htslib 0.0.5 → 0.0.6

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.
@@ -0,0 +1,430 @@
1
+ # frozen_string_literal: true
2
+
3
+ module HTS
4
+ module LibHTS
5
+ attach_function \
6
+ :bcf_hdr_init,
7
+ [:string],
8
+ BcfHdr.by_ref
9
+
10
+ attach_function \
11
+ :bcf_hdr_destroy,
12
+ [BcfHdr],
13
+ :void
14
+
15
+ attach_function \
16
+ :bcf_init,
17
+ [],
18
+ Bcf1.by_ref
19
+
20
+ attach_function \
21
+ :bcf_destroy,
22
+ [Bcf1],
23
+ :void
24
+
25
+ attach_function \
26
+ :bcf_empty,
27
+ [Bcf1],
28
+ :void
29
+
30
+ attach_function \
31
+ :bcf_clear,
32
+ [Bcf1],
33
+ :void
34
+
35
+ attach_function \
36
+ :bcf_hdr_read,
37
+ [HtsFile],
38
+ BcfHdr.by_ref
39
+
40
+ attach_function \
41
+ :bcf_hdr_set_samples,
42
+ [BcfHdr, :string, :int],
43
+ :int
44
+
45
+ attach_function \
46
+ :bcf_subset_format,
47
+ [BcfHdr, Bcf1],
48
+ :int
49
+
50
+ attach_function \
51
+ :bcf_hdr_write,
52
+ [HtsFile, BcfHdr],
53
+ :int
54
+
55
+ attach_function \
56
+ :vcf_parse,
57
+ [KString, BcfHdr, Bcf1],
58
+ :int
59
+
60
+ attach_function \
61
+ :vcf_open_mode,
62
+ %i[string string string],
63
+ :int
64
+
65
+ attach_function \
66
+ :vcf_format,
67
+ [BcfHdr, Bcf1, KString],
68
+ :int
69
+
70
+ attach_function \
71
+ :bcf_read,
72
+ [HtsFile, BcfHdr, Bcf1],
73
+ :int
74
+
75
+ attach_function \
76
+ :bcf_unpack,
77
+ [Bcf1, :int],
78
+ :int
79
+
80
+ attach_function \
81
+ :bcf_dup,
82
+ [Bcf1],
83
+ Bcf1.by_ref
84
+
85
+ attach_function \
86
+ :bcf_copy,
87
+ [Bcf1, Bcf1],
88
+ Bcf1.by_ref
89
+
90
+ attach_function \
91
+ :bcf_write,
92
+ [HtsFile, BcfHdr, Bcf1],
93
+ :int
94
+
95
+ attach_function \
96
+ :vcf_hdr_read,
97
+ [HtsFile],
98
+ BcfHdr.by_ref
99
+
100
+ attach_function \
101
+ :vcf_hdr_write,
102
+ [HtsFile, BcfHdr],
103
+ :int
104
+
105
+ attach_function \
106
+ :vcf_read,
107
+ [HtsFile, BcfHdr, Bcf1],
108
+ :int
109
+
110
+ attach_function \
111
+ :vcf_write,
112
+ [HtsFile, BcfHdr, Bcf1],
113
+ :int
114
+
115
+ attach_function \
116
+ :bcf_readrec,
117
+ [BGZF, :pointer, :pointer, :pointer, :hts_pos_t, :hts_pos_t],
118
+ :int
119
+
120
+ attach_function \
121
+ :vcf_write_line,
122
+ [HtsFile, KString],
123
+ :int
124
+
125
+ attach_function \
126
+ :bcf_hdr_dup,
127
+ [BcfHdr],
128
+ BcfHdr.by_ref
129
+
130
+ attach_function \
131
+ :bcf_hdr_merge,
132
+ [BcfHdr, BcfHdr],
133
+ BcfHdr.by_ref
134
+
135
+ attach_function \
136
+ :bcf_hdr_add_sample,
137
+ [BcfHdr, :string],
138
+ :int
139
+
140
+ attach_function \
141
+ :bcf_hdr_set,
142
+ [BcfHdr, :string],
143
+ :int
144
+
145
+ attach_function \
146
+ :bcf_hdr_format,
147
+ [BcfHdr, :int, KString],
148
+ :int
149
+
150
+ attach_function \
151
+ :bcf_hdr_fmt_text,
152
+ [BcfHdr, :int, :pointer],
153
+ :string
154
+
155
+ attach_function \
156
+ :bcf_hdr_append,
157
+ [BcfHdr, :string],
158
+ :int
159
+
160
+ attach_function \
161
+ :bcf_hdr_printf,
162
+ [BcfHdr, :string, :varargs],
163
+ :int
164
+
165
+ attach_function \
166
+ :bcf_hdr_get_version,
167
+ [BcfHdr],
168
+ :string
169
+
170
+ attach_function \
171
+ :bcf_hdr_set_version,
172
+ [BcfHdr, :string],
173
+ :int
174
+
175
+ attach_function \
176
+ :bcf_hdr_remove,
177
+ [BcfHdr, :int, :string],
178
+ :void
179
+
180
+ attach_function \
181
+ :bcf_hdr_subset,
182
+ [BcfHdr, :int, :pointer, :pointer],
183
+ BcfHdr.by_ref
184
+
185
+ attach_function \
186
+ :bcf_hdr_seqnames,
187
+ [BcfHdr, :pointer],
188
+ :pointer
189
+
190
+ attach_function \
191
+ :bcf_hdr_parse,
192
+ [BcfHdr, :string],
193
+ :int
194
+
195
+ attach_function \
196
+ :bcf_hdr_sync,
197
+ [BcfHdr],
198
+ :int
199
+
200
+ attach_function \
201
+ :bcf_hdr_parse_line,
202
+ [BcfHdr, :string, :pointer],
203
+ BcfHrec.by_ref
204
+
205
+ attach_function \
206
+ :bcf_hrec_format,
207
+ [BcfHrec, KString],
208
+ :int
209
+
210
+ attach_function \
211
+ :bcf_hdr_add_hrec,
212
+ [BcfHdr, BcfHrec],
213
+ :int
214
+
215
+ attach_function \
216
+ :bcf_hdr_get_hrec,
217
+ [BcfHdr, :int, :string, :string, :string],
218
+ BcfHrec.by_ref
219
+
220
+ attach_function \
221
+ :bcf_hrec_dup,
222
+ [BcfHrec],
223
+ BcfHrec.by_ref
224
+
225
+ attach_function \
226
+ :bcf_hrec_add_key,
227
+ [BcfHrec, :string, :size_t],
228
+ :int
229
+
230
+ attach_function \
231
+ :bcf_hrec_set_val,
232
+ [BcfHrec, :int, :string, :size_t, :int],
233
+ :int
234
+
235
+ attach_function \
236
+ :bcf_hrec_find_key,
237
+ [BcfHrec, :string],
238
+ :int
239
+
240
+ attach_function \
241
+ :hrec_add_idx,
242
+ [BcfHrec, :int],
243
+ :int
244
+
245
+ attach_function \
246
+ :bcf_hrec_destroy,
247
+ [BcfHrec],
248
+ :void
249
+
250
+ attach_function \
251
+ :bcf_subset,
252
+ [BcfHdr, Bcf1, :int, :pointer],
253
+ :int
254
+
255
+ attach_function \
256
+ :bcf_translate,
257
+ [BcfHdr, BcfHdr, Bcf1],
258
+ :int
259
+
260
+ attach_function \
261
+ :bcf_get_variant_types,
262
+ [Bcf1],
263
+ :int
264
+
265
+ attach_function \
266
+ :bcf_get_variant_type,
267
+ [Bcf1, :int],
268
+ :int
269
+
270
+ attach_function \
271
+ :bcf_is_snp,
272
+ [Bcf1],
273
+ :int
274
+
275
+ attach_function \
276
+ :bcf_update_filter,
277
+ [BcfHdr, Bcf1, :pointer, :int],
278
+ :int
279
+
280
+ attach_function \
281
+ :bcf_add_filter,
282
+ [BcfHdr, Bcf1, :int],
283
+ :int
284
+
285
+ attach_function \
286
+ :bcf_remove_filter,
287
+ [BcfHdr, Bcf1, :int, :int],
288
+ :int
289
+
290
+ attach_function \
291
+ :bcf_has_filter,
292
+ [BcfHdr, Bcf1, :string],
293
+ :int
294
+
295
+ attach_function \
296
+ :bcf_update_alleles,
297
+ [BcfHdr, Bcf1, :pointer, :int],
298
+ :int
299
+
300
+ attach_function \
301
+ :bcf_update_alleles_str,
302
+ [BcfHdr, Bcf1, :string],
303
+ :int
304
+
305
+ attach_function \
306
+ :bcf_update_id,
307
+ [BcfHdr, Bcf1, :string],
308
+ :int
309
+
310
+ attach_function \
311
+ :bcf_add_id,
312
+ [BcfHdr, Bcf1, :string],
313
+ :int
314
+
315
+ attach_function \
316
+ :bcf_update_info,
317
+ [BcfHdr, Bcf1, :string, :pointer, :int, :int],
318
+ :int
319
+
320
+ attach_function \
321
+ :bcf_update_format_string,
322
+ [BcfHdr, Bcf1, :string, :pointer, :int],
323
+ :int
324
+
325
+ attach_function \
326
+ :bcf_update_format,
327
+ [BcfHdr, Bcf1, :string, :pointer, :int, :int],
328
+ :int
329
+
330
+ attach_function \
331
+ :bcf_get_fmt,
332
+ [BcfHdr, Bcf1, :string],
333
+ BcfFmt.by_ref
334
+
335
+ attach_function \
336
+ :bcf_get_info,
337
+ [BcfHdr, Bcf1, :string],
338
+ BcfInfo.by_ref
339
+
340
+ attach_function \
341
+ :bcf_get_fmt_id,
342
+ [Bcf1, :int],
343
+ BcfFmt.by_ref
344
+
345
+ attach_function \
346
+ :bcf_get_info_id,
347
+ [Bcf1, :int],
348
+ BcfInfo.by_ref
349
+
350
+ attach_function \
351
+ :bcf_get_info_values,
352
+ [BcfHdr, Bcf1, :string, :pointer, :pointer, :int],
353
+ :int
354
+
355
+ attach_function \
356
+ :bcf_get_format_string,
357
+ [BcfHdr, Bcf1, :string, :pointer, :pointer],
358
+ :int
359
+
360
+ attach_function \
361
+ :bcf_get_format_values,
362
+ [BcfHdr, Bcf1, :string, :pointer, :pointer, :int],
363
+ :int
364
+
365
+ attach_function \
366
+ :bcf_hdr_id2int,
367
+ [BcfHdr, :int, :string],
368
+ :int
369
+
370
+ attach_function \
371
+ :bcf_fmt_array,
372
+ [KString, :int, :int, :pointer],
373
+ :int
374
+
375
+ attach_function \
376
+ :bcf_fmt_sized_array,
377
+ [KString, :pointer],
378
+ :uint8_t
379
+
380
+ attach_function \
381
+ :bcf_enc_vchar,
382
+ [KString, :int, :string],
383
+ :int
384
+
385
+ attach_function \
386
+ :bcf_enc_vint,
387
+ [KString, :int, :pointer, :int],
388
+ :int
389
+
390
+ attach_function \
391
+ :bcf_enc_vfloat,
392
+ [KString, :int, :pointer],
393
+ :int
394
+
395
+ attach_function \
396
+ :bcf_index_load2,
397
+ %i[string string],
398
+ HtsIdx.by_ref
399
+
400
+ attach_function \
401
+ :bcf_index_load3,
402
+ %i[string string int],
403
+ HtsIdx.by_ref
404
+
405
+ attach_function \
406
+ :bcf_index_build,
407
+ %i[string int],
408
+ :int
409
+
410
+ attach_function \
411
+ :bcf_index_build2,
412
+ %i[string string int],
413
+ :int
414
+
415
+ attach_function \
416
+ :bcf_index_build3,
417
+ %i[string string int int],
418
+ :int
419
+
420
+ attach_function \
421
+ :bcf_idx_init,
422
+ [HtsFile, BcfHdr, :int, :string],
423
+ :int
424
+
425
+ attach_function \
426
+ :bcf_idx_save,
427
+ [HtsFile],
428
+ :int
429
+ end
430
+ end
data/lib/hts/version.rb CHANGED
@@ -1,5 +1,5 @@
1
1
  # frozen_string_literal: true
2
2
 
3
3
  module HTS
4
- VERSION = "0.0.5"
4
+ VERSION = "0.0.6"
5
5
  end
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: htslib
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.0.5
4
+ version: 0.0.6
5
5
  platform: ruby
6
6
  authors:
7
7
  - kojix2
8
- autorequire:
8
+ autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2021-12-26 00:00:00.000000000 Z
11
+ date: 2022-01-03 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: ffi
@@ -122,7 +122,7 @@ dependencies:
122
122
  - - ">="
123
123
  - !ruby/object:Gem::Version
124
124
  version: '0'
125
- description:
125
+ description:
126
126
  email:
127
127
  - 2xijok@gmail.com
128
128
  executables: []
@@ -152,8 +152,10 @@ files:
152
152
  - lib/hts/libhts/hts.rb
153
153
  - lib/hts/libhts/kfunc.rb
154
154
  - lib/hts/libhts/sam.rb
155
+ - lib/hts/libhts/sam_funcs.rb
155
156
  - lib/hts/libhts/tbx.rb
156
157
  - lib/hts/libhts/vcf.rb
158
+ - lib/hts/libhts/vcf_funcs.rb
157
159
  - lib/hts/tabix.rb
158
160
  - lib/hts/version.rb
159
161
  - lib/htslib.rb
@@ -161,7 +163,7 @@ homepage: https://github.com/kojix2/ruby-htslib
161
163
  licenses:
162
164
  - MIT
163
165
  metadata: {}
164
- post_install_message:
166
+ post_install_message:
165
167
  rdoc_options: []
166
168
  require_paths:
167
169
  - lib
@@ -177,7 +179,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
177
179
  version: '0'
178
180
  requirements: []
179
181
  rubygems_version: 3.3.3
180
- signing_key:
182
+ signing_key:
181
183
  specification_version: 4
182
184
  summary: HTSlib bindings for Ruby
183
185
  test_files: []