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 "0.1.17 (r973:277)"
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 size_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: match */
139 /*! @abstract CIGAR: insertion to the reference */
141 /*! @abstract CIGAR: deletion from the reference */
143 /*! @abstract CIGAR: skip on the reference (e.g. spliced alignment) */
144 #define BAM_CREF_SKIP 3
145 /*! @abstract CIGAR: clip on the read with clipped sequence present in qseq */
146 #define BAM_CSOFT_CLIP 4
147 /*! @abstract CIGAR: clip on the read with clipped sequence trimmed off */
148 #define BAM_CHARD_CLIP 5
149 /*! @abstract CIGAR: padding */
153 @abstract Structure for core alignment information.
154 @field tid chromosome ID, defined by bam_header_t
155 @field pos 0-based leftmost coordinate
156 @field strand strand; 0 for forward and 1 otherwise
157 @field bin bin calculated by bam_reg2bin()
158 @field qual mapping quality
159 @field l_qname length of the query name
160 @field flag bitwise flag
161 @field n_cigar number of CIGAR operations
162 @field l_qseq length of the query sequence (read)
167 uint32_t bin:16, qual:8, l_qname:8;
168 uint32_t flag:16, n_cigar:16;
176 @abstract Structure for one alignment.
177 @field core core information about the alignment
178 @field l_aux length of auxiliary data
179 @field data_len current length of bam1_t::data
180 @field m_data maximum length of bam1_t::data
181 @field data all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux
185 1. qname is zero tailing and core.l_qname includes the tailing '\0'.
186 2. l_qseq is calculated from the total length of an alignment block
187 on reading or from CIGAR.
191 int l_aux, data_len, m_data;
195 typedef struct __bam_iter_t *bam_iter_t;
197 #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
198 #define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
201 @abstract Get the CIGAR array
202 @param b pointer to an alignment
203 @return pointer to the CIGAR array
205 @discussion In the CIGAR array, each element is a 32-bit integer. The
206 lower 4 bits gives a CIGAR operation and the higher 28 bits keep the
209 #define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
212 @abstract Get the name of the query
213 @param b pointer to an alignment
214 @return pointer to the name string, null terminated
216 #define bam1_qname(b) ((char*)((b)->data))
219 @abstract Get query sequence
220 @param b pointer to an alignment
221 @return pointer to sequence
223 @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G,
224 8 for T and 15 for N. Two bases are packed in one byte with the base
225 at the higher 4 bits having smaller coordinate on the read. It is
226 recommended to use bam1_seqi() macro to get the base.
228 #define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)
231 @abstract Get query quality
232 @param b pointer to an alignment
233 @return pointer to quality string
235 #define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
238 @abstract Get a base on read
239 @param s Query sequence returned by bam1_seq()
240 @param i The i-th position, 0-based
241 @return 4-bit integer representing the base.
243 #define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
246 @abstract Get query sequence and quality
247 @param b pointer to an alignment
248 @return pointer to the concatenated auxiliary data
250 #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)
254 @abstract Round an integer to the next closest power-2 integer.
255 @param x integer to be rounded (in place)
256 @discussion x will be modified.
258 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
262 @abstract Whether the machine is big-endian; modified only in
265 extern int bam_is_be;
268 @abstract Verbose level between 0 and 3; 0 is supposed to disable all
269 debugging information, though this may not have been implemented.
271 extern int bam_verbose;
273 /*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
274 extern unsigned char bam_nt16_table[256];
276 /*! @abstract Table for converting a 4-bit encoded nucleotide to a letter. */
277 extern char *bam_nt16_rev_table;
279 extern char bam_nt16_nt4_table[];
285 /*********************
286 * Low-level SAM I/O *
287 *********************/
289 /*! @abstract TAM file handler */
290 typedef struct __tamFile_t *tamFile;
293 @abstract Open a SAM file for reading, either uncompressed or compressed by gzip/zlib.
294 @param fn SAM file name
295 @return SAM file handler
297 tamFile sam_open(const char *fn);
300 @abstract Close a SAM file handler
301 @param fp SAM file handler
303 void sam_close(tamFile fp);
306 @abstract Read one alignment from a SAM file handler
307 @param fp SAM file handler
308 @param header header information (ordered names of chromosomes)
309 @param b read alignment; all members in b will be updated
310 @return 0 if successful; otherwise negative
312 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b);
315 @abstract Read header information from a TAB-delimited list file.
316 @param fn_list file name for the list
317 @return a pointer to the header structure
319 @discussion Each line in this file consists of chromosome name and
320 the length of chromosome.
322 bam_header_t *sam_header_read2(const char *fn_list);
325 @abstract Read header from a SAM file (if present)
326 @param fp SAM file handler
327 @return pointer to header struct; 0 if no @SQ lines available
329 bam_header_t *sam_header_read(tamFile fp);
332 @abstract Parse @SQ lines a update a header struct
333 @param h pointer to the header struct to be updated
334 @return number of target sequences
336 @discussion bam_header_t::{n_targets,target_len,target_name} will
337 be destroyed in the first place.
339 int sam_header_parse(bam_header_t *h);
340 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
343 @abstract Parse @RG lines a update a header struct
344 @param h pointer to the header struct to be updated
345 @return number of @RG lines
347 @discussion bam_header_t::rg2lib will be destroyed in the first
350 int sam_header_parse_rg(bam_header_t *h);
352 #define sam_write1(header, b) bam_view1(header, b)
355 /********************************
356 * APIs for string dictionaries *
357 ********************************/
359 int bam_strmap_put(void *strmap, const char *rg, const char *lib);
360 const char *bam_strmap_get(const void *strmap, const char *rg);
361 void *bam_strmap_dup(const void*);
362 void *bam_strmap_init();
363 void bam_strmap_destroy(void *strmap);
366 /*********************
367 * Low-level BAM I/O *
368 *********************/
371 @abstract Initialize a header structure.
372 @return the pointer to the header structure
374 @discussion This function also modifies the global variable
377 bam_header_t *bam_header_init();
380 @abstract Destroy a header structure.
381 @param header pointer to the header
383 void bam_header_destroy(bam_header_t *header);
386 @abstract Read a header structure from BAM.
387 @param fp BAM file handler, opened by bam_open()
388 @return pointer to the header structure
390 @discussion The file position indicator must be placed at the
391 beginning of the file. Upon success, the position indicator will
392 be set at the start of the first alignment.
394 bam_header_t *bam_header_read(bamFile fp);
397 @abstract Write a header structure to BAM.
398 @param fp BAM file handler
399 @param header pointer to the header structure
400 @return always 0 currently
402 int bam_header_write(bamFile fp, const bam_header_t *header);
405 @abstract Read an alignment from BAM.
406 @param fp BAM file handler
407 @param b read alignment; all members are updated.
408 @return number of bytes read from the file
410 @discussion The file position indicator must be
411 placed right before an alignment. Upon success, this function
412 will set the position indicator to the start of the next
413 alignment. This function is not affected by the machine
416 int bam_read1(bamFile fp, bam1_t *b);
419 @abstract Write an alignment to BAM.
420 @param fp BAM file handler
421 @param c pointer to the bam1_core_t structure
422 @param data_len total length of variable size data related to
424 @param data pointer to the concatenated data
425 @return number of bytes written to the file
427 @discussion This function is not affected by the machine
430 int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);
433 @abstract Write an alignment to BAM.
434 @param fp BAM file handler
435 @param b alignment to write
436 @return number of bytes written to the file
438 @abstract It is equivalent to:
439 bam_write1_core(fp, &b->core, b->data_len, b->data)
441 int bam_write1(bamFile fp, const bam1_t *b);
444 @abstract Initiate a pointer to bam1_t struct
446 #define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
449 @abstract Free the memory allocated for an alignment.
450 @param b pointer to an alignment
452 #define bam_destroy1(b) do { \
453 if (b) { free((b)->data); free(b); } \
457 @abstract Format a BAM record in the SAM format
458 @param header pointer to the header structure
459 @param b alignment to print
460 @return a pointer to the SAM string
462 char *bam_format1(const bam_header_t *header, const bam1_t *b);
464 char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of);
467 @abstract Check whether a BAM record is plausibly valid
468 @param header associated header structure, or NULL if unavailable
469 @param b alignment to validate
470 @return 0 if the alignment is invalid; non-zero otherwise
472 @discussion Simple consistency check of some of the fields of the
473 alignment record. If the header is provided, several additional checks
474 are made. Not all fields are checked, so a non-zero result is not a
475 guarantee that the record is valid. However it is usually good enough
476 to detect when bam_seek() has been called with a virtual file offset
477 that is not the offset of an alignment record.
479 int bam_validate1(const bam_header_t *header, const bam1_t *b);
481 const char *bam_get_library(bam_header_t *header, const bam1_t *b);
489 @abstract Structure for one alignment covering the pileup position.
490 @field b pointer to the alignment
491 @field qpos position of the read base at the pileup site, 0-based
492 @field indel indel length; 0 for no indel, positive for ins and negative for del
493 @field is_del 1 iff the base on the padded read is a deletion
494 @field level the level of the read in the "viewer" mode
496 @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
497 difference between the two functions is that the former does not
498 set bam_pileup1_t::level, while the later does. Level helps the
499 implementation of alignment viewers, but calculating this has some
506 uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, aux:28;
509 typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);
512 typedef struct __bam_plp_t *bam_plp_t;
514 bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data);
515 int bam_plp_push(bam_plp_t iter, const bam1_t *b);
516 const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
517 const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
518 void bam_plp_set_mask(bam_plp_t iter, int mask);
519 void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt);
520 void bam_plp_reset(bam_plp_t iter);
521 void bam_plp_destroy(bam_plp_t iter);
524 typedef struct __bam_mplp_t *bam_mplp_t;
526 bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data);
527 void bam_mplp_destroy(bam_mplp_t iter);
528 void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt);
529 int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
532 @abstract Type of function to be called by bam_plbuf_push().
533 @param tid chromosome ID as is defined in the header
534 @param pos start coordinate of the alignment, 0-based
535 @param n number of elements in pl array
536 @param pl array of alignments
537 @param data user provided data
538 @discussion See also bam_plbuf_push(), bam_plbuf_init() and bam_pileup1_t.
540 typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
548 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask);
549 void bam_plbuf_reset(bam_plbuf_t *buf);
550 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data);
551 void bam_plbuf_destroy(bam_plbuf_t *buf);
552 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
554 int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
556 struct __bam_lplbuf_t;
557 typedef struct __bam_lplbuf_t bam_lplbuf_t;
559 void bam_lplbuf_reset(bam_lplbuf_t *buf);
561 /*! @abstract bam_plbuf_init() equivalent with level calculated. */
562 bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data);
564 /*! @abstract bam_plbuf_destroy() equivalent with level calculated. */
565 void bam_lplbuf_destroy(bam_lplbuf_t *tv);
567 /*! @abstract bam_plbuf_push() equivalent with level calculated. */
568 int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);
571 /*********************
572 * BAM indexing APIs *
573 *********************/
575 struct __bam_index_t;
576 typedef struct __bam_index_t bam_index_t;
579 @abstract Build index for a BAM file.
580 @discussion Index file "fn.bai" will be created.
581 @param fn name of the BAM file
582 @return always 0 currently
584 int bam_index_build(const char *fn);
587 @abstract Load index from file "fn.bai".
588 @param fn name of the BAM file (NOT the index file)
589 @return pointer to the index structure
591 bam_index_t *bam_index_load(const char *fn);
594 @abstract Destroy an index structure.
595 @param idx pointer to the index structure
597 void bam_index_destroy(bam_index_t *idx);
600 @abstract Type of function to be called by bam_fetch().
601 @param b the alignment
602 @param data user provided data
604 typedef int (*bam_fetch_f)(const bam1_t *b, void *data);
607 @abstract Retrieve the alignments that are overlapped with the
610 @discussion A user defined function will be called for each
611 retrieved alignment ordered by its start position.
613 @param fp BAM file handler
614 @param idx pointer to the alignment index
615 @param tid chromosome ID as is defined in the header
616 @param beg start coordinate, 0-based
617 @param end end coordinate, 0-based
618 @param data user provided data (will be transferred to func)
619 @param func user defined function
621 int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
623 bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end);
624 int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b);
625 void bam_iter_destroy(bam_iter_t iter);
628 @abstract Parse a region in the format: "chr2:100,000-200,000".
629 @discussion bam_header_t::hash will be initialized if empty.
630 @param header pointer to the header structure
631 @param str string to be parsed
632 @param ref_id the returned chromosome ID
633 @param begin the returned start coordinate
634 @param end the returned end coordinate
635 @return 0 on success; -1 on failure
637 int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
640 /**************************
641 * APIs for optional tags *
642 **************************/
645 @abstract Retrieve data of a tag
646 @param b pointer to an alignment struct
647 @param tag two-character tag to be retrieved
649 @return pointer to the type and data. The first character is the
650 type that can be 'iIsScCdfAZH'.
652 @discussion Use bam_aux2?() series to convert the returned data to
653 the corresponding type.
655 uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]);
657 int32_t bam_aux2i(const uint8_t *s);
658 float bam_aux2f(const uint8_t *s);
659 double bam_aux2d(const uint8_t *s);
660 char bam_aux2A(const uint8_t *s);
661 char *bam_aux2Z(const uint8_t *s);
663 int bam_aux_del(bam1_t *b, uint8_t *s);
664 void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
665 uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
673 @abstract Calculate the rightmost coordinate of an alignment on the
676 @param c pointer to the bam1_core_t structure
677 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
678 @return the rightmost coordinate, 0-based
680 uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar);
683 @abstract Calculate the length of the query sequence from CIGAR.
684 @param c pointer to the bam1_core_t structure
685 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
686 @return length of the query sequence
688 int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar);
695 @abstract Calculate the minimum bin that contains a region [beg,end).
696 @param beg start of the region, 0-based
697 @param end end of the region, 0-based
700 static inline int bam_reg2bin(uint32_t beg, uint32_t end)
703 if (beg>>14 == end>>14) return 4681 + (beg>>14);
704 if (beg>>17 == end>>17) return 585 + (beg>>17);
705 if (beg>>20 == end>>20) return 73 + (beg>>20);
706 if (beg>>23 == end>>23) return 9 + (beg>>23);
707 if (beg>>26 == end>>26) return 1 + (beg>>26);
712 @abstract Copy an alignment
713 @param bdst destination alignment struct
714 @param bsrc source alignment struct
715 @return pointer to the destination alignment struct
717 static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
719 uint8_t *data = bdst->data;
720 int m_data = bdst->m_data; // backup data and m_data
721 if (m_data < bsrc->data_len) { // double the capacity
722 m_data = bsrc->data_len; kroundup32(m_data);
723 data = (uint8_t*)realloc(data, m_data);
725 memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
726 *bdst = *bsrc; // copy the rest
727 // restore the backup
728 bdst->m_data = m_data;
734 @abstract Duplicate an alignment
735 @param src source alignment struct
736 @return pointer to the destination alignment struct
738 static inline bam1_t *bam_dup1(const bam1_t *src)
743 b->m_data = b->data_len;
744 b->data = (uint8_t*)calloc(b->data_len, 1);
745 memcpy(b->data, src->data, b->data_len);
749 static inline int bam_aux_type2size(int x)
751 if (x == 'C' || x == 'c' || x == 'A') return 1;
752 else if (x == 'S' || x == 's') return 2;
753 else if (x == 'I' || x == 'i' || x == 'f') return 4;