comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bam.h @ 0:74f5ea818cea

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1 /* The MIT License
2
3 Copyright (c) 2008 Genome Research Ltd (GRL).
4
5 Permission is hereby granted, free of charge, to any person obtaining
6 a copy of this software and associated documentation files (the
7 "Software"), to deal in the Software without restriction, including
8 without limitation the rights to use, copy, modify, merge, publish,
9 distribute, sublicense, and/or sell copies of the Software, and to
10 permit persons to whom the Software is furnished to do so, subject to
11 the following conditions:
12
13 The above copyright notice and this permission notice shall be
14 included in all copies or substantial portions of the Software.
15
16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
17 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
18 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
19 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
20 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
21 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
22 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
23 SOFTWARE.
24 */
25
26 /* Contact: Heng Li <lh3@sanger.ac.uk> */
27
28 #ifndef BAM_BAM_H
29 #define BAM_BAM_H
30
31 /*!
32 @header
33
34 BAM library provides I/O and various operations on manipulating files
35 in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map)
36 format. It now supports importing from or exporting to TAM, sorting,
37 merging, generating pileup, and quickly retrieval of reads overlapped
38 with a specified region.
39
40 @copyright Genome Research Ltd.
41 */
42
43 #include <stdint.h>
44 #include <stdlib.h>
45 #include <string.h>
46 #include <stdio.h>
47
48 #ifndef BAM_LITE
49 #define BAM_VIRTUAL_OFFSET16
50 #include "bgzf.h"
51 /*! @abstract BAM file handler */
52 typedef BGZF *bamFile;
53 #define bam_open(fn, mode) bgzf_open(fn, mode)
54 #define bam_dopen(fd, mode) bgzf_fdopen(fd, mode)
55 #define bam_close(fp) bgzf_close(fp)
56 #define bam_read(fp, buf, size) bgzf_read(fp, buf, size)
57 #define bam_write(fp, buf, size) bgzf_write(fp, buf, size)
58 #define bam_tell(fp) bgzf_tell(fp)
59 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
60 #else
61 #define BAM_TRUE_OFFSET
62 #include <zlib.h>
63 typedef gzFile bamFile;
64 #define bam_open(fn, mode) gzopen(fn, mode)
65 #define bam_dopen(fd, mode) gzdopen(fd, mode)
66 #define bam_close(fp) gzclose(fp)
67 #define bam_read(fp, buf, size) gzread(fp, buf, size)
68 /* no bam_write/bam_tell/bam_seek() here */
69 #endif
70
71 /*! @typedef
72 @abstract Structure for the alignment header.
73 @field n_targets number of reference sequences
74 @field target_name names of the reference sequences
75 @field target_len lengths of the referene sequences
76 @field hash hash table for fast name lookup
77 @field rg2lib hash table for @RG-ID -> LB lookup
78 @field l_text length of the plain text in the header
79 @field text plain text
80
81 @discussion Field hash points to null by default. It is a private
82 member.
83 */
84 typedef struct {
85 int32_t n_targets;
86 char **target_name;
87 uint32_t *target_len;
88 void *hash, *rg2lib;
89 int l_text;
90 char *text;
91 } bam_header_t;
92
93 /*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */
94 #define BAM_FPAIRED 1
95 /*! @abstract the read is mapped in a proper pair */
96 #define BAM_FPROPER_PAIR 2
97 /*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */
98 #define BAM_FUNMAP 4
99 /*! @abstract the mate is unmapped */
100 #define BAM_FMUNMAP 8
101 /*! @abstract the read is mapped to the reverse strand */
102 #define BAM_FREVERSE 16
103 /*! @abstract the mate is mapped to the reverse strand */
104 #define BAM_FMREVERSE 32
105 /*! @abstract this is read1 */
106 #define BAM_FREAD1 64
107 /*! @abstract this is read2 */
108 #define BAM_FREAD2 128
109 /*! @abstract not primary alignment */
110 #define BAM_FSECONDARY 256
111 /*! @abstract QC failure */
112 #define BAM_FQCFAIL 512
113 /*! @abstract optical or PCR duplicate */
114 #define BAM_FDUP 1024
115
116 #define BAM_OFDEC 0
117 #define BAM_OFHEX 1
118 #define BAM_OFSTR 2
119
120 /*! @abstract defautl mask for pileup */
121 #define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)
122
123 #define BAM_CORE_SIZE sizeof(bam1_core_t)
124
125 /**
126 * Describing how CIGAR operation/length is packed in a 32-bit integer.
127 */
128 #define BAM_CIGAR_SHIFT 4
129 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1)
130
131 /*
132 CIGAR operations.
133 */
134 /*! @abstract CIGAR: match */
135 #define BAM_CMATCH 0
136 /*! @abstract CIGAR: insertion to the reference */
137 #define BAM_CINS 1
138 /*! @abstract CIGAR: deletion from the reference */
139 #define BAM_CDEL 2
140 /*! @abstract CIGAR: skip on the reference (e.g. spliced alignment) */
141 #define BAM_CREF_SKIP 3
142 /*! @abstract CIGAR: clip on the read with clipped sequence present in qseq */
143 #define BAM_CSOFT_CLIP 4
144 /*! @abstract CIGAR: clip on the read with clipped sequence trimmed off */
145 #define BAM_CHARD_CLIP 5
146 /*! @abstract CIGAR: padding */
147 #define BAM_CPAD 6
148
149 /*! @typedef
150 @abstract Structure for core alignment information.
151 @field tid chromosome ID, defined by bam_header_t
152 @field pos 0-based leftmost coordinate
153 @field strand strand; 0 for forward and 1 otherwise
154 @field bin bin calculated by bam_reg2bin()
155 @field qual mapping quality
156 @field l_qname length of the query name
157 @field flag bitwise flag
158 @field n_cigar number of CIGAR operations
159 @field l_qseq length of the query sequence (read)
160 */
161 typedef struct {
162 int32_t tid;
163 int32_t pos;
164 uint32_t bin:16, qual:8, l_qname:8;
165 uint32_t flag:16, n_cigar:16;
166 int32_t l_qseq;
167 int32_t mtid;
168 int32_t mpos;
169 int32_t isize;
170 } bam1_core_t;
171
172 /*! @typedef
173 @abstract Structure for one alignment.
174 @field core core information about the alignment
175 @field l_aux length of auxiliary data
176 @field data_len current length of bam1_t::data
177 @field m_data maximum length of bam1_t::data
178 @field data all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux
179
180 @discussion Notes:
181
182 1. qname is zero tailing and core.l_qname includes the tailing '\0'.
183 2. l_qseq is calculated from the total length of an alignment block
184 on reading or from CIGAR.
185 */
186 typedef struct {
187 bam1_core_t core;
188 int l_aux, data_len, m_data;
189 uint8_t *data;
190 } bam1_t;
191
192 #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
193 #define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
194
195 /*! @function
196 @abstract Get the CIGAR array
197 @param b pointer to an alignment
198 @return pointer to the CIGAR array
199
200 @discussion In the CIGAR array, each element is a 32-bit integer. The
201 lower 4 bits gives a CIGAR operation and the higher 28 bits keep the
202 length of a CIGAR.
203 */
204 #define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
205
206 /*! @function
207 @abstract Get the name of the query
208 @param b pointer to an alignment
209 @return pointer to the name string, null terminated
210 */
211 #define bam1_qname(b) ((char*)((b)->data))
212
213 /*! @function
214 @abstract Get query sequence
215 @param b pointer to an alignment
216 @return pointer to sequence
217
218 @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G,
219 8 for T and 15 for N. Two bases are packed in one byte with the base
220 at the higher 4 bits having smaller coordinate on the read. It is
221 recommended to use bam1_seqi() macro to get the base.
222 */
223 #define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)
224
225 /*! @function
226 @abstract Get query quality
227 @param b pointer to an alignment
228 @return pointer to quality string
229 */
230 #define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + ((b)->core.l_qseq + 1)/2)
231
232 /*! @function
233 @abstract Get a base on read
234 @param s Query sequence returned by bam1_seq()
235 @param i The i-th position, 0-based
236 @return 4-bit integer representing the base.
237 */
238 #define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
239
240 /*! @function
241 @abstract Get query sequence and quality
242 @param b pointer to an alignment
243 @return pointer to the concatenated auxiliary data
244 */
245 #define bam1_aux(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (b)->core.l_qseq + ((b)->core.l_qseq + 1)/2)
246
247 #ifndef kroundup32
248 /*! @function
249 @abstract Round an integer to the next closest power-2 integer.
250 @param x integer to be rounded (in place)
251 @discussion x will be modified.
252 */
253 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
254 #endif
255
256 /*!
257 @abstract Whether the machine is big-endian; modified only in
258 bam_header_init().
259 */
260 extern int bam_is_be;
261
262 /*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
263 extern unsigned char bam_nt16_table[256];
264
265 /*! @abstract Table for converting a 4-bit encoded nucleotide to a letter. */
266 extern char *bam_nt16_rev_table;
267
268 extern char bam_nt16_nt4_table[];
269
270 #ifdef __cplusplus
271 extern "C" {
272 #endif
273
274 /*! @abstract TAM file handler */
275 typedef struct __tamFile_t *tamFile;
276
277 /*!
278 @abstract Open a SAM file for reading, either uncompressed or compressed by gzip/zlib.
279 @param fn SAM file name
280 @return SAM file handler
281 */
282 tamFile sam_open(const char *fn);
283
284 /*!
285 @abstract Close a SAM file handler
286 @param fp SAM file handler
287 */
288 void sam_close(tamFile fp);
289
290 /*!
291 @abstract Read one alignment from a SAM file handler
292 @param fp SAM file handler
293 @param header header information (ordered names of chromosomes)
294 @param b read alignment; all members in b will be updated
295 @return 0 if successful; otherwise negative
296 */
297 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b);
298
299 /*!
300 @abstract Read header information from a TAB-delimited list file.
301 @param fn_list file name for the list
302 @return a pointer to the header structure
303
304 @discussion Each line in this file consists of chromosome name and
305 the length of chromosome.
306 */
307 bam_header_t *sam_header_read2(const char *fn_list);
308
309 /*!
310 @abstract Read header from a SAM file (if present)
311 @param fp SAM file handler
312 @return pointer to header struct; 0 if no @SQ lines available
313 */
314 bam_header_t *sam_header_read(tamFile fp);
315
316 /*!
317 @abstract Parse @SQ lines a update a header struct
318 @param h pointer to the header struct to be updated
319 @return number of target sequences
320
321 @discussion bam_header_t::{n_targets,target_len,target_name} will
322 be destroyed in the first place.
323 */
324 int sam_header_parse(bam_header_t *h);
325
326 /*!
327 @abstract Parse @RG lines a update a header struct
328 @param h pointer to the header struct to be updated
329 @return number of @RG lines
330
331 @discussion bam_header_t::rg2lib will be destroyed in the first
332 place.
333 */
334 int sam_header_parse_rg(bam_header_t *h);
335
336 #define sam_write1(header, b) bam_view1(header, b)
337
338 int bam_strmap_put(void *strmap, const char *rg, const char *lib);
339 const char *bam_strmap_get(const void *strmap, const char *rg);
340 void *bam_strmap_dup(const void*);
341 void *bam_strmap_init();
342 void bam_strmap_destroy(void *strmap);
343
344 /*!
345 @abstract Initialize a header structure.
346 @return the pointer to the header structure
347
348 @discussion This function also modifies the global variable
349 bam_is_be.
350 */
351 bam_header_t *bam_header_init();
352
353 /*!
354 @abstract Destroy a header structure.
355 @param header pointer to the header
356 */
357 void bam_header_destroy(bam_header_t *header);
358
359 /*!
360 @abstract Read a header structure from BAM.
361 @param fp BAM file handler, opened by bam_open()
362 @return pointer to the header structure
363
364 @discussion The file position indicator must be placed at the
365 beginning of the file. Upon success, the position indicator will
366 be set at the start of the first alignment.
367 */
368 bam_header_t *bam_header_read(bamFile fp);
369
370 /*!
371 @abstract Write a header structure to BAM.
372 @param fp BAM file handler
373 @param header pointer to the header structure
374 @return always 0 currently
375 */
376 int bam_header_write(bamFile fp, const bam_header_t *header);
377
378 /*!
379 @abstract Read an alignment from BAM.
380 @param fp BAM file handler
381 @param b read alignment; all members are updated.
382 @return number of bytes read from the file
383
384 @discussion The file position indicator must be
385 placed right before an alignment. Upon success, this function
386 will set the position indicator to the start of the next
387 alignment. This function is not affected by the machine
388 endianness.
389 */
390 int bam_read1(bamFile fp, bam1_t *b);
391
392 /*!
393 @abstract Write an alignment to BAM.
394 @param fp BAM file handler
395 @param c pointer to the bam1_core_t structure
396 @param data_len total length of variable size data related to
397 the alignment
398 @param data pointer to the concatenated data
399 @return number of bytes written to the file
400
401 @discussion This function is not affected by the machine
402 endianness.
403 */
404 int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);
405
406 /*!
407 @abstract Write an alignment to BAM.
408 @param fp BAM file handler
409 @param b alignment to write
410 @return number of bytes written to the file
411
412 @abstract It is equivalent to:
413 bam_write1_core(fp, &b->core, b->data_len, b->data)
414 */
415 int bam_write1(bamFile fp, const bam1_t *b);
416
417 /*! @function
418 @abstract Initiate a pointer to bam1_t struct
419 */
420 #define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
421
422 /*! @function
423 @abstract Free the memory allocated for an alignment.
424 @param b pointer to an alignment
425 */
426 #define bam_destroy1(b) do { \
427 free((b)->data); free(b); \
428 } while (0)
429
430 /*!
431 @abstract Format a BAM record in the SAM format
432 @param header pointer to the header structure
433 @param b alignment to print
434 @return a pointer to the SAM string
435 */
436 char *bam_format1(const bam_header_t *header, const bam1_t *b);
437
438 char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of);
439
440 /*! @typedef
441 @abstract Structure for one alignment covering the pileup position.
442 @field b pointer to the alignment
443 @field qpos position of the read base at the pileup site, 0-based
444 @field indel indel length; 0 for no indel, positive for ins and negative for del
445 @field is_del 1 iff the base on the padded read is a deletion
446 @field level the level of the read in the "viewer" mode
447
448 @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
449 difference between the two functions is that the former does not
450 set bam_pileup1_t::level, while the later does. Level helps the
451 implementation of alignment viewers, but calculating this has some
452 overhead.
453 */
454 typedef struct {
455 bam1_t *b;
456 int32_t qpos;
457 int indel, level;
458 uint32_t is_del:1, is_head:1, is_tail:1;
459 } bam_pileup1_t;
460
461 struct __bam_plbuf_t;
462 /*! @abstract pileup buffer */
463 typedef struct __bam_plbuf_t bam_plbuf_t;
464
465 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask);
466
467 /*! @typedef
468 @abstract Type of function to be called by bam_plbuf_push().
469 @param tid chromosome ID as is defined in the header
470 @param pos start coordinate of the alignment, 0-based
471 @param n number of elements in pl array
472 @param pl array of alignments
473 @param data user provided data
474 @discussion See also bam_plbuf_push(), bam_plbuf_init() and bam_pileup1_t.
475 */
476 typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
477
478 /*!
479 @abstract Reset a pileup buffer for another pileup process
480 @param buf the pileup buffer to be reset
481 */
482 void bam_plbuf_reset(bam_plbuf_t *buf);
483
484 /*!
485 @abstract Initialize a buffer for pileup.
486 @param func fucntion to be called by bam_pileup_core()
487 @param data user provided data
488 @return pointer to the pileup buffer
489 */
490 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data);
491
492 /*!
493 @abstract Destroy a pileup buffer.
494 @param buf pointer to the pileup buffer
495 */
496 void bam_plbuf_destroy(bam_plbuf_t *buf);
497
498 /*!
499 @abstract Push an alignment to the pileup buffer.
500 @param b alignment to be pushed
501 @param buf pileup buffer
502 @see bam_plbuf_init()
503 @return always 0 currently
504
505 @discussion If all the alignments covering a particular site have
506 been collected, this function will call the user defined function
507 as is provided to bam_plbuf_init(). The coordinate of the site and
508 all the alignments will be transferred to the user defined
509 function as function parameters.
510
511 When all the alignments are pushed to the buffer, this function
512 needs to be called with b equal to NULL. This will flush the
513 buffer. A pileup buffer can only be reused when bam_plbuf_reset()
514 is called.
515 */
516 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
517
518 int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
519
520 struct __bam_lplbuf_t;
521 typedef struct __bam_lplbuf_t bam_lplbuf_t;
522
523 void bam_lplbuf_reset(bam_lplbuf_t *buf);
524
525 /*! @abstract bam_plbuf_init() equivalent with level calculated. */
526 bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data);
527
528 /*! @abstract bam_plbuf_destroy() equivalent with level calculated. */
529 void bam_lplbuf_destroy(bam_lplbuf_t *tv);
530
531 /*! @abstract bam_plbuf_push() equivalent with level calculated. */
532 int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);
533
534 struct __bam_index_t;
535 typedef struct __bam_index_t bam_index_t;
536
537 /*!
538 @abstract Build index for a BAM file.
539 @discussion Index file "fn.bai" will be created.
540 @param fn name of the BAM file
541 @return always 0 currently
542 */
543 int bam_index_build(const char *fn);
544
545 /*!
546 @abstract Load index from file "fn.bai".
547 @param fn name of the BAM file (NOT the index file)
548 @return pointer to the index structure
549 */
550 bam_index_t *bam_index_load(const char *fn);
551
552 /*!
553 @abstract Destroy an index structure.
554 @param idx pointer to the index structure
555 */
556 void bam_index_destroy(bam_index_t *idx);
557
558 /*! @typedef
559 @abstract Type of function to be called by bam_fetch().
560 @param b the alignment
561 @param data user provided data
562 */
563 typedef int (*bam_fetch_f)(const bam1_t *b, void *data);
564
565 /*!
566 @abstract Retrieve the alignments that are overlapped with the
567 specified region.
568
569 @discussion A user defined function will be called for each
570 retrieved alignment ordered by its start position.
571
572 @param fp BAM file handler
573 @param idx pointer to the alignment index
574 @param tid chromosome ID as is defined in the header
575 @param beg start coordinate, 0-based
576 @param end end coordinate, 0-based
577 @param data user provided data (will be transferred to func)
578 @param func user defined function
579 */
580 int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
581
582 /*!
583 @abstract Parse a region in the format: "chr2:100,000-200,000".
584 @discussion bam_header_t::hash will be initialized if empty.
585 @param header pointer to the header structure
586 @param str string to be parsed
587 @param ref_id the returned chromosome ID
588 @param begin the returned start coordinate
589 @param end the returned end coordinate
590 @return 0 on success; -1 on failure
591 */
592 int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
593
594 /*!
595 @abstract Retrieve data of a tag
596 @param b pointer to an alignment struct
597 @param tag two-character tag to be retrieved
598
599 @return pointer to the type and data. The first character is the
600 type that can be 'iIsScCdfAZH'.
601
602 @discussion Use bam_aux2?() series to convert the returned data to
603 the corresponding type.
604 */
605 uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]);
606
607 int32_t bam_aux2i(const uint8_t *s);
608 float bam_aux2f(const uint8_t *s);
609 double bam_aux2d(const uint8_t *s);
610 char bam_aux2A(const uint8_t *s);
611 char *bam_aux2Z(const uint8_t *s);
612
613 int bam_aux_del(bam1_t *b, uint8_t *s);
614 void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
615 uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
616
617 /*!
618 @abstract Calculate the rightmost coordinate of an alignment on the
619 reference genome.
620
621 @param c pointer to the bam1_core_t structure
622 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
623 @return the rightmost coordinate, 0-based
624 */
625 uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar);
626
627 /*!
628 @abstract Calculate the length of the query sequence from CIGAR.
629 @param c pointer to the bam1_core_t structure
630 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
631 @return length of the query sequence
632 */
633 int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar);
634
635 typedef struct {
636 int32_t qbeg, qend;
637 int32_t tbeg, tend;
638 int32_t cbeg, cend;
639 } bam_segreg_t;
640
641 int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg);
642
643 #ifdef __cplusplus
644 }
645 #endif
646
647 /*!
648 @abstract Calculate the minimum bin that contains a region [beg,end).
649 @param beg start of the region, 0-based
650 @param end end of the region, 0-based
651 @return bin
652 */
653 static inline int bam_reg2bin(uint32_t beg, uint32_t end)
654 {
655 --end;
656 if (beg>>14 == end>>14) return 4681 + (beg>>14);
657 if (beg>>17 == end>>17) return 585 + (beg>>17);
658 if (beg>>20 == end>>20) return 73 + (beg>>20);
659 if (beg>>23 == end>>23) return 9 + (beg>>23);
660 if (beg>>26 == end>>26) return 1 + (beg>>26);
661 return 0;
662 }
663
664 /*!
665 @abstract Copy an alignment
666 @param bdst destination alignment struct
667 @param bsrc source alignment struct
668 @return pointer to the destination alignment struct
669 */
670 static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
671 {
672 uint8_t *data = bdst->data;
673 int m_data = bdst->m_data; // backup data and m_data
674 if (m_data < bsrc->m_data) { // double the capacity
675 m_data = bsrc->m_data; kroundup32(m_data);
676 data = (uint8_t*)realloc(data, m_data);
677 }
678 memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
679 *bdst = *bsrc; // copy the rest
680 // restore the backup
681 bdst->m_data = m_data;
682 bdst->data = data;
683 return bdst;
684 }
685
686 /*!
687 @abstract Duplicate an alignment
688 @param src source alignment struct
689 @return pointer to the destination alignment struct
690 */
691 static inline bam1_t *bam_dup1(const bam1_t *src)
692 {
693 bam1_t *b;
694 b = bam_init1();
695 *b = *src;
696 b->m_data = b->data_len;
697 b->data = (uint8_t*)calloc(b->data_len, 1);
698 memcpy(b->data, src->data, b->data_len);
699 return b;
700 }
701
702 #endif