bio-polymarker 1.3.2

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Files changed (177) hide show
  1. checksums.yaml +7 -0
  2. data/.travis.yml +24 -0
  3. data/Gemfile +23 -0
  4. data/README.md +205 -0
  5. data/Rakefile +61 -0
  6. data/SECURITY.md +16 -0
  7. data/VERSION +1 -0
  8. data/bin/bfr.rb +128 -0
  9. data/bin/blast_triads.rb +166 -0
  10. data/bin/blast_triads_promoters.rb +192 -0
  11. data/bin/count_variations.rb +36 -0
  12. data/bin/filter_blat_by_target_coverage.rb +69 -0
  13. data/bin/filter_exonerate_by_identity.rb +38 -0
  14. data/bin/find_best_blat_hit.rb +33 -0
  15. data/bin/find_best_exonerate.rb +17 -0
  16. data/bin/get_longest_hsp_blastx_triads.rb +66 -0
  17. data/bin/hexaploid_primers.rb +168 -0
  18. data/bin/homokaryot_primers.rb +183 -0
  19. data/bin/mafft_triads.rb +120 -0
  20. data/bin/mafft_triads_promoters.rb +403 -0
  21. data/bin/map_markers_to_contigs.rb +66 -0
  22. data/bin/marker_to_vcf.rb +241 -0
  23. data/bin/markers_in_region.rb +42 -0
  24. data/bin/mask_triads.rb +169 -0
  25. data/bin/polymarker.rb +410 -0
  26. data/bin/polymarker_capillary.rb +443 -0
  27. data/bin/polymarker_deletions.rb +350 -0
  28. data/bin/snp_position_to_polymarker.rb +101 -0
  29. data/bin/snps_between_bams.rb +107 -0
  30. data/bin/tag_stats.rb +75 -0
  31. data/bin/vcfLineToTable.rb +56 -0
  32. data/bin/vcfToPolyMarker.rb +82 -0
  33. data/bio-polymarker.gemspec +227 -0
  34. data/conf/defaults.rb +1 -0
  35. data/conf/primer3_config/dangle.dh +128 -0
  36. data/conf/primer3_config/dangle.ds +128 -0
  37. data/conf/primer3_config/interpretations/dangle_i.dh +131 -0
  38. data/conf/primer3_config/interpretations/dangle_i.ds +131 -0
  39. data/conf/primer3_config/interpretations/loops_i.dh +34 -0
  40. data/conf/primer3_config/interpretations/loops_i.ds +31 -0
  41. data/conf/primer3_config/interpretations/stack_i.dh +257 -0
  42. data/conf/primer3_config/interpretations/stack_i.ds +256 -0
  43. data/conf/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
  44. data/conf/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
  45. data/conf/primer3_config/interpretations/tetraloop_i.dh +79 -0
  46. data/conf/primer3_config/interpretations/tetraloop_i.ds +81 -0
  47. data/conf/primer3_config/interpretations/triloop_i.dh +21 -0
  48. data/conf/primer3_config/interpretations/triloop_i.ds +18 -0
  49. data/conf/primer3_config/interpretations/tstack2_i.dh +256 -0
  50. data/conf/primer3_config/interpretations/tstack2_i.ds +256 -0
  51. data/conf/primer3_config/interpretations/tstack_i.dh +256 -0
  52. data/conf/primer3_config/interpretations/tstack_i.ds +256 -0
  53. data/conf/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
  54. data/conf/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
  55. data/conf/primer3_config/loops.dh +30 -0
  56. data/conf/primer3_config/loops.ds +30 -0
  57. data/conf/primer3_config/stack.dh +256 -0
  58. data/conf/primer3_config/stack.ds +256 -0
  59. data/conf/primer3_config/stackmm.dh +256 -0
  60. data/conf/primer3_config/stackmm.ds +256 -0
  61. data/conf/primer3_config/tetraloop.dh +77 -0
  62. data/conf/primer3_config/tetraloop.ds +77 -0
  63. data/conf/primer3_config/triloop.dh +16 -0
  64. data/conf/primer3_config/triloop.ds +16 -0
  65. data/conf/primer3_config/tstack.dh +256 -0
  66. data/conf/primer3_config/tstack2.dh +256 -0
  67. data/conf/primer3_config/tstack2.ds +256 -0
  68. data/conf/primer3_config/tstack_tm_inf.ds +256 -0
  69. data/lib/bio/BFRTools.rb +465 -0
  70. data/lib/bio/BIOExtensions.rb +153 -0
  71. data/lib/bio/PolyploidTools/ChromosomeArm.rb +63 -0
  72. data/lib/bio/PolyploidTools/ExonContainer.rb +245 -0
  73. data/lib/bio/PolyploidTools/Marker.rb +175 -0
  74. data/lib/bio/PolyploidTools/Mask.rb +116 -0
  75. data/lib/bio/PolyploidTools/NoSNPSequence.rb +292 -0
  76. data/lib/bio/PolyploidTools/PrimerRegion.rb +30 -0
  77. data/lib/bio/PolyploidTools/SNP.rb +804 -0
  78. data/lib/bio/PolyploidTools/SNPMutant.rb +86 -0
  79. data/lib/bio/PolyploidTools/SNPSequence.rb +55 -0
  80. data/lib/bio/db/blast.rb +114 -0
  81. data/lib/bio/db/exonerate.rb +333 -0
  82. data/lib/bio/db/primer3.rb +820 -0
  83. data/lib/bio-polymarker.rb +28 -0
  84. data/test/data/7B_amplicon_test.fa +12 -0
  85. data/test/data/7B_amplicon_test.fa.fai +1 -0
  86. data/test/data/7B_amplicon_test_reference.fa +110 -0
  87. data/test/data/7B_amplicon_test_reference.fa.fai +3 -0
  88. data/test/data/7B_marker_test.txt +1 -0
  89. data/test/data/BS00068396_51.fa +2 -0
  90. data/test/data/BS00068396_51_blast.tab +4 -0
  91. data/test/data/BS00068396_51_contigs.aln +1412 -0
  92. data/test/data/BS00068396_51_contigs.dnd +7 -0
  93. data/test/data/BS00068396_51_contigs.fa +8 -0
  94. data/test/data/BS00068396_51_contigs.fa.fai +4 -0
  95. data/test/data/BS00068396_51_contigs.fa.nhr +0 -0
  96. data/test/data/BS00068396_51_contigs.fa.nin +0 -0
  97. data/test/data/BS00068396_51_contigs.fa.nsq +0 -0
  98. data/test/data/BS00068396_51_contigs.nhr +0 -0
  99. data/test/data/BS00068396_51_contigs.nin +0 -0
  100. data/test/data/BS00068396_51_contigs.nsq +0 -0
  101. data/test/data/BS00068396_51_exonerate.tab +6 -0
  102. data/test/data/BS00068396_51_for_polymarker.txt +1 -0
  103. data/test/data/BS00068396_51_genes.txt +14 -0
  104. data/test/data/IWGSC_CSS_1AL_scaff_1455974.fa +112 -0
  105. data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa +2304 -0
  106. data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai +11 -0
  107. data/test/data/LIB1716.bam +0 -0
  108. data/test/data/LIB1716.bam.bai +0 -0
  109. data/test/data/LIB1719.bam +0 -0
  110. data/test/data/LIB1719.bam.bai +0 -0
  111. data/test/data/LIB1721.bam +0 -0
  112. data/test/data/LIB1721.bam.bai +0 -0
  113. data/test/data/LIB1722.bam +0 -0
  114. data/test/data/LIB1722.bam.bai +0 -0
  115. data/test/data/PST130_7067.csv +1 -0
  116. data/test/data/PST130_7067.fa +2 -0
  117. data/test/data/PST130_7067.fa.fai +1 -0
  118. data/test/data/PST130_7067.fa.ndb +0 -0
  119. data/test/data/PST130_7067.fa.nhr +0 -0
  120. data/test/data/PST130_7067.fa.nin +0 -0
  121. data/test/data/PST130_7067.fa.not +0 -0
  122. data/test/data/PST130_7067.fa.nsq +0 -0
  123. data/test/data/PST130_7067.fa.ntf +0 -0
  124. data/test/data/PST130_7067.fa.nto +0 -0
  125. data/test/data/PST130_reverse_primer.csv +1 -0
  126. data/test/data/S22380157.fa +16 -0
  127. data/test/data/S22380157.fa.fai +1 -0
  128. data/test/data/S22380157.vcf +67 -0
  129. data/test/data/S58861868/LIB1716.bam +0 -0
  130. data/test/data/S58861868/LIB1716.sam +651 -0
  131. data/test/data/S58861868/LIB1719.bam +0 -0
  132. data/test/data/S58861868/LIB1719.sam +805 -0
  133. data/test/data/S58861868/LIB1721.bam +0 -0
  134. data/test/data/S58861868/LIB1721.sam +1790 -0
  135. data/test/data/S58861868/LIB1722.bam +0 -0
  136. data/test/data/S58861868/LIB1722.sam +1271 -0
  137. data/test/data/S58861868/S58861868.fa +16 -0
  138. data/test/data/S58861868/S58861868.fa.fai +1 -0
  139. data/test/data/S58861868/S58861868.vcf +76 -0
  140. data/test/data/S58861868/header.txt +9 -0
  141. data/test/data/S58861868/merged.bam +0 -0
  142. data/test/data/S58861868/merged_reheader.bam +0 -0
  143. data/test/data/S58861868/merged_reheader.bam.bai +0 -0
  144. data/test/data/Test3Aspecific.csv +2 -0
  145. data/test/data/Test3Aspecific_contigs.fa +6 -0
  146. data/test/data/bfr_out_test.csv +5 -0
  147. data/test/data/chr1A_C1145499T/chr1A_C1145499T.csv +1 -0
  148. data/test/data/chr1A_G540414846C/chr1A_G540414846C.csv +1 -0
  149. data/test/data/chr1A_G540414846C/chr1A_G540414846C.fa +2 -0
  150. data/test/data/chr1A_T517634750C/chr1A_T517634750C.csv +1 -0
  151. data/test/data/chr2D_C112180134A/chr2D_C112180134A.csv +1 -0
  152. data/test/data/chr4D_C14473543T/chr4D_C14473543T.csv +1 -0
  153. data/test/data/chr4D_C14473543T/chr4D_C14473543T.fa +2 -0
  154. data/test/data/headerMergeed.txt +9 -0
  155. data/test/data/headerS2238015 +1 -0
  156. data/test/data/mergedLibs.bam +0 -0
  157. data/test/data/mergedLibsReheader.bam +0 -0
  158. data/test/data/mergedLibsSorted.bam +0 -0
  159. data/test/data/mergedLibsSorted.bam.bai +0 -0
  160. data/test/data/patological_cases5D.csv +1 -0
  161. data/test/data/primer_3_input_header_test +5 -0
  162. data/test/data/short_primer_design_test.csv +10 -0
  163. data/test/data/some_tests/some_tests.csv +201 -0
  164. data/test/data/test_from_mutant.csv +3 -0
  165. data/test/data/test_iselect.csv +196 -0
  166. data/test/data/test_iselect_reference.fa +1868 -0
  167. data/test/data/test_iselect_reference.fa.fai +934 -0
  168. data/test/data/test_primer3_error.csv +4 -0
  169. data/test/data/test_primer3_error_contigs.fa +10 -0
  170. data/test/test_bfr.rb +135 -0
  171. data/test/test_blast.rb +47 -0
  172. data/test/test_exon_container.rb +17 -0
  173. data/test/test_exonearate.rb +48 -0
  174. data/test/test_integration.rb +76 -0
  175. data/test/test_snp_parsing.rb +121 -0
  176. data/test/test_wrong_selection.sh +5 -0
  177. metadata +356 -0
metadata ADDED
@@ -0,0 +1,356 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: bio-polymarker
3
+ version: !ruby/object:Gem::Version
4
+ version: 1.3.2
5
+ platform: ruby
6
+ authors:
7
+ - Rob Ellis
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+ date: 2024-09-25 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
14
+ name: bio
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - ">="
18
+ - !ruby/object:Gem::Version
19
+ version: 1.5.1
20
+ type: :runtime
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - ">="
25
+ - !ruby/object:Gem::Version
26
+ version: 1.5.1
27
+ - !ruby/object:Gem::Dependency
28
+ name: bio-samtools-wrapper
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - ">="
32
+ - !ruby/object:Gem::Version
33
+ version: 2.7.0
34
+ type: :runtime
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - ">="
39
+ - !ruby/object:Gem::Version
40
+ version: 2.7.0
41
+ - !ruby/object:Gem::Dependency
42
+ name: descriptive_statistics
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - ">="
46
+ - !ruby/object:Gem::Version
47
+ version: '0'
48
+ type: :runtime
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
52
+ - - ">="
53
+ - !ruby/object:Gem::Version
54
+ version: '0'
55
+ - !ruby/object:Gem::Dependency
56
+ name: systemu
57
+ requirement: !ruby/object:Gem::Requirement
58
+ requirements:
59
+ - - ">="
60
+ - !ruby/object:Gem::Version
61
+ version: 2.5.2
62
+ type: :runtime
63
+ prerelease: false
64
+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
66
+ - - ">="
67
+ - !ruby/object:Gem::Version
68
+ version: 2.5.2
69
+ - !ruby/object:Gem::Dependency
70
+ name: shoulda
71
+ requirement: !ruby/object:Gem::Requirement
72
+ requirements:
73
+ - - ">="
74
+ - !ruby/object:Gem::Version
75
+ version: '2.10'
76
+ type: :development
77
+ prerelease: false
78
+ version_requirements: !ruby/object:Gem::Requirement
79
+ requirements:
80
+ - - ">="
81
+ - !ruby/object:Gem::Version
82
+ version: '2.10'
83
+ - !ruby/object:Gem::Dependency
84
+ name: test-unit
85
+ requirement: !ruby/object:Gem::Requirement
86
+ requirements:
87
+ - - ">="
88
+ - !ruby/object:Gem::Version
89
+ version: '0'
90
+ type: :development
91
+ prerelease: false
92
+ version_requirements: !ruby/object:Gem::Requirement
93
+ requirements:
94
+ - - ">="
95
+ - !ruby/object:Gem::Version
96
+ version: '0'
97
+ - !ruby/object:Gem::Dependency
98
+ name: juwelier
99
+ requirement: !ruby/object:Gem::Requirement
100
+ requirements:
101
+ - - ">="
102
+ - !ruby/object:Gem::Version
103
+ version: '0'
104
+ type: :development
105
+ prerelease: false
106
+ version_requirements: !ruby/object:Gem::Requirement
107
+ requirements:
108
+ - - ">="
109
+ - !ruby/object:Gem::Version
110
+ version: '0'
111
+ - !ruby/object:Gem::Dependency
112
+ name: sorted_set
113
+ requirement: !ruby/object:Gem::Requirement
114
+ requirements:
115
+ - - ">="
116
+ - !ruby/object:Gem::Version
117
+ version: '0'
118
+ type: :development
119
+ prerelease: false
120
+ version_requirements: !ruby/object:Gem::Requirement
121
+ requirements:
122
+ - - ">="
123
+ - !ruby/object:Gem::Version
124
+ version: '0'
125
+ description: Repository of tools developed at Crop Genetics in JIC to work with polyploid
126
+ wheat
127
+ email: rob.ellis@jic.ac.uk
128
+ executables:
129
+ - bfr.rb
130
+ - blast_triads.rb
131
+ - blast_triads_promoters.rb
132
+ - count_variations.rb
133
+ - filter_blat_by_target_coverage.rb
134
+ - filter_exonerate_by_identity.rb
135
+ - find_best_blat_hit.rb
136
+ - find_best_exonerate.rb
137
+ - get_longest_hsp_blastx_triads.rb
138
+ - hexaploid_primers.rb
139
+ - homokaryot_primers.rb
140
+ - mafft_triads.rb
141
+ - mafft_triads_promoters.rb
142
+ - map_markers_to_contigs.rb
143
+ - marker_to_vcf.rb
144
+ - markers_in_region.rb
145
+ - mask_triads.rb
146
+ - polymarker.rb
147
+ - polymarker_capillary.rb
148
+ - polymarker_deletions.rb
149
+ - snp_position_to_polymarker.rb
150
+ - snps_between_bams.rb
151
+ - tag_stats.rb
152
+ - vcfLineToTable.rb
153
+ - vcfToPolyMarker.rb
154
+ extensions: []
155
+ extra_rdoc_files:
156
+ - README.md
157
+ files:
158
+ - ".travis.yml"
159
+ - Gemfile
160
+ - README.md
161
+ - Rakefile
162
+ - SECURITY.md
163
+ - VERSION
164
+ - bin/bfr.rb
165
+ - bin/blast_triads.rb
166
+ - bin/blast_triads_promoters.rb
167
+ - bin/count_variations.rb
168
+ - bin/filter_blat_by_target_coverage.rb
169
+ - bin/filter_exonerate_by_identity.rb
170
+ - bin/find_best_blat_hit.rb
171
+ - bin/find_best_exonerate.rb
172
+ - bin/get_longest_hsp_blastx_triads.rb
173
+ - bin/hexaploid_primers.rb
174
+ - bin/homokaryot_primers.rb
175
+ - bin/mafft_triads.rb
176
+ - bin/mafft_triads_promoters.rb
177
+ - bin/map_markers_to_contigs.rb
178
+ - bin/marker_to_vcf.rb
179
+ - bin/markers_in_region.rb
180
+ - bin/mask_triads.rb
181
+ - bin/polymarker.rb
182
+ - bin/polymarker_capillary.rb
183
+ - bin/polymarker_deletions.rb
184
+ - bin/snp_position_to_polymarker.rb
185
+ - bin/snps_between_bams.rb
186
+ - bin/tag_stats.rb
187
+ - bin/vcfLineToTable.rb
188
+ - bin/vcfToPolyMarker.rb
189
+ - bio-polymarker.gemspec
190
+ - conf/defaults.rb
191
+ - conf/primer3_config/dangle.dh
192
+ - conf/primer3_config/dangle.ds
193
+ - conf/primer3_config/interpretations/dangle_i.dh
194
+ - conf/primer3_config/interpretations/dangle_i.ds
195
+ - conf/primer3_config/interpretations/loops_i.dh
196
+ - conf/primer3_config/interpretations/loops_i.ds
197
+ - conf/primer3_config/interpretations/stack_i.dh
198
+ - conf/primer3_config/interpretations/stack_i.ds
199
+ - conf/primer3_config/interpretations/stackmm_i_mm.dh
200
+ - conf/primer3_config/interpretations/stackmm_i_mm.ds
201
+ - conf/primer3_config/interpretations/tetraloop_i.dh
202
+ - conf/primer3_config/interpretations/tetraloop_i.ds
203
+ - conf/primer3_config/interpretations/triloop_i.dh
204
+ - conf/primer3_config/interpretations/triloop_i.ds
205
+ - conf/primer3_config/interpretations/tstack2_i.dh
206
+ - conf/primer3_config/interpretations/tstack2_i.ds
207
+ - conf/primer3_config/interpretations/tstack_i.dh
208
+ - conf/primer3_config/interpretations/tstack_i.ds
209
+ - conf/primer3_config/interpretations/tstack_tm_inf_i.dh
210
+ - conf/primer3_config/interpretations/tstack_tm_inf_i.ds
211
+ - conf/primer3_config/loops.dh
212
+ - conf/primer3_config/loops.ds
213
+ - conf/primer3_config/stack.dh
214
+ - conf/primer3_config/stack.ds
215
+ - conf/primer3_config/stackmm.dh
216
+ - conf/primer3_config/stackmm.ds
217
+ - conf/primer3_config/tetraloop.dh
218
+ - conf/primer3_config/tetraloop.ds
219
+ - conf/primer3_config/triloop.dh
220
+ - conf/primer3_config/triloop.ds
221
+ - conf/primer3_config/tstack.dh
222
+ - conf/primer3_config/tstack2.dh
223
+ - conf/primer3_config/tstack2.ds
224
+ - conf/primer3_config/tstack_tm_inf.ds
225
+ - lib/bio-polymarker.rb
226
+ - lib/bio/BFRTools.rb
227
+ - lib/bio/BIOExtensions.rb
228
+ - lib/bio/PolyploidTools/ChromosomeArm.rb
229
+ - lib/bio/PolyploidTools/ExonContainer.rb
230
+ - lib/bio/PolyploidTools/Marker.rb
231
+ - lib/bio/PolyploidTools/Mask.rb
232
+ - lib/bio/PolyploidTools/NoSNPSequence.rb
233
+ - lib/bio/PolyploidTools/PrimerRegion.rb
234
+ - lib/bio/PolyploidTools/SNP.rb
235
+ - lib/bio/PolyploidTools/SNPMutant.rb
236
+ - lib/bio/PolyploidTools/SNPSequence.rb
237
+ - lib/bio/db/blast.rb
238
+ - lib/bio/db/exonerate.rb
239
+ - lib/bio/db/primer3.rb
240
+ - test/data/7B_amplicon_test.fa
241
+ - test/data/7B_amplicon_test.fa.fai
242
+ - test/data/7B_amplicon_test_reference.fa
243
+ - test/data/7B_amplicon_test_reference.fa.fai
244
+ - test/data/7B_marker_test.txt
245
+ - test/data/BS00068396_51.fa
246
+ - test/data/BS00068396_51_blast.tab
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+ - test/data/BS00068396_51_contigs.aln
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+ - test/data/BS00068396_51_contigs.dnd
249
+ - test/data/BS00068396_51_contigs.fa
250
+ - test/data/BS00068396_51_contigs.fa.fai
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+ - test/data/BS00068396_51_contigs.fa.nhr
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+ - test/data/BS00068396_51_contigs.fa.nin
253
+ - test/data/BS00068396_51_contigs.fa.nsq
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+ - test/data/BS00068396_51_contigs.nhr
255
+ - test/data/BS00068396_51_contigs.nin
256
+ - test/data/BS00068396_51_contigs.nsq
257
+ - test/data/BS00068396_51_exonerate.tab
258
+ - test/data/BS00068396_51_for_polymarker.txt
259
+ - test/data/BS00068396_51_genes.txt
260
+ - test/data/IWGSC_CSS_1AL_scaff_1455974.fa
261
+ - test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa
262
+ - test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai
263
+ - test/data/LIB1716.bam
264
+ - test/data/LIB1716.bam.bai
265
+ - test/data/LIB1719.bam
266
+ - test/data/LIB1719.bam.bai
267
+ - test/data/LIB1721.bam
268
+ - test/data/LIB1721.bam.bai
269
+ - test/data/LIB1722.bam
270
+ - test/data/LIB1722.bam.bai
271
+ - test/data/PST130_7067.csv
272
+ - test/data/PST130_7067.fa
273
+ - test/data/PST130_7067.fa.fai
274
+ - test/data/PST130_7067.fa.ndb
275
+ - test/data/PST130_7067.fa.nhr
276
+ - test/data/PST130_7067.fa.nin
277
+ - test/data/PST130_7067.fa.not
278
+ - test/data/PST130_7067.fa.nsq
279
+ - test/data/PST130_7067.fa.ntf
280
+ - test/data/PST130_7067.fa.nto
281
+ - test/data/PST130_reverse_primer.csv
282
+ - test/data/S22380157.fa
283
+ - test/data/S22380157.fa.fai
284
+ - test/data/S22380157.vcf
285
+ - test/data/S58861868/LIB1716.bam
286
+ - test/data/S58861868/LIB1716.sam
287
+ - test/data/S58861868/LIB1719.bam
288
+ - test/data/S58861868/LIB1719.sam
289
+ - test/data/S58861868/LIB1721.bam
290
+ - test/data/S58861868/LIB1721.sam
291
+ - test/data/S58861868/LIB1722.bam
292
+ - test/data/S58861868/LIB1722.sam
293
+ - test/data/S58861868/S58861868.fa
294
+ - test/data/S58861868/S58861868.fa.fai
295
+ - test/data/S58861868/S58861868.vcf
296
+ - test/data/S58861868/header.txt
297
+ - test/data/S58861868/merged.bam
298
+ - test/data/S58861868/merged_reheader.bam
299
+ - test/data/S58861868/merged_reheader.bam.bai
300
+ - test/data/Test3Aspecific.csv
301
+ - test/data/Test3Aspecific_contigs.fa
302
+ - test/data/bfr_out_test.csv
303
+ - test/data/chr1A_C1145499T/chr1A_C1145499T.csv
304
+ - test/data/chr1A_G540414846C/chr1A_G540414846C.csv
305
+ - test/data/chr1A_G540414846C/chr1A_G540414846C.fa
306
+ - test/data/chr1A_T517634750C/chr1A_T517634750C.csv
307
+ - test/data/chr2D_C112180134A/chr2D_C112180134A.csv
308
+ - test/data/chr4D_C14473543T/chr4D_C14473543T.csv
309
+ - test/data/chr4D_C14473543T/chr4D_C14473543T.fa
310
+ - test/data/headerMergeed.txt
311
+ - test/data/headerS2238015
312
+ - test/data/mergedLibs.bam
313
+ - test/data/mergedLibsReheader.bam
314
+ - test/data/mergedLibsSorted.bam
315
+ - test/data/mergedLibsSorted.bam.bai
316
+ - test/data/patological_cases5D.csv
317
+ - test/data/primer_3_input_header_test
318
+ - test/data/short_primer_design_test.csv
319
+ - test/data/some_tests/some_tests.csv
320
+ - test/data/test_from_mutant.csv
321
+ - test/data/test_iselect.csv
322
+ - test/data/test_iselect_reference.fa
323
+ - test/data/test_iselect_reference.fa.fai
324
+ - test/data/test_primer3_error.csv
325
+ - test/data/test_primer3_error_contigs.fa
326
+ - test/test_bfr.rb
327
+ - test/test_blast.rb
328
+ - test/test_exon_container.rb
329
+ - test/test_exonearate.rb
330
+ - test/test_integration.rb
331
+ - test/test_snp_parsing.rb
332
+ - test/test_wrong_selection.sh
333
+ homepage: https://github.com/cb2e6f/bio-polymarker
334
+ licenses:
335
+ - MIT
336
+ metadata: {}
337
+ post_install_message:
338
+ rdoc_options: []
339
+ require_paths:
340
+ - lib
341
+ required_ruby_version: !ruby/object:Gem::Requirement
342
+ requirements:
343
+ - - ">="
344
+ - !ruby/object:Gem::Version
345
+ version: '0'
346
+ required_rubygems_version: !ruby/object:Gem::Requirement
347
+ requirements:
348
+ - - ">="
349
+ - !ruby/object:Gem::Version
350
+ version: '0'
351
+ requirements: []
352
+ rubygems_version: 3.5.16
353
+ signing_key:
354
+ specification_version: 4
355
+ summary: Tool to work with polyploids, NGS and molecular biology
356
+ test_files: []