bio-maf 0.3.2-java → 1.0.0-java

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (33) hide show
  1. data/Gemfile +3 -0
  2. data/README.md +34 -3
  3. data/bin/maf_bgzip +56 -0
  4. data/bin/maf_index +0 -6
  5. data/bio-maf.gemspec +3 -2
  6. data/features/bgzf.feature +62 -0
  7. data/features/maf-indexing.feature +10 -0
  8. data/features/maf-querying.feature +9 -0
  9. data/features/step_definitions/convert_steps.rb +1 -1
  10. data/features/support/env.rb +2 -0
  11. data/lib/bio/maf/index.rb +35 -13
  12. data/lib/bio/maf/maf.rb +3 -1
  13. data/lib/bio/maf/parser.rb +135 -39
  14. data/lib/bio/maf/writer.rb +4 -4
  15. data/man/maf_bgzip.1 +101 -0
  16. data/man/maf_bgzip.1.ronn +85 -0
  17. data/man/maf_extract.1 +5 -2
  18. data/man/maf_extract.1.ronn +4 -1
  19. data/man/maf_index.1 +3 -3
  20. data/man/maf_index.1.ronn +3 -2
  21. data/man/maf_tile.1 +5 -2
  22. data/man/maf_tile.1.ronn +4 -1
  23. data/man/maf_to_fasta.1 +1 -1
  24. data/spec/bio/maf/index_spec.rb +7 -0
  25. data/spec/bio/maf/parser_spec.rb +13 -0
  26. data/spec/spec_helper.rb +2 -0
  27. data/test/data/gap-1.kct +0 -0
  28. data/test/data/mm8.chrM.maf +2421 -0
  29. data/test/data/mm8.chrM.maf.bgz +0 -0
  30. data/test/data/mm8_chr7_tiny.kct +0 -0
  31. data/test/data/mm8_chr7_tiny.maf.gz +0 -0
  32. data/test/data/mm8_chrM_tiny.kct +0 -0
  33. metadata +30 -2
data/test/data/mm8.chrM.maf.bgz ADDED
Binary file
data/test/data/mm8_chr7_tiny.kct CHANGED
Binary file
data/test/data/mm8_chr7_tiny.maf.gz ADDED
Binary file
data/test/data/mm8_chrM_tiny.kct CHANGED
Binary file
metadata CHANGED
@@ -2,14 +2,14 @@
2
2
  name: bio-maf
3
3
  version: !ruby/object:Gem::Version
4
4
  prerelease:
5
- version: 0.3.2
5
+ version: 1.0.0
6
6
  platform: java
7
7
  authors:
8
8
  - Clayton Wheeler
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2012-07-26 00:00:00.000000000 Z
12
+ date: 2012-08-02 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: bio-alignment
@@ -27,6 +27,22 @@ dependencies:
27
27
  none: false
28
28
  prerelease: false
29
29
  type: :runtime
30
+ - !ruby/object:Gem::Dependency
31
+ name: bio-bgzf
32
+ version_requirements: !ruby/object:Gem::Requirement
33
+ requirements:
34
+ - - ~>
35
+ - !ruby/object:Gem::Version
36
+ version: 0.2.0
37
+ none: false
38
+ requirement: !ruby/object:Gem::Requirement
39
+ requirements:
40
+ - - ~>
41
+ - !ruby/object:Gem::Version
42
+ version: 0.2.0
43
+ none: false
44
+ prerelease: false
45
+ type: :runtime
30
46
  - !ruby/object:Gem::Dependency
31
47
  name: bio-genomic-interval
32
48
  version_requirements: !ruby/object:Gem::Requirement
@@ -79,6 +95,7 @@ description: Multiple Alignment Format parser for BioRuby.
79
95
  email: cswh@umich.edu
80
96
  executables:
81
97
  - find_overlaps
98
+ - maf_bgzip
82
99
  - maf_count
83
100
  - maf_dump_blocks
84
101
  - maf_extract
@@ -111,6 +128,7 @@ files:
111
128
  - benchmarks/sort_bench
112
129
  - benchmarks/split_bench
113
130
  - bin/find_overlaps
131
+ - bin/maf_bgzip
114
132
  - bin/maf_count
115
133
  - bin/maf_dump_blocks
116
134
  - bin/maf_extract
@@ -122,6 +140,7 @@ files:
122
140
  - bin/maf_write
123
141
  - bin/random_ranges
124
142
  - bio-maf.gemspec
143
+ - features/bgzf.feature
125
144
  - features/block-joining.feature
126
145
  - features/dir-access.feature
127
146
  - features/gap-removal.feature
@@ -159,6 +178,8 @@ files:
159
178
  - lib/bio/ucsc/genomic-interval-bin.rb
160
179
  - lib/bio/ucsc/ucsc_bin.rb
161
180
  - man/.gitignore
181
+ - man/maf_bgzip.1
182
+ - man/maf_bgzip.1.ronn
162
183
  - man/maf_extract.1
163
184
  - man/maf_extract.1.ronn
164
185
  - man/maf_index.1
@@ -185,8 +206,11 @@ files:
185
206
  - test/data/gap-filled1.fa
186
207
  - test/data/gap-sp1.fa
187
208
  - test/data/gap-sp1.fa.gz
209
+ - test/data/mm8.chrM.maf
210
+ - test/data/mm8.chrM.maf.bgz
188
211
  - test/data/mm8_chr7_tiny.kct
189
212
  - test/data/mm8_chr7_tiny.maf
213
+ - test/data/mm8_chr7_tiny.maf.gz
190
214
  - test/data/mm8_chr7_tiny_slice1.maf
191
215
  - test/data/mm8_chr7_tiny_slice2.maf
192
216
  - test/data/mm8_chr7_tiny_slice3.maf
@@ -233,6 +257,7 @@ signing_key:
233
257
  specification_version: 3
234
258
  summary: MAF parser for BioRuby
235
259
  test_files:
260
+ - features/bgzf.feature
236
261
  - features/block-joining.feature
237
262
  - features/dir-access.feature
238
263
  - features/gap-removal.feature
@@ -274,8 +299,11 @@ test_files:
274
299
  - test/data/gap-filled1.fa
275
300
  - test/data/gap-sp1.fa
276
301
  - test/data/gap-sp1.fa.gz
302
+ - test/data/mm8.chrM.maf
303
+ - test/data/mm8.chrM.maf.bgz
277
304
  - test/data/mm8_chr7_tiny.kct
278
305
  - test/data/mm8_chr7_tiny.maf
306
+ - test/data/mm8_chr7_tiny.maf.gz
279
307
  - test/data/mm8_chr7_tiny_slice1.maf
280
308
  - test/data/mm8_chr7_tiny_slice2.maf
281
309
  - test/data/mm8_chr7_tiny_slice3.maf