGAGAAGAGAAAGGTGTTTCAAATCAAATATG
+RAC875_c9697_1091,7B,GTGTATTTGCATGGTAAGTATGGAGCCGTACCTCCACTCATCTGGGTCGG[T/C]GGATCAACATCGAGGACATGACCAGGAGGGGGTGGGTGGGTGTTTGTCTG
+RAC875_c97040_104,1A,CCTGGCGAGGAAAACCACATCAATGGGACACAAAATGTAGAACCCAATGA[A/G]TGGTTTCATGAGATGGCCCCGATGGCACACAGACTCCTTTCAGCTTTAAT
+RAC875_c9706_2240,7A,TCACTTTCTGGTCGCACTTCCACCAGTTGTGTGATATCTTTGTTCACGAC[A/G]CTCCTCCCACCCATCTGAATCTCAACAGGCTTTGTCAGCACTTTACGTGC
+RAC875_c97462_415,2B,CGCTAAAGAATTATTTCCGTGGGCAAAATGATCTATACCTGCTACAAATT[A/G]acactgccaagattgcagatggcttaatttatgaggcagctgatggctgt
+RAC875_c9791_2297,1B,TTGTCAGAGGCTACACCAGCTTCGGGTGTTTGAGCAATCCAAGAAGGTAT[A/C]GTCACACAGTAACTCCAGCCTGTTTGAGGGTTATGTGGCCAGACGGTGTT
+RAC875_c9795_209,3B,CAAACTAAGTTGCACGCCGTTGGGATGGTCCTCCGTGGCGACCCTCACCG[A/C]AGCATCTGCTTCCTCCAGCTCGACGTCAGTTGCTTTTTTCACACAGAAGC
+RAC875_c97988_123,2B,CTTCTAGAAACACCGTTGTATTCCTCCTCGGACTGTTCCTCTCGTCCGTC[A/G]CGATGAGCAACGCGGCAAGAATGCTAGAGGAGGAGATGGCTCTGTCCAAA
+RAC875_c97988_87,2B,GAAGCGTAGAACAACCATAGGCGCCCAGAAAAATGGCTTCTAGAAACACC[A/G]TTGTATTCCTCCTCGGACTGTTCCTCTCGTCCGTCGCGATGAGCAACGCG
+RAC875_c982_710,6B,TGGGAGCCATAGTTGTTTGGGCAGGAGCAAAATGCCTTTGTGATGGTCGA[T/G]AGCTGGACATGGGTCTCGATGCCGATAACAGATTCAAAACCTTGTATCTT
+RAC875_c98608_173,5B,CTACAGAAGATGAGATCGTCGCTGCAGACGGTGGAGGCCCTGCTCGAAGA[T/C]GCTGAGAGGCGGTCCATCACGGATCAGGCGGTGCGTCTGTGGCTGGGGCG
+RAC875_c98794_101,3D,cataaatcgtcatacatatagagaggggaatccagggcaatctcagggtt[A/G]GGGAGCAATCCAGCAATGATCACCAGCACCTGAAAGTACCATGTCTCAAG
+RAC875_c99286_60,6A,GCAGATTAAGGTCAGAGGAAGCATCTGCTACGAGGAACATCTTCGTCTTC[A/G]ACCTACAGGTGGAATATGCAGAGCAAGCACGGGCGTGCATCCGTGCCGCC
+RAC875_c99286_90,6A,CGAGGAACATCTTCGTCTTCAACCTACAGGTGGAATATGCAGAGCAAGCA[T/C]GGGCGTGCATCCGTGCCGCCTTGGGTAGCCACCCCAGATTCGTCGTGCCC
+RAC875_c9932_705,2B,TGCCGATGCAGATGTCCAGCAATGATAAGGTTGCTACGCTCAAAGAACAA[T/C]GGATGGTACATAAGCGAGCACAGGGAATTCCACAACCACTCTCTTACAGA
+RAC875_c9934_252,5A,TAGAGTCGGACGCGTCGTGATGGCCGCAGCGGCCAAGCATCTGACGCCGG[T/C]CGTCTTGGAGCTCGGTGGCAAATGCCCGGTGGTTGTCGATTCAAACGTCG
+RAC875_c9934_814,5A,CTCCAGAACCAGTTCGAGGGGGCCATTTCTGCAGGAGGAATGCTCTTCAA[T/C]gacaccagcatacatctcacaaacccatacctgccatttggaggagttgg
+RAC875_c99584_503,4B,GGTCTTTGCCCTCGACGGCGTGATCCTTACCGGCTTCCACCGTCTCGGAC[A/G]CCTTCCCCATGGCCTCGTCGCCCATCTTTTTAGCCGCCTCGGTAGTCTCG
+RAC875_c998_939,6A,TCAAAACACTCACCCTTGGTGTGTCCTTTTCTCTTGCAATGGTCACAAAG[T/C]AATTTGCTTTTATCCACCTTACCAAAGGAATTTGTAGCACGACGAGGTTG
+RAC875_c999_612,2D,GACAAGTTCATGGTGCACATCGAAACCCATGGACAGCCAGAGAAGTCGCA[T/C]AGCTTCAGGGATTTCATTGATAAGTGCCTCAGCCTGCTGACCAAGGGCAA
+RAC875_c9994_887,4B,TGGGGACTTGGGAGGCGATCGTAAAAGCGGTGTGCTACAGTGTAATGCAC[T/G]AGCAATATGTGAAGATTTTTTTAAGGAGGGGGTTAATAAACAATCAGAAA
+RAC875_c99953_224,2B,GTCGAGACTTACGAGCTTGGGGAGAGTGGCTCACACTATGTGGATGACCA[T/C]GATGGAGAGGAACGAGTTAAAAGTGCTCTTGCACATATTGGCACTCATGC
+RAC875_c9998_353,7A,GGTACACAATGTAGCAATATTGTGGAGCATTTCGGATTTACACATCTTAG[T/C]GCTGGAGAGCTGTTGCGCTCAGAAATCAAGTCTGGTTCTGACAATGGAAC
+RAC875_rep_c100137_114,6B,GACCCACGGATCATTGCAGTCAGCGGCAATGCCATCAAGTCACAAATATG[T/C]GATTGTTCTGAATTGGACCAAGAGCTTGGGTCCTTGATCGTCCGGTGAAT
+RAC875_rep_c101430_180,6A,GTTGAACATAGGGGTTCTTGGCCTGAGCATGCAAGTGTATGGCCGGGACA[A/G]TCGTTACGTGATTAATATGTTGGGAAAATCAGTAATGGTCGAGCAAACCG
+RAC875_rep_c101664_297,2D,ggcttatggtttatcacctcaggtgccatccatctgtaggtgccagtttc[A/G]GCAGTCATATCTCCCTCTTGCGATCGTTGACGAGAGACACCAAAATCTGC
+RAC875_rep_c101933_656,1B,ATTCATCCCAACCCCCCATATGTGGCATCCAGATCGTACATAGCACTAGA[T/C]GGATCCACATCTAGGTCCCCTGTGTAGTTGTAGTCATCACCATTGCTCTC
+RAC875_rep_c102406_205,4D,TGAGAGGTCGACCCAGGCTACTAGGCCTAAATCTCCTTTTATGGTGATTG[T/C]CTTGTATGTGGTGAGCTGGTAGGGGACTGAATCGACATTCACCAGCACTT
+RAC875_rep_c102406_390,4D,ACGAAGGTGCAGTCAGGTTTGCCATTGCTCACAATGGCAAAGGAGTGATC[A/G]TTGACTGGGTGGTCGTCGCCCGGCTGCTTGATGTGCTTGAGCTCAGGGAC
+RAC875_rep_c102485_468,2B,ATGCAGACCCCACGCCGAGCCTCATGGTAGTATTTGACCAAAAGATTAAC[A/G]caatcggcctttagtatatcgttgcatccatgtcgcagtgaagtttctgt
+RAC875_rep_c102601_57,2D,GGCGTCCGCATCAAGCCGTGGGAGAACTCCCCTACCAAGAGCCTCGCCGC[A/G]CGCATGCTGTTCGAGAACATGGTGATGAAGGACGTGCAGACCCCCATCAT
+RAC875_rep_c102709_719,3B,TATCGCAATGCCTTTCTTTTTAAAAGATTGCCTTCTTTCGTGAGGTGTTT[A/G]cattggtctttcagtaaacagaaccttgattcactgtgctgaattttgtt
+RAC875_rep_c103893_601,2D,CCATGATGAGTTAATACAACATACGCTTTGCCATTCGCCCTTTGTGGTGT[T/C]GAAGCTTGCAGTGTAGCCAATAGTATCCCATTCGTAGCTAGTTCTTATGA
+RAC875_rep_c104133_1757,1B,TGTTCTTTTTCATGCTATCATGTAGGTTATTGTGATTGTAGAAAAATCTA[T/C]AGATCTGCTTAGCACTTTTAACTATCACGCCAATCTCACGAAACTTAGCA
+RAC875_rep_c104133_703,1B,ATCGTCCCTCCTTGCAAGACGAGAAACTTTCCTACTTGAGTTAAGCAAAC[A/G]TATTTTCTCAAACACGGCGCTAGCAGCATCAACTCCATCCAAGATTGCAT
+RAC875_rep_c104197_411,6B,ACTCTTTTGAGCATTGCAAAGCATTATGAAACCGGTGAACCTCTTCCAGA[A/G]GAAATCTATGCTAAGCTTGTGGCTGCAAAGAATTTCCGTGCTGGCACCTT
+RAC875_rep_c104674_867,7B,CTTGACATTCTAGAGGGCAAACCAGACTTGATCATTGGCAACTACACTGA[T/C]GGCAACTTGGTGGCGTCCCTCATGTCAAGCAAACTAGGAGTCACACAGGG
+RAC875_rep_c104893_620,6B,TTAGCGTCCGTCTTCTTCACATTCTCCCTCGGAACCAAGACTCACTACTA[T/C]GGAAAGACGCTGCTCCACGGAGGAGCCGAGTACAGAGCCACCGGACGTGG
+RAC875_rep_c104943_272,7A,CTGAYYCCCCATGACACTGTTTCTGTCCTTCAAGCATGTATCCAAGTAGA[A/G]GTCGTTTACCTGGTATCTATCATCAGGAGAGAATGGATATTTGTTAAGCT
+RAC875_rep_c104986_200,1A,GTCACAATGTCCAGTAAAGATATCCCTGGGGCGGAGGTCCAGGCTTACAA[T/C]GATGAAATCCCCATTAAGTTAGGTCAACTTGATGGTGATCGCATTGGCTC
+RAC875_rep_c105012_111,7B,ATCCCAGGTTAGGCTAGATTTGGTAAAGCTTCTGCGACAAGATAGCGAAA[T/C]AGACAACACGTGGAAGGACAGCAAAAGGATTCCCCACAGAACAGCCAGAA
+RAC875_rep_c105053_57,2A,GCATCCATCTTTCCAGTCCGTTCAACGATTGAATATTTTATAGCAATGGC[A/G]actgtagcccttgtgtttgctgctgggctagttgtgcgttccttcagagc
+RAC875_rep_c105085_313,7B,GCTGATCCGGCGGGGCAGGATGGACAAGCACATCGAGATGTCCTACTGCC[A/G]CTTTGAGGGCTTCAAGGTGCTCGCCAAGAACTACCTAGATGTCATTGAGC
+RAC875_rep_c105150_589,2D,GGAGGAAGAATATCCCAGTGCTCGTAGATGCTTCCAGTTTGCTTCTCTTC[A/G]TTGTCAATGAGAATGCTGTATGTGGCATCAGGGCGGATGATCAAAGTGTA
+RAC875_rep_c105184_88,3B,GCATTTGAAGATGAGCATGATATACCAGAACCCGTAGAAGAAAATTATGC[T/C]GGCTATCATTCAGAAGTTGAGGATGATAGGCACAAATTTGAAGACGAAGA
+RAC875_rep_c105224_352,6B,gatctcctgaagatgatcaaggaggtggcgttccctatgaacatattgct[A/G]TCCCTCGCGCTCTCCATCTTCGTTAGGGGCGACCAGGCCAACTTCGAGAT
+RAC875_rep_c105265_79,4D,TCAACAGAGAACCTTTCAGCAGCTTCGTGGAGCACGAAGTATCCATATTT[A/G]TTTATGCAGTTGGGATTGGCGTGCATCCCATAGAGCTCAGGTGCCATGCC
+RAC875_rep_c105375_810,5D,CCACTTGGATTCGCCAAGAAACTTGGGTTTCTTGCAGGCAGCTCAACACC[A/G]GGTCCTGTTCTTGTTGTTTGCATGGGCACTGACACGTACCGACCAGCCTC
+RAC875_rep_c105380_216,6B,TGTTTTGATCCTTCTCACCGTCCACCGATGATGGCCCGACAGAAATCAGG[A/G]AAGGAGAAAAGGATGTTGTTGTCATGGTCGTCGGAACGACTTGCCGTGGA
+RAC875_rep_c105400_1131,1B,AGAGCTGCTTCAGTTTGTGTTCGCCTATCGCTTTCATTTTGTAGCTGGCC[A/G]TGAATACTGTGAATTTCCTCTCTCTTCCGTTCCACATCTTTCATCAGGAT
+RAC875_rep_c105462_468,4A,TTGTCCAGGACCTTGTCGACCAAGTAGCCTTCACCCTGGTCATCCTTGAT[A/G]CTGAAGATATCAGCAGTGATCTCGACCAAGAAACTGAGGAGCTCGCCCTT
+RAC875_rep_c105487_241,1D,TTATCATCTGCTCCATTGTCAATAGTACTGGCAATGTCTTCACAACATGG[A/G]TCTGTCACATTTTTGTGCAAAGTGGCAGCTTGGACAGCAGAGACAGGAAT
+RAC875_rep_c105500_301,6B,GTCACAAATACCATGAAAAAGGGATCGCTGCTGCAACGTTTCTTCGACGG[T/C]GATGATGAATTCCGCAATAGCAGACTGAAGCTTATACCGGCCGTTCCGAA
+RAC875_rep_c105537_890,5B,ATTGCAAATGAGTGGACATTTGTTCCTGCAGTTCTTAGTTGATGCAGCAA[T/C]GTGCATTGAACAGTGGAGACTAAATTGGTACAGGACAAACCAAGGTAAGT
+RAC875_rep_c105658_115,1B,agaggtgattgaatacgcttaaactcagtctgaggattctgcaagttgaa[T/G]ATCACAATATTGCGATCAGCTGTTCCCACAATCATAAGGGGATAATTCAC
+RAC875_rep_c105697_366,1A,TAATGTGATGACACATCCGAAGTGCGAGATTACTCAAGCATGGGGTGTGC[A/G]CAATGAAGCGCATCCCGGCATCAGTTACCGCATGACACAATATAAGCTCG
+RAC875_rep_c105718_304,4D,GGAGCTGTTGCTGTACTAGGCCTTATTGCTGCATTAGGGTTCTATTGCTA[T/C]AAGAGAAAGCAGAAGCCTTCCGGAAGGGTGCAGAGTCCACATGCTATGGT
+RAC875_rep_c105718_412,4D,CCCCGGCACTCAGGGTCAGATCCTGACATGGTAAAGATCACAGTTGCTGG[T/G]GGAAATGCCAATGGTGGTGCGGCCACGAGCGAGCCATATAGCCAGGCAAG
+RAC875_rep_c105718_585,4D,GTGACCAACAACTTCAGTCAGGAGAACATCCTTGGTCGTGGTGGGTTTGG[T/C]ACTGTCTACAAGGGTGAGCTCCATGATGGTACAAAAATTGCTGTGAAGCG
+RAC875_rep_c105718_672,4D,ATTGCTGTGAAGCGAATGGAGTCTGGTGTTATGGGCAACAAGGGGTTAAA[T/C]GAGTTCAAATCAGAGATTTCTGTGCTGACCAAGGTCCGTCATCGGAACCT
+RAC875_rep_c105803_144,7D,ACTCGTACCGGTGTTTGTTCATGTGGGACACCTTCAAGTTCTTCGTACTC[A/G]GCTGCGTCCAGTTCCCGCAAGTCATTGGGCTCAAAGAACTTTGGGAGTAG
+RAC875_rep_c105881_260,4A,CTCCATTTTTCTTCTGCTCTTTCTTCTGATAAATTATCACAAGAGCCTAT[T/C]GCGTCATCTTGGCCATTAACATCAGAACCATCATTTTCAATTGATTTCCG
+RAC875_rep_c105884_546,5A,TCCATGATAGCAGCAAGCACAAATCGGTTATCCAAACTCCAGACAATCAT[A/G]TTGACACCACGAGGAGTTGGCTGATGTCTTTGTCGTGGACCACCACGAAT
+RAC875_rep_c105919_164,7B,atgcacagggatgaggaggtgaactacttcccttcaaggtttgatcctac[T/C]CGTCATGCTGAACAGTACCCTATCCCTCCTCGCGTTCTATCTGGCTGCCG
+RAC875_rep_c105922_169,4D,GGGCCAGTGAGCCAACACCTGTTTGAGTGGAAAGAACACAATTTGCAGCC[A/G]TTGGAATGGAAGAGGCGACTCAGCATTGCGCTTGATGTTGCAAGAGGTGT
+RAC875_rep_c105927_650,5B,CGAAGTTCACTGACGCTGAACCAGGATCCTCTTCGCCTCTAAGAAAAATT[A/G]TTCCTGCCAGAAGCAGTACCCCAGGGAGTGATCCTCACAAAACAGCCAAA
+RAC875_rep_c105937_467,6B,CAGAGTATCAGTTCTGATGCTCATGTTAGCCATGCTATGGTGGTTCTCCG[T/C]AAGCTCTTTACGGATGCTGCTGTACCAGATCCAGTGGCGTCAGTTGTCAC
+RAC875_rep_c105942_155,1B,AGGCAAAACTTAAAAACGAATGGTTCCAGGAACATAGTTCTATATCCTTG[A/C]AGATAACTGGCTATAGCAAAACGACTCAACGCCTCAGAATCAGGCCTTGG
+RAC875_rep_c106035_443,7B,TCAGTCCAGTCATCCACAATCTTCTGCCACTCGAATCCAGAAGGGTTGAA[A/C]AGGAAGGGTGCAAAGAGCCAGGTGCCCACCATAAACCACATGGAAACAGT
+RAC875_rep_c106039_66,5B,TTCATTCTAGTTTTTCGAATTCCTCTTCAAGCCCCAAAGAATAATGCGGC[A/G]CAGTTACAGAAACAGCAACAAAAGGTGGTCGGGGAAGATGTACAATGTGG
+RAC875_rep_c106093_670,1D,ATGCCATTTCTACTCAGAAGAACCAAGGATGAAGTCTTATCGGATCTTCC[A/G]GAGAAGATTATCCAGGACAGACATTGCAATCTCAGCCACTTACAGCTGAA
+RAC875_rep_c106109_130,7B,ACTGAAGATTATCCTCCTGATACTCCTAAGCCATCAGTTGTGATACGGCC[T/C]CCTGCTGAAGTAGAGAAGGATGTACCTCGTAAGAAGGTCATTATCAAGCA
+RAC875_rep_c106151_123,4A,CCCATTCTCAATGGCGAGTAGAAGCCCATCATGTACAACATAATCATTGG[A/G]TGAAAATTGGTCAGCCACCCTGACTTCTGTGATGTCTTTGAATGCAGAAG
+RAC875_rep_c106158_701,4A,AATGATGAGAGCTCTAATTTTATCAACTCACTAGACACCATGACCACTCC[T/G]CCAAGATACATCATCGGCCTAGAGTTGTCTGGCAAGATGGAAAGGCCCCC
+RAC875_rep_c106170_204,3D,GAAATCTTTTATGTCCCCCAGCGACCATATACAGCTGTCGGAACACTTCG[T/C]GACCAGTTAATCTATCCACTTACAGCAGATCAGGAAACCGAACCACTTAG
+RAC875_rep_c106177_206,4B,ATTTGCATGGTCTATGGTGGCATCAATTGCACCATCTCTTATGGCCTTGG[T/C]TACGATGCACTCCGCATCAGCAACAGGATTCTCAGTGTCTAGCCTTAGCT
+RAC875_rep_c106241_304,5A,ATGATCCTTCCTACTGGAGCTGCCTCATTCAAGGAGGCAATGAAGATGGG[T/C]gttgaagtgtaccacaacttgaagtctgttatcaagaagaagtatgggca
+RAC875_rep_c106322_1091,4B,TGAACTTCCCAAGATCACGAAGTGCTATAGTTTTGAGATATATGGTCTCC[A/G]TTACTAGATTAACAGTATGCAAGGACATTGGTGGATAACTGGAATGTGGA
+RAC875_rep_c106400_276,2B,CCCGATCTTTGCATCGACACGATCACAAAGAACCGAACAGGATTACACGA[A/G]cattccgccctgctgtaaccctttggctttgggaagtgcacgtagggcag
+RAC875_rep_c106488_130,5A,CTTGCGTTAGTCTCATGGCAGGCCACTGCTTCTGATCCTAGCCCACTCCA[A/G]gacttttgtgtcgccgacatgaattcaccagtccgtgtcaatgggtttgt
+RAC875_rep_c106533_93,7A,AATCGCATCCAAGGCGACTGTGGTGCGGTTGACTTAACCATAGCACGTGT[T/C]GATGACGCAGTCATGGCGAATATTGAAGTTGCCGTGTCAGAAGTGCAGAG
+RAC875_rep_c106565_185,3B,CCGACAATGAGCGAGGTCATAGAGATGCTGGAAGGTGGCTTCGATGGCCT[T/G]CAGATGCCTTCCAGGCCATTCTTCTGTGATGATGAGCACACCGCTGTTCC
+RAC875_rep_c106566_197,2B,ctgaccacattcaatgaagttgacatgaccaatttgatgaagctgcggtc[T/G]GACTACAAGGATGAATTTGTCAAGAAGCATGGTGTCAAACTGGGTCTGAT
+RAC875_rep_c106588_205,7D,AYGATTACATGATGGCTGAGGAAGCTCCCTCCATTTCCAGCAGCGATCAG[A/G]TCCGTGATCCAGAGGTAGCAGAACGACCCATGGCTATGGTACGACCTGCT
+RAC875_rep_c106636_232,3A,CTTTAGGCATCGCCCGAGGAACGGAGTACCTGCATCAAGGTTGCAACCAG[T/C]GCATCCTCCACTTTGACATCAAACCGCACAACATCTTGCTGGACTACAAC
+RAC875_rep_c106876_558,1B,ttatgatcagattaagaagatgaacaccttcggctattttctggtactta[T/C]TGCGCCTTGCATAATCTTCGTGATGAATGTGCTTTGGTTCTCCAAGATCC
+RAC875_rep_c106976_263,7A,ATCACCATCTCCCTGCTGTGGGTCGCCATCAACCCGCCGTCGCAGAACTC[A/G]CAGATCGGAGGCTCCTTCCAGTTCCCCTGATCGATGAAGCTAGCTTCCTC
+RAC875_rep_c107031_84,2B,AATTAGGTCTTGCAGCAGGCGCCCCACCTCCAGAATAGGAACTATGAGGT[T/G]GTTGCTGCTGCCACTGTTGGGCTCCTGCATATGGTGCAGGCTGGTAGACC
+RAC875_rep_c107110_137,3B,AAGAGATAATCACCGTGGCCAAGGCGGCCAACGCTCATGAGTTCATATCG[A/G]GCTTGCCACAGGGATACAACACTAACGTTGGTGAGAGAGGAACACAACTA

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.9.5
+  version: 0.9.6
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
@@ -271,6 +271,7 @@ files:
 - 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
@@ -286,6 +287,7 @@ files:
 - 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