3 Copyright (c) 2008-2010 Genome Research Ltd (GRL).
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:
13 The above copyright notice and this permission notice shall be
14 included in all copies or substantial portions of the Software.
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
26 /* Contact: Heng Li <lh3@sanger.ac.uk> */
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 SAM, sorting,
37 merging, generating pileup, and quickly retrieval of reads overlapped
38 with a specified region.
40 @copyright Genome Research Ltd.
43 #define BAM_VERSION "0.1.18-r580"
51 #define BAM_VIRTUAL_OFFSET16
53 /*! @abstract BAM file handler */
54 typedef BGZF *bamFile;
55 #define bam_open(fn, mode) bgzf_open(fn, mode)
56 #define bam_dopen(fd, mode) bgzf_fdopen(fd, mode)
57 #define bam_close(fp) bgzf_close(fp)
58 #define bam_read(fp, buf, size) bgzf_read(fp, buf, size)
59 #define bam_write(fp, buf, size) bgzf_write(fp, buf, size)
60 #define bam_tell(fp) bgzf_tell(fp)
61 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
63 #define BAM_TRUE_OFFSET
65 typedef gzFile bamFile;
66 #define bam_open(fn, mode) gzopen(fn, mode)
67 #define bam_dopen(fd, mode) gzdopen(fd, mode)
68 #define bam_close(fp) gzclose(fp)
69 #define bam_read(fp, buf, size) gzread(fp, buf, size)
70 /* no bam_write/bam_tell/bam_seek() here */
74 @abstract Structure for the alignment header.
75 @field n_targets number of reference sequences
76 @field target_name names of the reference sequences
77 @field target_len lengths of the referene sequences
78 @field dict header dictionary
79 @field hash hash table for fast name lookup
80 @field rg2lib hash table for @RG-ID -> LB lookup
81 @field l_text length of the plain text in the header
82 @field text plain text
84 @discussion Field hash points to null by default. It is a private
91 void *dict, *hash, *rg2lib;
92 uint32_t l_text, n_text;
96 /*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */
98 /*! @abstract the read is mapped in a proper pair */
99 #define BAM_FPROPER_PAIR 2
100 /*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */
102 /*! @abstract the mate is unmapped */
103 #define BAM_FMUNMAP 8
104 /*! @abstract the read is mapped to the reverse strand */
105 #define BAM_FREVERSE 16
106 /*! @abstract the mate is mapped to the reverse strand */
107 #define BAM_FMREVERSE 32
108 /*! @abstract this is read1 */
109 #define BAM_FREAD1 64
110 /*! @abstract this is read2 */
111 #define BAM_FREAD2 128
112 /*! @abstract not primary alignment */
113 #define BAM_FSECONDARY 256
114 /*! @abstract QC failure */
115 #define BAM_FQCFAIL 512
116 /*! @abstract optical or PCR duplicate */
117 #define BAM_FDUP 1024
123 /*! @abstract defautl mask for pileup */
124 #define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)
126 #define BAM_CORE_SIZE sizeof(bam1_core_t)
129 * Describing how CIGAR operation/length is packed in a 32-bit integer.
131 #define BAM_CIGAR_SHIFT 4
132 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1)
137 /*! @abstract CIGAR: M = match or mismatch*/
139 /*! @abstract CIGAR: I = insertion to the reference */
141 /*! @abstract CIGAR: D = deletion from the reference */
143 /*! @abstract CIGAR: N = skip on the reference (e.g. spliced alignment) */
144 #define BAM_CREF_SKIP 3
145 /*! @abstract CIGAR: S = clip on the read with clipped sequence
147 #define BAM_CSOFT_CLIP 4
148 /*! @abstract CIGAR: H = clip on the read with clipped sequence trimmed off */
149 #define BAM_CHARD_CLIP 5
150 /*! @abstract CIGAR: P = padding */
152 /*! @abstract CIGAR: equals = match */
154 /*! @abstract CIGAR: X = mismatch */
158 #define BAM_CIGAR_STR "MIDNSHP=XB"
159 #define BAM_CIGAR_TYPE 0x3C1A7
161 #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
162 #define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)
163 #define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])
164 #define bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o))
165 #define bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3) // bit 1: consume query; bit 2: consume reference
168 @abstract Structure for core alignment information.
169 @field tid chromosome ID, defined by bam_header_t
170 @field pos 0-based leftmost coordinate
171 @field bin bin calculated by bam_reg2bin()
172 @field qual mapping quality
173 @field l_qname length of the query name
174 @field flag bitwise flag
175 @field n_cigar number of CIGAR operations
176 @field l_qseq length of the query sequence (read)
181 uint32_t bin:16, qual:8, l_qname:8;
182 uint32_t flag:16, n_cigar:16;
190 @abstract Structure for one alignment.
191 @field core core information about the alignment
192 @field l_aux length of auxiliary data
193 @field data_len current length of bam1_t::data
194 @field m_data maximum length of bam1_t::data
195 @field data all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux
199 1. qname is zero tailing and core.l_qname includes the tailing '\0'.
200 2. l_qseq is calculated from the total length of an alignment block
201 on reading or from CIGAR.
202 3. cigar data is encoded 4 bytes per CIGAR operation.
203 4. seq is nybble-encoded according to bam_nt16_table.
207 int l_aux, data_len, m_data;
211 typedef struct __bam_iter_t *bam_iter_t;
213 #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
214 #define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
217 @abstract Get the CIGAR array
218 @param b pointer to an alignment
219 @return pointer to the CIGAR array
221 @discussion In the CIGAR array, each element is a 32-bit integer. The
222 lower 4 bits gives a CIGAR operation and the higher 28 bits keep the
225 #define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
228 @abstract Get the name of the query
229 @param b pointer to an alignment
230 @return pointer to the name string, null terminated
232 #define bam1_qname(b) ((char*)((b)->data))
235 @abstract Get query sequence
236 @param b pointer to an alignment
237 @return pointer to sequence
239 @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G,
240 8 for T and 15 for N. Two bases are packed in one byte with the base
241 at the higher 4 bits having smaller coordinate on the read. It is
242 recommended to use bam1_seqi() macro to get the base.
244 #define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)
247 @abstract Get query quality
248 @param b pointer to an alignment
249 @return pointer to quality string
251 #define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
254 @abstract Get a base on read
255 @param s Query sequence returned by bam1_seq()
256 @param i The i-th position, 0-based
257 @return 4-bit integer representing the base.
259 //#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
260 #define bam1_seqi(s, i) ((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf)
262 #define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((~(i)&1)<<2) )
265 @abstract Get query sequence and quality
266 @param b pointer to an alignment
267 @return pointer to the concatenated auxiliary data
269 #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)
273 @abstract Round an integer to the next closest power-2 integer.
274 @param x integer to be rounded (in place)
275 @discussion x will be modified.
277 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
281 @abstract Whether the machine is big-endian; modified only in
284 extern int bam_is_be;
287 @abstract Verbose level between 0 and 3; 0 is supposed to disable all
288 debugging information, though this may not have been implemented.
290 extern int bam_verbose;
294 /*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
295 extern unsigned char bam_nt16_table[256];
297 /*! @abstract Table for converting a 4-bit encoded nucleotide to a letter. */
298 extern char *bam_nt16_rev_table;
300 extern char bam_nt16_nt4_table[];
306 /*********************
307 * Low-level SAM I/O *
308 *********************/
310 /*! @abstract TAM file handler */
311 typedef struct __tamFile_t *tamFile;
314 @abstract Open a SAM file for reading, either uncompressed or compressed by gzip/zlib.
315 @param fn SAM file name
316 @return SAM file handler
318 tamFile sam_open(const char *fn);
321 @abstract Close a SAM file handler
322 @param fp SAM file handler
324 void sam_close(tamFile fp);
327 @abstract Read one alignment from a SAM file handler
328 @param fp SAM file handler
329 @param header header information (ordered names of chromosomes)
330 @param b read alignment; all members in b will be updated
331 @return 0 if successful; otherwise negative
333 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b);
336 @abstract Read header information from a TAB-delimited list file.
337 @param fn_list file name for the list
338 @return a pointer to the header structure
340 @discussion Each line in this file consists of chromosome name and
341 the length of chromosome.
343 bam_header_t *sam_header_read2(const char *fn_list);
346 @abstract Read header from a SAM file (if present)
347 @param fp SAM file handler
348 @return pointer to header struct; 0 if no @SQ lines available
350 bam_header_t *sam_header_read(tamFile fp);
353 @abstract Parse @SQ lines a update a header struct
354 @param h pointer to the header struct to be updated
355 @return number of target sequences
357 @discussion bam_header_t::{n_targets,target_len,target_name} will
358 be destroyed in the first place.
360 int sam_header_parse(bam_header_t *h);
361 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
364 @abstract Parse @RG lines a update a header struct
365 @param h pointer to the header struct to be updated
366 @return number of @RG lines
368 @discussion bam_header_t::rg2lib will be destroyed in the first
371 int sam_header_parse_rg(bam_header_t *h);
373 #define sam_write1(header, b) bam_view1(header, b)
376 /********************************
377 * APIs for string dictionaries *
378 ********************************/
380 int bam_strmap_put(void *strmap, const char *rg, const char *lib);
381 const char *bam_strmap_get(const void *strmap, const char *rg);
382 void *bam_strmap_dup(const void*);
383 void *bam_strmap_init();
384 void bam_strmap_destroy(void *strmap);
387 /*********************
388 * Low-level BAM I/O *
389 *********************/
392 @abstract Initialize a header structure.
393 @return the pointer to the header structure
395 @discussion This function also modifies the global variable
398 bam_header_t *bam_header_init();
401 @abstract Destroy a header structure.
402 @param header pointer to the header
404 void bam_header_destroy(bam_header_t *header);
407 @abstract Read a header structure from BAM.
408 @param fp BAM file handler, opened by bam_open()
409 @return pointer to the header structure
411 @discussion The file position indicator must be placed at the
412 beginning of the file. Upon success, the position indicator will
413 be set at the start of the first alignment.
415 bam_header_t *bam_header_read(bamFile fp);
418 @abstract Write a header structure to BAM.
419 @param fp BAM file handler
420 @param header pointer to the header structure
421 @return always 0 currently
423 int bam_header_write(bamFile fp, const bam_header_t *header);
426 @abstract Read an alignment from BAM.
427 @param fp BAM file handler
428 @param b read alignment; all members are updated.
429 @return number of bytes read from the file
431 @discussion The file position indicator must be
432 placed right before an alignment. Upon success, this function
433 will set the position indicator to the start of the next
434 alignment. This function is not affected by the machine
437 int bam_read1(bamFile fp, bam1_t *b);
439 int bam_remove_B(bam1_t *b);
442 @abstract Write an alignment to BAM.
443 @param fp BAM file handler
444 @param c pointer to the bam1_core_t structure
445 @param data_len total length of variable size data related to
447 @param data pointer to the concatenated data
448 @return number of bytes written to the file
450 @discussion This function is not affected by the machine
453 int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);
456 @abstract Write an alignment to BAM.
457 @param fp BAM file handler
458 @param b alignment to write
459 @return number of bytes written to the file
461 @abstract It is equivalent to:
462 bam_write1_core(fp, &b->core, b->data_len, b->data)
464 int bam_write1(bamFile fp, const bam1_t *b);
467 @abstract Initiate a pointer to bam1_t struct
469 #define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
472 @abstract Free the memory allocated for an alignment.
473 @param b pointer to an alignment
475 #define bam_destroy1(b) do { \
476 if (b) { free((b)->data); free(b); } \
480 @abstract Format a BAM record in the SAM format
481 @param header pointer to the header structure
482 @param b alignment to print
483 @return a pointer to the SAM string
485 char *bam_format1(const bam_header_t *header, const bam1_t *b);
487 char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of);
490 @abstract Check whether a BAM record is plausibly valid
491 @param header associated header structure, or NULL if unavailable
492 @param b alignment to validate
493 @return 0 if the alignment is invalid; non-zero otherwise
495 @discussion Simple consistency check of some of the fields of the
496 alignment record. If the header is provided, several additional checks
497 are made. Not all fields are checked, so a non-zero result is not a
498 guarantee that the record is valid. However it is usually good enough
499 to detect when bam_seek() has been called with a virtual file offset
500 that is not the offset of an alignment record.
502 int bam_validate1(const bam_header_t *header, const bam1_t *b);
504 const char *bam_get_library(bam_header_t *header, const bam1_t *b);
512 @abstract Structure for one alignment covering the pileup position.
513 @field b pointer to the alignment
514 @field qpos position of the read base at the pileup site, 0-based
515 @field indel indel length; 0 for no indel, positive for ins and negative for del
516 @field is_del 1 iff the base on the padded read is a deletion
517 @field level the level of the read in the "viewer" mode
519 @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
520 difference between the two functions is that the former does not
521 set bam_pileup1_t::level, while the later does. Level helps the
522 implementation of alignment viewers, but calculating this has some
529 uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, aux:28;
532 typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);
535 typedef struct __bam_plp_t *bam_plp_t;
537 bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data);
538 int bam_plp_push(bam_plp_t iter, const bam1_t *b);
539 const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
540 const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
541 void bam_plp_set_mask(bam_plp_t iter, int mask);
542 void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt);
543 void bam_plp_reset(bam_plp_t iter);
544 void bam_plp_destroy(bam_plp_t iter);
547 typedef struct __bam_mplp_t *bam_mplp_t;
549 bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data);
550 void bam_mplp_destroy(bam_mplp_t iter);
551 void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt);
552 int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
555 @abstract Type of function to be called by bam_plbuf_push().
556 @param tid chromosome ID as is defined in the header
557 @param pos start coordinate of the alignment, 0-based
558 @param n number of elements in pl array
559 @param pl array of alignments
560 @param data user provided data
561 @discussion See also bam_plbuf_push(), bam_plbuf_init() and bam_pileup1_t.
563 typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
571 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask);
572 void bam_plbuf_reset(bam_plbuf_t *buf);
573 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data);
574 void bam_plbuf_destroy(bam_plbuf_t *buf);
575 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
577 int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
579 struct __bam_lplbuf_t;
580 typedef struct __bam_lplbuf_t bam_lplbuf_t;
582 void bam_lplbuf_reset(bam_lplbuf_t *buf);
584 /*! @abstract bam_plbuf_init() equivalent with level calculated. */
585 bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data);
587 /*! @abstract bam_plbuf_destroy() equivalent with level calculated. */
588 void bam_lplbuf_destroy(bam_lplbuf_t *tv);
590 /*! @abstract bam_plbuf_push() equivalent with level calculated. */
591 int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);
594 /*********************
595 * BAM indexing APIs *
596 *********************/
598 struct __bam_index_t;
599 typedef struct __bam_index_t bam_index_t;
602 @abstract Build index for a BAM file.
603 @discussion Index file "fn.bai" will be created.
604 @param fn name of the BAM file
605 @return always 0 currently
607 int bam_index_build(const char *fn);
610 @abstract Load index from file "fn.bai".
611 @param fn name of the BAM file (NOT the index file)
612 @return pointer to the index structure
614 bam_index_t *bam_index_load(const char *fn);
617 @abstract Destroy an index structure.
618 @param idx pointer to the index structure
620 void bam_index_destroy(bam_index_t *idx);
623 @abstract Type of function to be called by bam_fetch().
624 @param b the alignment
625 @param data user provided data
627 typedef int (*bam_fetch_f)(const bam1_t *b, void *data);
630 @abstract Retrieve the alignments that are overlapped with the
633 @discussion A user defined function will be called for each
634 retrieved alignment ordered by its start position.
636 @param fp BAM file handler
637 @param idx pointer to the alignment index
638 @param tid chromosome ID as is defined in the header
639 @param beg start coordinate, 0-based
640 @param end end coordinate, 0-based
641 @param data user provided data (will be transferred to func)
642 @param func user defined function
644 int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
646 bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end);
647 int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b);
648 void bam_iter_destroy(bam_iter_t iter);
651 @abstract Parse a region in the format: "chr2:100,000-200,000".
652 @discussion bam_header_t::hash will be initialized if empty.
653 @param header pointer to the header structure
654 @param str string to be parsed
655 @param ref_id the returned chromosome ID
656 @param begin the returned start coordinate
657 @param end the returned end coordinate
658 @return 0 on success; -1 on failure
660 int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
663 /**************************
664 * APIs for optional tags *
665 **************************/
668 @abstract Retrieve data of a tag
669 @param b pointer to an alignment struct
670 @param tag two-character tag to be retrieved
672 @return pointer to the type and data. The first character is the
673 type that can be 'iIsScCdfAZH'.
675 @discussion Use bam_aux2?() series to convert the returned data to
676 the corresponding type.
678 uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]);
680 int32_t bam_aux2i(const uint8_t *s);
681 float bam_aux2f(const uint8_t *s);
682 double bam_aux2d(const uint8_t *s);
683 char bam_aux2A(const uint8_t *s);
684 char *bam_aux2Z(const uint8_t *s);
686 int bam_aux_del(bam1_t *b, uint8_t *s);
687 void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
688 uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
696 @abstract Calculate the rightmost coordinate of an alignment on the
699 @param c pointer to the bam1_core_t structure
700 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
701 @return the rightmost coordinate, 0-based
703 uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar);
706 @abstract Calculate the length of the query sequence from CIGAR.
707 @param c pointer to the bam1_core_t structure
708 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
709 @return length of the query sequence
711 int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar);
718 @abstract Calculate the minimum bin that contains a region [beg,end).
719 @param beg start of the region, 0-based
720 @param end end of the region, 0-based
723 static inline int bam_reg2bin(uint32_t beg, uint32_t end)
726 if (beg>>14 == end>>14) return 4681 + (beg>>14);
727 if (beg>>17 == end>>17) return 585 + (beg>>17);
728 if (beg>>20 == end>>20) return 73 + (beg>>20);
729 if (beg>>23 == end>>23) return 9 + (beg>>23);
730 if (beg>>26 == end>>26) return 1 + (beg>>26);
735 @abstract Copy an alignment
736 @param bdst destination alignment struct
737 @param bsrc source alignment struct
738 @return pointer to the destination alignment struct
740 static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
742 uint8_t *data = bdst->data;
743 int m_data = bdst->m_data; // backup data and m_data
744 if (m_data < bsrc->data_len) { // double the capacity
745 m_data = bsrc->data_len; kroundup32(m_data);
746 data = (uint8_t*)realloc(data, m_data);
748 memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
749 *bdst = *bsrc; // copy the rest
750 // restore the backup
751 bdst->m_data = m_data;
757 @abstract Duplicate an alignment
758 @param src source alignment struct
759 @return pointer to the destination alignment struct
761 static inline bam1_t *bam_dup1(const bam1_t *src)
766 b->m_data = b->data_len;
767 b->data = (uint8_t*)calloc(b->data_len, 1);
768 memcpy(b->data, src->data, b->data_len);
772 static inline int bam_aux_type2size(int x)
774 if (x == 'C' || x == 'c' || x == 'A') return 1;
775 else if (x == 'S' || x == 's') return 2;
776 else if (x == 'I' || x == 'i' || x == 'f' || x == 'F') return 4;
780 /*********************************
781 *** Compatibility with htslib ***
782 *********************************/
784 typedef bam_header_t bam_hdr_t;
786 #define bam_get_qname(b) bam1_qname(b)
787 #define bam_get_cigar(b) bam1_cigar(b)
789 #define bam_hdr_read(fp) bam_header_read(fp)
790 #define bam_hdr_write(fp, h) bam_header_write(fp, h)
791 #define bam_hdr_destroy(fp) bam_header_destroy(fp)