3 Copyright (c) 2008 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 TAM, sorting,
37 merging, generating pileup, and quickly retrieval of reads overlapped
38 with a specified region.
40 @copyright Genome Research Ltd.
49 #define BAM_VIRTUAL_OFFSET16
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)
61 #define BAM_TRUE_OFFSET
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 */
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 dict header dictionary
77 @field hash hash table for fast name lookup
78 @field rg2lib hash table for @RG-ID -> LB lookup
79 @field l_text length of the plain text in the header
80 @field text plain text
82 @discussion Field hash points to null by default. It is a private
89 void *dict, *hash, *rg2lib;
90 size_t l_text, n_text;
94 /*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */
96 /*! @abstract the read is mapped in a proper pair */
97 #define BAM_FPROPER_PAIR 2
98 /*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */
100 /*! @abstract the mate is unmapped */
101 #define BAM_FMUNMAP 8
102 /*! @abstract the read is mapped to the reverse strand */
103 #define BAM_FREVERSE 16
104 /*! @abstract the mate is mapped to the reverse strand */
105 #define BAM_FMREVERSE 32
106 /*! @abstract this is read1 */
107 #define BAM_FREAD1 64
108 /*! @abstract this is read2 */
109 #define BAM_FREAD2 128
110 /*! @abstract not primary alignment */
111 #define BAM_FSECONDARY 256
112 /*! @abstract QC failure */
113 #define BAM_FQCFAIL 512
114 /*! @abstract optical or PCR duplicate */
115 #define BAM_FDUP 1024
121 /*! @abstract defautl mask for pileup */
122 #define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)
124 #define BAM_CORE_SIZE sizeof(bam1_core_t)
127 * Describing how CIGAR operation/length is packed in a 32-bit integer.
129 #define BAM_CIGAR_SHIFT 4
130 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1)
135 /*! @abstract CIGAR: match */
137 /*! @abstract CIGAR: insertion to the reference */
139 /*! @abstract CIGAR: deletion from the reference */
141 /*! @abstract CIGAR: skip on the reference (e.g. spliced alignment) */
142 #define BAM_CREF_SKIP 3
143 /*! @abstract CIGAR: clip on the read with clipped sequence present in qseq */
144 #define BAM_CSOFT_CLIP 4
145 /*! @abstract CIGAR: clip on the read with clipped sequence trimmed off */
146 #define BAM_CHARD_CLIP 5
147 /*! @abstract CIGAR: padding */
151 @abstract Structure for core alignment information.
152 @field tid chromosome ID, defined by bam_header_t
153 @field pos 0-based leftmost coordinate
154 @field strand strand; 0 for forward and 1 otherwise
155 @field bin bin calculated by bam_reg2bin()
156 @field qual mapping quality
157 @field l_qname length of the query name
158 @field flag bitwise flag
159 @field n_cigar number of CIGAR operations
160 @field l_qseq length of the query sequence (read)
165 uint32_t bin:16, qual:8, l_qname:8;
166 uint32_t flag:16, n_cigar:16;
174 @abstract Structure for one alignment.
175 @field core core information about the alignment
176 @field l_aux length of auxiliary data
177 @field data_len current length of bam1_t::data
178 @field m_data maximum length of bam1_t::data
179 @field data all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux
183 1. qname is zero tailing and core.l_qname includes the tailing '\0'.
184 2. l_qseq is calculated from the total length of an alignment block
185 on reading or from CIGAR.
189 int l_aux, data_len, m_data;
193 typedef struct __bam_iterf_t *bam_iterf_t;
195 #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
196 #define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
199 @abstract Get the CIGAR array
200 @param b pointer to an alignment
201 @return pointer to the CIGAR array
203 @discussion In the CIGAR array, each element is a 32-bit integer. The
204 lower 4 bits gives a CIGAR operation and the higher 28 bits keep the
207 #define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
210 @abstract Get the name of the query
211 @param b pointer to an alignment
212 @return pointer to the name string, null terminated
214 #define bam1_qname(b) ((char*)((b)->data))
217 @abstract Get query sequence
218 @param b pointer to an alignment
219 @return pointer to sequence
221 @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G,
222 8 for T and 15 for N. Two bases are packed in one byte with the base
223 at the higher 4 bits having smaller coordinate on the read. It is
224 recommended to use bam1_seqi() macro to get the base.
226 #define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)
229 @abstract Get query quality
230 @param b pointer to an alignment
231 @return pointer to quality string
233 #define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + ((b)->core.l_qseq + 1)/2)
236 @abstract Get a base on read
237 @param s Query sequence returned by bam1_seq()
238 @param i The i-th position, 0-based
239 @return 4-bit integer representing the base.
241 #define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
244 @abstract Get query sequence and quality
245 @param b pointer to an alignment
246 @return pointer to the concatenated auxiliary data
248 #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)
252 @abstract Round an integer to the next closest power-2 integer.
253 @param x integer to be rounded (in place)
254 @discussion x will be modified.
256 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
260 @abstract Whether the machine is big-endian; modified only in
263 extern int bam_is_be;
265 /*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
266 extern unsigned char bam_nt16_table[256];
268 /*! @abstract Table for converting a 4-bit encoded nucleotide to a letter. */
269 extern char *bam_nt16_rev_table;
271 extern char bam_nt16_nt4_table[];
277 /*********************
278 * Low-level SAM I/O *
279 *********************/
281 /*! @abstract TAM file handler */
282 typedef struct __tamFile_t *tamFile;
285 @abstract Open a SAM file for reading, either uncompressed or compressed by gzip/zlib.
286 @param fn SAM file name
287 @return SAM file handler
289 tamFile sam_open(const char *fn);
292 @abstract Close a SAM file handler
293 @param fp SAM file handler
295 void sam_close(tamFile fp);
298 @abstract Read one alignment from a SAM file handler
299 @param fp SAM file handler
300 @param header header information (ordered names of chromosomes)
301 @param b read alignment; all members in b will be updated
302 @return 0 if successful; otherwise negative
304 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b);
307 @abstract Read header information from a TAB-delimited list file.
308 @param fn_list file name for the list
309 @return a pointer to the header structure
311 @discussion Each line in this file consists of chromosome name and
312 the length of chromosome.
314 bam_header_t *sam_header_read2(const char *fn_list);
317 @abstract Read header from a SAM file (if present)
318 @param fp SAM file handler
319 @return pointer to header struct; 0 if no @SQ lines available
321 bam_header_t *sam_header_read(tamFile fp);
324 @abstract Parse @SQ lines a update a header struct
325 @param h pointer to the header struct to be updated
326 @return number of target sequences
328 @discussion bam_header_t::{n_targets,target_len,target_name} will
329 be destroyed in the first place.
331 int sam_header_parse(bam_header_t *h);
334 @abstract Parse @RG lines a update a header struct
335 @param h pointer to the header struct to be updated
336 @return number of @RG lines
338 @discussion bam_header_t::rg2lib will be destroyed in the first
341 int sam_header_parse_rg(bam_header_t *h);
343 #define sam_write1(header, b) bam_view1(header, b)
346 /********************************
347 * APIs for string dictionaries *
348 ********************************/
350 int bam_strmap_put(void *strmap, const char *rg, const char *lib);
351 const char *bam_strmap_get(const void *strmap, const char *rg);
352 void *bam_strmap_dup(const void*);
353 void *bam_strmap_init();
354 void bam_strmap_destroy(void *strmap);
357 /*********************
358 * Low-level BAM I/O *
359 *********************/
362 @abstract Initialize a header structure.
363 @return the pointer to the header structure
365 @discussion This function also modifies the global variable
368 bam_header_t *bam_header_init();
371 @abstract Destroy a header structure.
372 @param header pointer to the header
374 void bam_header_destroy(bam_header_t *header);
377 @abstract Read a header structure from BAM.
378 @param fp BAM file handler, opened by bam_open()
379 @return pointer to the header structure
381 @discussion The file position indicator must be placed at the
382 beginning of the file. Upon success, the position indicator will
383 be set at the start of the first alignment.
385 bam_header_t *bam_header_read(bamFile fp);
388 @abstract Write a header structure to BAM.
389 @param fp BAM file handler
390 @param header pointer to the header structure
391 @return always 0 currently
393 int bam_header_write(bamFile fp, const bam_header_t *header);
396 @abstract Read an alignment from BAM.
397 @param fp BAM file handler
398 @param b read alignment; all members are updated.
399 @return number of bytes read from the file
401 @discussion The file position indicator must be
402 placed right before an alignment. Upon success, this function
403 will set the position indicator to the start of the next
404 alignment. This function is not affected by the machine
407 int bam_read1(bamFile fp, bam1_t *b);
410 @abstract Write an alignment to BAM.
411 @param fp BAM file handler
412 @param c pointer to the bam1_core_t structure
413 @param data_len total length of variable size data related to
415 @param data pointer to the concatenated data
416 @return number of bytes written to the file
418 @discussion This function is not affected by the machine
421 int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);
424 @abstract Write an alignment to BAM.
425 @param fp BAM file handler
426 @param b alignment to write
427 @return number of bytes written to the file
429 @abstract It is equivalent to:
430 bam_write1_core(fp, &b->core, b->data_len, b->data)
432 int bam_write1(bamFile fp, const bam1_t *b);
435 @abstract Initiate a pointer to bam1_t struct
437 #define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
440 @abstract Free the memory allocated for an alignment.
441 @param b pointer to an alignment
443 #define bam_destroy1(b) do { \
444 if (b) { free((b)->data); free(b); } \
448 @abstract Format a BAM record in the SAM format
449 @param header pointer to the header structure
450 @param b alignment to print
451 @return a pointer to the SAM string
453 char *bam_format1(const bam_header_t *header, const bam1_t *b);
455 char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of);
457 const char *bam_get_library(bam_header_t *header, const bam1_t *b);
465 @abstract Structure for one alignment covering the pileup position.
466 @field b pointer to the alignment
467 @field qpos position of the read base at the pileup site, 0-based
468 @field indel indel length; 0 for no indel, positive for ins and negative for del
469 @field is_del 1 iff the base on the padded read is a deletion
470 @field level the level of the read in the "viewer" mode
472 @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
473 difference between the two functions is that the former does not
474 set bam_pileup1_t::level, while the later does. Level helps the
475 implementation of alignment viewers, but calculating this has some
482 uint32_t is_del:1, is_head:1, is_tail:1;
485 typedef int (*bam_plp_auto_f)(bam1_t *b, void *data);
488 typedef struct __bam_plp_t *bam_plp_t;
490 bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data);
491 int bam_plp_push(bam_plp_t iter, const bam1_t *b);
492 const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
493 const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
494 void bam_plp_set_mask(bam_plp_t iter, int mask);
495 void bam_plp_reset(bam_plp_t iter);
496 void bam_plp_destroy(bam_plp_t iter);
499 typedef struct __bam_mplp_t *bam_mplp_t;
501 bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data);
502 void bam_mplp_destroy(bam_mplp_t iter);
503 int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
506 @abstract Type of function to be called by bam_plbuf_push().
507 @param tid chromosome ID as is defined in the header
508 @param pos start coordinate of the alignment, 0-based
509 @param n number of elements in pl array
510 @param pl array of alignments
511 @param data user provided data
512 @discussion See also bam_plbuf_push(), bam_plbuf_init() and bam_pileup1_t.
514 typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
522 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask);
523 void bam_plbuf_reset(bam_plbuf_t *buf);
524 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data);
525 void bam_plbuf_destroy(bam_plbuf_t *buf);
526 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
528 int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
530 struct __bam_lplbuf_t;
531 typedef struct __bam_lplbuf_t bam_lplbuf_t;
533 void bam_lplbuf_reset(bam_lplbuf_t *buf);
535 /*! @abstract bam_plbuf_init() equivalent with level calculated. */
536 bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data);
538 /*! @abstract bam_plbuf_destroy() equivalent with level calculated. */
539 void bam_lplbuf_destroy(bam_lplbuf_t *tv);
541 /*! @abstract bam_plbuf_push() equivalent with level calculated. */
542 int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);
545 /*********************
546 * BAM indexing APIs *
547 *********************/
549 struct __bam_index_t;
550 typedef struct __bam_index_t bam_index_t;
553 @abstract Build index for a BAM file.
554 @discussion Index file "fn.bai" will be created.
555 @param fn name of the BAM file
556 @return always 0 currently
558 int bam_index_build(const char *fn);
561 @abstract Load index from file "fn.bai".
562 @param fn name of the BAM file (NOT the index file)
563 @return pointer to the index structure
565 bam_index_t *bam_index_load(const char *fn);
568 @abstract Destroy an index structure.
569 @param idx pointer to the index structure
571 void bam_index_destroy(bam_index_t *idx);
574 @abstract Type of function to be called by bam_fetch().
575 @param b the alignment
576 @param data user provided data
578 typedef int (*bam_fetch_f)(const bam1_t *b, void *data);
581 @abstract Retrieve the alignments that are overlapped with the
584 @discussion A user defined function will be called for each
585 retrieved alignment ordered by its start position.
587 @param fp BAM file handler
588 @param idx pointer to the alignment index
589 @param tid chromosome ID as is defined in the header
590 @param beg start coordinate, 0-based
591 @param end end coordinate, 0-based
592 @param data user provided data (will be transferred to func)
593 @param func user defined function
595 int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
597 bam_iterf_t bam_iterf_query(const bam_index_t *idx, int tid, int beg, int end);
598 int bam_iterf_read(bamFile fp, bam_iterf_t iter, bam1_t *b);
599 void bam_iterf_destroy(bam_iterf_t iter);
602 @abstract Parse a region in the format: "chr2:100,000-200,000".
603 @discussion bam_header_t::hash will be initialized if empty.
604 @param header pointer to the header structure
605 @param str string to be parsed
606 @param ref_id the returned chromosome ID
607 @param begin the returned start coordinate
608 @param end the returned end coordinate
609 @return 0 on success; -1 on failure
611 int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
614 /**************************
615 * APIs for optional tags *
616 **************************/
619 @abstract Retrieve data of a tag
620 @param b pointer to an alignment struct
621 @param tag two-character tag to be retrieved
623 @return pointer to the type and data. The first character is the
624 type that can be 'iIsScCdfAZH'.
626 @discussion Use bam_aux2?() series to convert the returned data to
627 the corresponding type.
629 uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]);
631 int32_t bam_aux2i(const uint8_t *s);
632 float bam_aux2f(const uint8_t *s);
633 double bam_aux2d(const uint8_t *s);
634 char bam_aux2A(const uint8_t *s);
635 char *bam_aux2Z(const uint8_t *s);
637 int bam_aux_del(bam1_t *b, uint8_t *s);
638 void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
639 uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
647 @abstract Calculate the rightmost coordinate of an alignment on the
650 @param c pointer to the bam1_core_t structure
651 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
652 @return the rightmost coordinate, 0-based
654 uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar);
657 @abstract Calculate the length of the query sequence from CIGAR.
658 @param c pointer to the bam1_core_t structure
659 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
660 @return length of the query sequence
662 int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar);
669 @abstract Calculate the minimum bin that contains a region [beg,end).
670 @param beg start of the region, 0-based
671 @param end end of the region, 0-based
674 static inline int bam_reg2bin(uint32_t beg, uint32_t end)
677 if (beg>>14 == end>>14) return 4681 + (beg>>14);
678 if (beg>>17 == end>>17) return 585 + (beg>>17);
679 if (beg>>20 == end>>20) return 73 + (beg>>20);
680 if (beg>>23 == end>>23) return 9 + (beg>>23);
681 if (beg>>26 == end>>26) return 1 + (beg>>26);
686 @abstract Copy an alignment
687 @param bdst destination alignment struct
688 @param bsrc source alignment struct
689 @return pointer to the destination alignment struct
691 static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
693 uint8_t *data = bdst->data;
694 int m_data = bdst->m_data; // backup data and m_data
695 if (m_data < bsrc->m_data) { // double the capacity
696 m_data = bsrc->m_data; kroundup32(m_data);
697 data = (uint8_t*)realloc(data, m_data);
699 memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
700 *bdst = *bsrc; // copy the rest
701 // restore the backup
702 bdst->m_data = m_data;
708 @abstract Duplicate an alignment
709 @param src source alignment struct
710 @return pointer to the destination alignment struct
712 static inline bam1_t *bam_dup1(const bam1_t *src)
717 b->m_data = b->data_len;
718 b->data = (uint8_t*)calloc(b->data_len, 1);
719 memcpy(b->data, src->data, b->data_len);