htslib 0.1.0 → 0.2.2

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 (31) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +30 -11
  3. data/lib/hts/bam/aux.rb +1 -0
  4. data/lib/hts/bam/cigar.rb +5 -7
  5. data/lib/hts/bam/flag.rb +5 -0
  6. data/lib/hts/bam/header.rb +1 -0
  7. data/lib/hts/bam/record.rb +7 -4
  8. data/lib/hts/bam.rb +128 -35
  9. data/lib/hts/bcf/format.rb +4 -4
  10. data/lib/hts/bcf/header.rb +1 -0
  11. data/lib/hts/bcf/header_record.rb +11 -0
  12. data/lib/hts/bcf/info.rb +3 -2
  13. data/lib/hts/bcf/record.rb +31 -30
  14. data/lib/hts/bcf.rb +183 -30
  15. data/lib/hts/faidx.rb +62 -21
  16. data/lib/hts/hts.rb +54 -2
  17. data/lib/hts/libhts/bgzf.rb +5 -5
  18. data/lib/hts/libhts/constants.rb +42 -20
  19. data/lib/hts/libhts/cram.rb +312 -279
  20. data/lib/hts/libhts/hfile.rb +29 -11
  21. data/lib/hts/libhts/hts.rb +158 -25
  22. data/lib/hts/libhts/sam.rb +695 -94
  23. data/lib/hts/libhts/sam_funcs.rb +131 -588
  24. data/lib/hts/libhts/tbx.rb +1 -1
  25. data/lib/hts/libhts/tbx_funcs.rb +25 -0
  26. data/lib/hts/libhts/vcf.rb +460 -234
  27. data/lib/hts/libhts/vcf_funcs.rb +277 -424
  28. data/lib/hts/libhts.rb +1 -0
  29. data/lib/hts/tbx.rb +39 -8
  30. data/lib/hts/version.rb +1 -1
  31. metadata +5 -3
data/lib/hts/libhts/cram.rb CHANGED
@@ -2,291 +2,324 @@
2
2
 
3
3
  module HTS
4
4
  module LibHTS
5
- #
6
- # attach_function \
7
- # :cram_fd_get_header,
8
- # [CramFd],
9
- # SamHdr.by_ref
10
- #
11
- # attach_function \
12
- # :cram_fd_set_header,
13
- # [CramFd, SamHdr.by_ref],
14
- # :void
15
- #
16
- # attach_function \
17
- # :cram_fd_get_version,
18
- # [CramFd],
19
- # :int
20
- #
21
- # attach_function \
22
- # :cram_fd_set_version,
23
- # [CramFd, :int],
24
- # :void
25
- #
26
- # attach_function \
27
- # :cram_major_vers,
28
- # [CramFd],
29
- # :int
30
- #
31
- # attach_function \
32
- # :cram_minor_vers,
33
- # [CramFd],
34
- # :int
35
- #
36
- # attach_function \
37
- # :cram_fd_get_fp,
38
- # [CramFd],
39
- # HFile.by_ref
40
- #
41
- # attach_function \
42
- # :cram_fd_set_fp,
43
- # [CramFd, HFile],
44
- # :void
45
- #
46
- # attach_function \
47
- # :cram_container_get_length,
48
- # [CramContainer],
49
- # :int32
50
- #
51
- # attach_function \
52
- # :cram_container_set_length,
53
- # [CramContainer, :int32],
54
- # :void
55
- #
56
- # attach_function \
57
- # :cram_container_get_num_blocks,
58
- # [CramContainer],
59
- # :int32
60
- #
61
- # attach_function \
62
- # :cram_container_set_num_blocks,
63
- # [CramContainer, :int32],
64
- # :void
65
- #
66
- # attach_function \
67
- # :cram_container_get_landmarks,
68
- # [CramContainer, :int32],
69
- # :pointer
70
- #
71
- # attach_function \
72
- # :cram_container_set_landmarks,
73
- # [CramContainer, :Int32, :pointer],
74
- # :void
75
- #
76
- # attach_function \
77
- # :cram_container_is_empty,
78
- # [CramFd],
79
- # :int
80
- #
81
- # attach_function \
82
- # :cram_block_get_content_id,
83
- # [CramBlock],
84
- # :int32
85
- #
86
- # attach_function \
87
- # :cram_block_get_comp_size,
88
- # [CramBlock],
89
- # :int32
90
- #
91
- # attach_function \
92
- # :cram_block_get_uncomp_size,
93
- # [CramBlock],
94
- # :int32
95
- #
96
- # attach_function \
97
- # :cram_block_get_crc32,
98
- # [CramBlock],
99
- # :int32
100
- #
101
- # attach_function \
102
- # :cram_block_get_data,
103
- # [CramBlock],
104
- # :pointer
105
- #
106
- # attach_function \
107
- # :cram_block_get_content_type,
108
- # [CramBlock],
109
- # CramContentType # ?
110
- #
111
- # attach_function \
112
- # :cram_block_set_content_id,
113
- # [CramBlock, :int32],
114
- # :void
115
- #
116
- # attach_function \
117
- # :cram_block_set_comp_size,
118
- # [CramBlock, :int32],
119
- # :void
120
- #
121
- # attach_function \
122
- # :cram_block_set_uncomp_size,
123
- # [CramBlock, :int32],
124
- # :void
125
- #
126
- # attach_function \
127
- # :cram_block_set_crc32,
128
- # [CramBlock, :int32],
129
- # :void
130
- #
131
- # attach_function \
132
- # :cram_block_set_data,
133
- # [CramBlock, :pointer],
134
- # :void
135
- #
136
- # attach_function \
137
- # :cram_block_append,
138
- # [CramBlock, :pointer, :int],
139
- # :int
140
- #
141
- # attach_function \
142
- # :cram_block_update_size,
143
- # [CramBlock],
144
- # :void
145
- #
146
- # attach_function \
147
- # :cram_block_get_offset,
148
- # [CramBlock],
149
- # :size_t
150
- #
151
- # attach_function \
152
- # :cram_block_set_offset,
153
- # [CramBlock, :size_t],
154
- # :void
155
- #
156
- # attach_function \
157
- # :cram_block_size,
158
- # [CramBlock],
159
- # :uint32
160
- #
161
- # attach_function \
162
- # :cram_transcode_rg,
163
- # [CramFd, CramFd, CramContainer, :int, :pointer, :pointer],
164
- # :int
165
- #
166
- # attach_function \
167
- # :cram_copy_slice,
168
- # [CramFd, CramFd, :int32],
169
- # :int
170
- #
171
- # attach_function \
172
- # :cram_new_block,
173
- # [CramContentType, :int],
174
- # CramBlock
175
- #
176
- # attach_function \
177
- # :cram_read_block,
178
- # [CramFd],
179
- # CramBlock
180
- #
181
- # attach_function \
182
- # :cram_write_block,
183
- # [CramFd, CramBlock],
184
- # :int
185
- #
186
- # attach_function \
187
- # :cram_free_block,
188
- # [CramBlock],
189
- # :void
190
- #
191
- # attach_function \
192
- # :cram_uncompress_block,
193
- # [CramBlock],
194
- # :int
195
- #
196
- # attach_function \
197
- # :cram_compress_block,
198
- # [CramFd, CramBlock, CramMetrics, :int, :int],
199
- # :int
200
- #
5
+ typedef :pointer, :cram_fd
6
+ typedef :pointer, :cram_container
7
+ typedef :pointer, :cram_block
8
+ typedef :pointer, :cram_metrics
9
+
10
+ attach_function \
11
+ :cram_fd_get_header,
12
+ [:cram_fd],
13
+ SamHdr.by_ref
14
+
15
+ attach_function \
16
+ :cram_fd_set_header,
17
+ [:cram_fd, SamHdr.by_ref],
18
+ :void
19
+
20
+ attach_function \
21
+ :cram_fd_get_version,
22
+ [:cram_fd],
23
+ :int
24
+
25
+ attach_function \
26
+ :cram_fd_set_version,
27
+ %i[cram_fd int],
28
+ :void
29
+
30
+ attach_function \
31
+ :cram_major_vers,
32
+ [:cram_fd],
33
+ :int
34
+
35
+ attach_function \
36
+ :cram_minor_vers,
37
+ [:cram_fd],
38
+ :int
39
+
40
+ attach_function \
41
+ :cram_fd_get_fp,
42
+ [:cram_fd],
43
+ HFile.by_ref
44
+
45
+ attach_function \
46
+ :cram_fd_set_fp,
47
+ [:cram_fd, HFile],
48
+ :void
49
+
50
+ attach_function \
51
+ :cram_container_get_length,
52
+ [:cram_container],
53
+ :int32
54
+
55
+ attach_function \
56
+ :cram_container_set_length,
57
+ %i[cram_container int32],
58
+ :void
59
+
60
+ attach_function \
61
+ :cram_container_get_num_blocks,
62
+ [:cram_container],
63
+ :int32
64
+
65
+ attach_function \
66
+ :cram_container_set_num_blocks,
67
+ %i[cram_container int32],
68
+ :void
69
+
70
+ attach_function \
71
+ :cram_container_get_landmarks,
72
+ %i[cram_container int32],
73
+ :pointer
74
+
75
+ attach_function \
76
+ :cram_container_set_landmarks,
77
+ %i[cram_container int32 pointer],
78
+ :void
79
+
80
+ attach_function \
81
+ :cram_container_is_empty,
82
+ [:cram_fd],
83
+ :int
84
+
85
+ attach_function \
86
+ :cram_block_get_content_id,
87
+ [:cram_block],
88
+ :int32
89
+
90
+ attach_function \
91
+ :cram_block_get_comp_size,
92
+ [:cram_block],
93
+ :int32
94
+
95
+ attach_function \
96
+ :cram_block_get_uncomp_size,
97
+ [:cram_block],
98
+ :int32
99
+
100
+ attach_function \
101
+ :cram_block_get_crc32,
102
+ [:cram_block],
103
+ :int32
104
+
105
+ attach_function \
106
+ :cram_block_get_data,
107
+ [:cram_block],
108
+ :pointer
109
+
110
+ attach_function \
111
+ :cram_block_get_content_type,
112
+ [:cram_block],
113
+ CramContentType
114
+
115
+ attach_function \
116
+ :cram_block_set_content_id,
117
+ %i[cram_block int32],
118
+ :void
119
+
120
+ attach_function \
121
+ :cram_block_set_comp_size,
122
+ %i[cram_block int32],
123
+ :void
124
+
125
+ attach_function \
126
+ :cram_block_set_uncomp_size,
127
+ %i[cram_block int32],
128
+ :void
129
+
130
+ attach_function \
131
+ :cram_block_set_crc32,
132
+ %i[cram_block int32],
133
+ :void
134
+
135
+ attach_function \
136
+ :cram_block_set_data,
137
+ %i[cram_block pointer],
138
+ :void
139
+
140
+ attach_function \
141
+ :cram_block_append,
142
+ %i[cram_block pointer int],
143
+ :int
144
+
145
+ attach_function \
146
+ :cram_block_update_size,
147
+ [:cram_block],
148
+ :void
149
+
150
+ attach_function \
151
+ :cram_block_get_offset,
152
+ [:cram_block],
153
+ :size_t
154
+
155
+ attach_function \
156
+ :cram_block_set_offset,
157
+ %i[cram_block size_t],
158
+ :void
159
+
160
+ attach_function \
161
+ :cram_block_size,
162
+ [:cram_block],
163
+ :uint32
164
+
165
+ attach_function \
166
+ :cram_transcode_rg,
167
+ %i[cram_fd cram_fd cram_container int pointer pointer],
168
+ :int
169
+
170
+ attach_function \
171
+ :cram_copy_slice,
172
+ %i[cram_fd cram_fd int32],
173
+ :int
174
+
175
+ attach_function \
176
+ :cram_slice_hdr_get_num_blocks,
177
+ [:pointer],
178
+ :int32
179
+
180
+ attach_function \
181
+ :cram_slice_hdr_get_embed_ref_id,
182
+ [:pointer],
183
+ :int
184
+
185
+ attach_function \
186
+ :cram_slice_hdr_get_coords,
187
+ %i[pointer pointer pointer pointer],
188
+ :void
189
+
190
+ attach_function \
191
+ :cram_decode_slice_header,
192
+ %i[pointer pointer],
193
+ :pointer
194
+
195
+ attach_function \
196
+ :cram_free_slice_header,
197
+ [:pointer],
198
+ :void
199
+
200
+ attach_function \
201
+ :cram_new_block,
202
+ [CramContentType, :int],
203
+ :cram_block
204
+
205
+ attach_function \
206
+ :cram_read_block,
207
+ [:cram_fd],
208
+ :cram_block
209
+
210
+ attach_function \
211
+ :cram_write_block,
212
+ %i[cram_fd cram_block],
213
+ :int
214
+
215
+ attach_function \
216
+ :cram_free_block,
217
+ [:cram_block],
218
+ :void
219
+
220
+ attach_function \
221
+ :cram_uncompress_block,
222
+ [:cram_block],
223
+ :int
224
+
225
+ attach_function \
226
+ :cram_compress_block,
227
+ %i[cram_fd cram_block cram_metrics int int],
228
+ :int
229
+
201
230
  # attach_function \
202
231
  # :cram_compress_block2,
203
- # [CramFd, CramSlice, CramBlock, CramMetrics, :int, :int],
204
- # :int
205
- #
206
- # attach_function \
207
- # :cram_new_container,
208
- # [:int, :int],
209
- # CramContainer
210
- #
211
- # attach_function \
212
- # :cram_free_container,
213
- # [CramContainer],
214
- # :void
215
- #
216
- # attach_function \
217
- # :cram_read_container,
218
- # [CramFd],
219
- # CramContainer
220
- #
221
- # attach_function \
222
- # :cram_write_container,
223
- # [CramFd, CramContainer],
224
- # :int
225
- #
226
- # attach_function \
227
- # :cram_store_container,
228
- # [CramFd, CramContainer, :string, :pointer],
229
- # :int
230
- #
231
- # attach_function \
232
- # :cram_container_size,
233
- # [CramContainer],
232
+ # %i[cram_fd cram_slice cram_block cram_metrics int int],
234
233
  # :int
235
- #
236
- # attach_function \
237
- # :cram_open,
238
- # [:string, :string],
239
- # CramFd
240
- #
241
- # attach_function \
242
- # :cram_dopen,
243
- # [:pointer, :string, :string],
244
- # CramFd
245
- #
246
- # attach_function \
247
- # :cram_close,
248
- # [CramFd],
249
- # :int
250
- #
234
+
235
+ attach_function \
236
+ :cram_new_container,
237
+ %i[int int],
238
+ :cram_container
239
+
240
+ attach_function \
241
+ :cram_free_container,
242
+ [:cram_container],
243
+ :void
244
+
245
+ attach_function \
246
+ :cram_read_container,
247
+ [:cram_fd],
248
+ :cram_container
249
+
250
+ attach_function \
251
+ :cram_write_container,
252
+ %i[cram_fd cram_container],
253
+ :int
254
+
255
+ attach_function \
256
+ :cram_store_container,
257
+ %i[cram_fd cram_container string pointer],
258
+ :int
259
+
260
+ attach_function \
261
+ :cram_container_size,
262
+ [:cram_container],
263
+ :int
264
+
265
+ attach_function \
266
+ :cram_open,
267
+ %i[string string],
268
+ :cram_fd
269
+
270
+ attach_function \
271
+ :cram_dopen,
272
+ %i[pointer string string],
273
+ :cram_fd
274
+
275
+ attach_function \
276
+ :cram_close,
277
+ [:cram_fd],
278
+ :int
251
279
 
252
280
  attach_function \
253
281
  :cram_seek,
254
- %i[pointer off_t int], :int # FIXME: pointer should be CramFd
282
+ %i[pointer off_t int],
283
+ :int # FIXME: pointer should be :cram_fd
255
284
 
256
- #
257
- # attach_function \
258
- # :cram_flush,
259
- # [CramFd],
260
- # :int
261
- #
262
- # attach_function \
263
- # :cram_eof,
264
- # [CramFd],
265
- # :int
266
- #
267
- # attach_function \
268
- # :cram_set_option,
269
- # [CramFd, HtsFmtOption, ...], # vararg!
270
- # :int
271
- #
272
- # attach_function \
273
- # :cram_set_voption,
274
- # [CramFd, HtsFmtOption, VaList],
275
- # :int
276
- #
277
- # attach_function \
278
- # :cram_set_header,
279
- # [CramFd, SamHdr.by_ref],
280
- # :int
281
- #
282
- # attach_function \
283
- # :cram_check_eof = :cram_check_EOF,
284
- # [CramFd], :int
285
- #
286
- # attach_function \
287
- # :cram_get_refs,
288
- # [HtsFile],
289
- # RefsT # what is RefsT
290
- #
285
+ attach_function \
286
+ :cram_flush,
287
+ [:cram_fd],
288
+ :int
289
+
290
+ attach_function \
291
+ :cram_eof,
292
+ [:cram_fd],
293
+ :int
294
+
295
+ attach_function \
296
+ :cram_set_option,
297
+ [:cram_fd, HtsFmtOption, :varargs],
298
+ :int
299
+
300
+ attach_function \
301
+ :cram_set_voption,
302
+ [:cram_fd, HtsFmtOption, :pointer], # va_list
303
+ :int
304
+
305
+ attach_function \
306
+ :cram_set_header,
307
+ [:cram_fd, SamHdr.by_ref],
308
+ :int
309
+
310
+ attach_function \
311
+ :cram_check_EOF,
312
+ [:cram_fd],
313
+ :int
314
+
315
+ attach_function \
316
+ :int32_put_blk,
317
+ %i[cram_block int32_t],
318
+ :int
319
+
320
+ attach_function \
321
+ :cram_get_refs,
322
+ [HtsFile.by_ref],
323
+ :pointer # refs_t
291
324
  end
292
325
  end