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 TAM (Text Alignment/Mapping)
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 #if _IOLIB == 1 && !defined(_NO_RAZF)
50 #define BAM_TRUE_OFFSET
52 /*! @abstract BAM file handler */
53 typedef RAZF *bamFile;
54 #define bam_open(fn, mode) razf_open(fn, mode)
55 #define bam_dopen(fd, mode) razf_dopen(fd, mode)
56 #define bam_close(fp) razf_close(fp)
57 #define bam_read(fp, buf, size) razf_read(fp, buf, size)
58 #define bam_write(fp, buf, size) razf_write(fp, buf, size)
59 #define bam_tell(fp) razf_tell(fp)
60 #define bam_seek(fp, pos, dir) razf_seek(fp, pos, dir)
62 #define BAM_VIRTUAL_OFFSET16
64 /*! @abstract BAM file handler */
65 typedef BGZF *bamFile;
66 #define bam_open(fn, mode) bgzf_open(fn, mode)
67 #define bam_dopen(fd, mode) bgzf_fdopen(fd, mode)
68 #define bam_close(fp) bgzf_close(fp)
69 #define bam_read(fp, buf, size) bgzf_read(fp, buf, size)
70 #define bam_write(fp, buf, size) bgzf_write(fp, buf, size)
71 #define bam_tell(fp) bgzf_tell(fp)
72 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
74 #define BAM_VIRTUAL_OFFSET16
76 /*! @abstract BAM file handler */
77 typedef RAZF *bamFile;
78 #define bam_open(fn, mode) razf_open2(fn, mode)
79 #define bam_dopen(fd, mode) razf_dopen2(fd, mode)
80 #define bam_close(fp) razf_close(fp)
81 #define bam_read(fp, buf, size) razf_read(fp, buf, size)
82 #define bam_write(fp, buf, size) razf_write(fp, buf, size)
83 #define bam_tell(fp) razf_tell2(fp)
84 #define bam_seek(fp, pos, dir) razf_seek2(fp, pos, dir)
88 @abstract Structure for the alignment header.
89 @field n_targets number of reference sequences
90 @field target_name names of the reference sequences
91 @field target_len lengths of the referene sequences
92 @field hash hash table for fast name lookup
93 @field l_text length of the plain text in the header
94 @field text plain text
96 @discussion Field hash points to null by default. It is a private
102 uint32_t *target_len;
108 /*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */
109 #define BAM_FPAIRED 1
110 /*! @abstract the read is mapped in a proper pair */
111 #define BAM_FPROPER_PAIR 2
112 /*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */
114 /*! @abstract the mate is unmapped */
115 #define BAM_FMUNMAP 8
116 #define BAM_FREVERSE 16
117 #define BAM_FMREVERSE 32
118 #define BAM_FREAD1 64
119 #define BAM_FREAD2 128
120 #define BAM_FSECONDARY 256
121 #define BAM_FQCFAIL 512
122 #define BAM_FDUP 1024
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 #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)
258 @abstract Round an integer to the next closest power-2 integer.
259 @param x integer to be rounded (in place)
260 @discussion x will be modified.
262 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
266 @abstract Whether the machine is big-endian; modified only in
269 extern int bam_is_be;
271 /*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
272 extern unsigned char bam_nt16_table[256];
274 /*! @abstract Table for converting a 4-bit encoded nucleotide to a letter. */
275 extern char *bam_nt16_rev_table;
277 extern char bam_nt16_nt4_table[];
283 /*! @abstract TAM file handler */
284 typedef struct __tamFile_t *tamFile;
287 @abstract Open a TAM file, either uncompressed or compressed by gzip/zlib.
288 @param fn TAM file name
289 @return TAM file handler
291 tamFile sam_open(const char *fn);
294 @abstract Close a TAM file handler
295 @param fp TAM file handler
297 void sam_close(tamFile fp);
300 @abstract Read one alignment from a TAM file handler
301 @param fp TAM file handler
302 @param header header information (ordered names of chromosomes)
303 @param b read alignment; all members in b will be updated
304 @return 0 if successful; otherwise negative
306 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b);
309 @abstract Read header information from a TAB-delimited list file.
310 @param fn_list file name for the list
311 @return a pointer to the header structure
313 @discussion Each line in this file consists of chromosome name and
314 the length of chromosome.
316 bam_header_t *sam_header_read2(const char *fn_list);
318 bam_header_t *sam_header_read(tamFile fp);
319 int sam_header_parse(bam_header_t *h);
321 #define sam_write1(header, b) bam_view1(header, b)
324 @abstract Initialize a header structure.
325 @return the pointer to the header structure
327 @discussion This function also modifies the global variable
330 bam_header_t *bam_header_init();
333 @abstract Destroy a header structure.
334 @param header pointer to the header
336 void bam_header_destroy(bam_header_t *header);
339 @abstract Read a header structure from BAM.
340 @param fp BAM file handler, opened by bam_open()
341 @return pointer to the header structure
343 @discussion The file position indicator must be placed at the
344 beginning of the file. Upon success, the position indicator will
345 be set at the start of the first alignment.
347 bam_header_t *bam_header_read(bamFile fp);
350 @abstract Write a header structure to BAM.
351 @param fp BAM file handler
352 @param header pointer to the header structure
353 @return always 0 currently
355 int bam_header_write(bamFile fp, const bam_header_t *header);
358 @abstract Read an alignment from BAM.
359 @param fp BAM file handler
360 @param b read alignment; all members are updated.
361 @return number of bytes read from the file
363 @discussion The file position indicator must be
364 placed right before an alignment. Upon success, this function
365 will set the position indicator to the start of the next
366 alignment. This function is not affected by the machine
369 int bam_read1(bamFile fp, bam1_t *b);
372 @abstract Write an alignment to BAM.
373 @param fp BAM file handler
374 @param c pointer to the bam1_core_t structure
375 @param data_len total length of variable size data related to
377 @param data pointer to the concatenated data
378 @return number of bytes written to the file
380 @discussion This function is not affected by the machine
383 int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);
386 @abstract Write an alignment to BAM.
387 @param fp BAM file handler
388 @param b alignment to write
389 @return number of bytes written to the file
391 @abstract It is equivalent to:
392 bam_write1_core(fp, &b->core, b->data_len, b->data)
394 int bam_write1(bamFile fp, const bam1_t *b);
397 @abstract Initiate a pointer to bam1_t struct
399 #define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
402 @abstract Free the memory allocated for an alignment.
403 @param b pointer to an alignment
405 #define bam_destroy1(b) do { \
406 free((b)->data); free(b); \
410 @abstract Format a BAM record in the SAM format
411 @param header pointer to the header structure
412 @param b alignment to print
413 @return a pointer to the SAM string
415 char *bam_format1(const bam_header_t *header, const bam1_t *b);
418 @abstract Merge multiple sorted BAM.
419 @param is_by_qname whether to sort by query name
420 @param out output BAM file name
421 @param n number of files to be merged
422 @param fn names of files to be merged
424 @discussion Padding information may NOT correctly maintained. This
425 function is NOT thread safe.
427 void bam_merge_core(int is_by_qname, const char *out, int n, char * const *fn);
430 @abstract Sort an unsorted BAM file based on the chromosome order
431 and the leftmost position of an alignment
433 @param is_by_qname whether to sort by query name
434 @param fn name of the file to be sorted
435 @param prefix prefix of the output and the temporary files; upon
436 sucessess, prefix.bam will be written.
437 @param max_mem approxiate maximum memory (very inaccurate)
439 @discussion It may create multiple temporary subalignment files
440 and then merge them by calling bam_merge_core(). This function is
443 void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem);
446 @abstract Structure for one alignment covering the pileup position.
447 @field b pointer to the alignment
448 @field qpos position of the read base at the pileup site, 0-based
449 @field indel indel length; 0 for no indel, positive for ins and negative for del
450 @field is_del 1 iff the base on the padded read is a deletion
451 @field level the level of the read in the "viewer" mode
453 @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
454 difference between the two functions is that the former does not
455 set bam_pileup1_t::level, while the later does. Level helps the
456 implementation of alignment viewers, but calculating this has some
463 uint32_t is_del:1, is_head:1, is_tail:1;
466 struct __bam_plbuf_t;
467 /*! @abstract pileup buffer */
468 typedef struct __bam_plbuf_t bam_plbuf_t;
470 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask);
473 @abstract Type of function to be called by bam_plbuf_push().
474 @param tid chromosome ID as is defined in the header
475 @param pos start coordinate of the alignment, 0-based
476 @param n number of elements in pl array
477 @param pl array of alignments
478 @param data user provided data
479 @discussion See also bam_plbuf_push(), bam_plbuf_init() and bam_pileup1_t.
481 typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
483 void bam_plbuf_reset(bam_plbuf_t *buf);
486 @abstract Initialize a buffer for pileup.
487 @param func fucntion to be called by bam_pileup_core()
488 @param data user provided data
489 @return pointer to the pileup buffer
491 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data);
494 @abstract Destroy a pileup buffer.
495 @param buf pointer to the pileup buffer
497 void bam_plbuf_destroy(bam_plbuf_t *buf);
500 @abstract Push an alignment to the pileup buffer.
501 @param b alignment to be pushed
502 @param buf pileup buffer
503 @see bam_plbuf_init()
504 @return always 0 currently
506 @discussion If all the alignments covering a particular site have
507 been collected, this function will call the user defined function
508 as is provided to bam_plbuf_init(). The coordinate of the site the
509 all the alignments will be transferred to the user defined
510 function as function parameters.
512 When all the alignments are pushed to the buffer, this function
513 needs to be called with b equal to NULL. This will flush the
514 buffer. A pileup buffer cannot be reused.
516 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
518 struct __bam_lplbuf_t;
519 typedef struct __bam_lplbuf_t bam_lplbuf_t;
521 void bam_lplbuf_reset(bam_lplbuf_t *buf);
523 /*! @abstract bam_plbuf_init() equivalent with level calculated. */
524 bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data);
526 /*! @abstract bam_plbuf_destroy() equivalent with level calculated. */
527 void bam_lplbuf_destroy(bam_lplbuf_t *tv);
529 /*! @abstract bam_plbuf_push() equivalent with level calculated. */
530 int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);
532 /*! @abstract bam_plbuf_file() equivalent with level calculated. */
533 int bam_lpileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
535 struct __bam_index_t;
536 typedef struct __bam_index_t bam_index_t;
539 @abstract Build index for a BAM file.
540 @discussion Index file "fn.bai" will be created.
541 @param fn name of the BAM file
542 @return always 0 currently
544 int bam_index_build(const char *fn);
547 @abstract Load index from file "fn.bai".
548 @param fn name of the BAM file (NOT the index file)
549 @return pointer to the index structure
551 bam_index_t *bam_index_load(const char *fn);
554 @abstract Destroy an index structure.
555 @param idx pointer to the index structure
557 void bam_index_destroy(bam_index_t *idx);
560 @abstract Type of function to be called by bam_fetch().
561 @param b the alignment
562 @param data user provided data
564 typedef int (*bam_fetch_f)(const bam1_t *b, void *data);
567 @abstract Retrieve the alignments that are overlapped with the
570 @discussion A user defined function will be called for each
571 retrieved alignment ordered by its start position.
573 @param fp BAM file handler
574 @param idx pointer to the alignment index
575 @param tid chromosome ID as is defined in the header
576 @param beg start coordinate, 0-based
577 @param end end coordinate, 0-based
578 @param data user provided data (will be transferred to func)
579 @param func user defined function
581 int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
584 @abstract Parse a region in the format: "chr2:100,000-200,000".
585 @discussion bam_header_t::hash will be initialized if empty.
586 @param header pointer to the header structure
587 @param str string to be parsed
588 @param ref_id the returned chromosome ID
589 @param begin the returned start coordinate
590 @param end the returned end coordinate
592 void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
594 void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
595 // uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
596 uint8_t *bam_aux_get(bam1_t *b, const char tag[2]);
597 int32_t bam_aux2i(const uint8_t *s);
598 float bam_aux2f(const uint8_t *s);
599 double bam_aux2d(const uint8_t *s);
600 char bam_aux2A(const uint8_t *s);
601 char *bam_aux2Z(const uint8_t *s);
604 @abstract Get the color encoding the previous and current base
605 @param b pointer to an alignment
606 @param i The i-th position, 0-based
609 @discussion Returns 0 no color information is found.
611 char bam_aux_getCSi(bam1_t *b, int i);
614 @abstract Get the color quality of the color encoding the previous and current base
615 @param b pointer to an alignment
616 @param i The i-th position, 0-based
617 @return color quality
619 @discussion Returns 0 no color information is found.
621 char bam_aux_getCQi(bam1_t *b, int i);
624 @abstract Get the color error profile at the give position
625 @param b pointer to an alignment
626 @return the original color if the color was an error, '-' (dash) otherwise
628 @discussion Returns 0 no color information is found.
630 char bam_aux_getCEi(bam1_t *b, int i);
633 @abstract Calculate the rightmost coordinate of an alignment on the
636 @param c pointer to the bam1_core_t structure
637 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
638 @return the rightmost coordinate, 0-based
640 uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar);
643 @abstract Calculate the length of the query sequence from CIGAR.
644 @param c pointer to the bam1_core_t structure
645 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
646 @return length of the query sequence
648 int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar);
650 int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg);
657 @abstract Calculate the minimum bin that contains a region [beg,end).
658 @param beg start of the region, 0-based
659 @param end end of the region, 0-based
662 static inline int bam_reg2bin(uint32_t beg, uint32_t end)
665 if (beg>>14 == end>>14) return 4681 + (beg>>14);
666 if (beg>>17 == end>>17) return 585 + (beg>>17);
667 if (beg>>20 == end>>20) return 73 + (beg>>20);
668 if (beg>>23 == end>>23) return 9 + (beg>>23);
669 if (beg>>26 == end>>26) return 1 + (beg>>26);
673 static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
675 uint8_t *data = bdst->data;
676 int m_data = bdst->m_data; // backup data and m_data
677 if (m_data < bsrc->m_data) { // double the capacity
678 m_data = bsrc->m_data; kroundup32(m_data);
679 data = (uint8_t*)realloc(data, m_data);
681 memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
682 *bdst = *bsrc; // copy the rest
683 // restore the backup
684 bdst->m_data = m_data;
689 static inline bam1_t *bam_dup1(const bam1_t *src)
694 b->m_data = b->data_len;
695 b->data = (uint8_t*)calloc(b->data_len, 1);
696 memcpy(b->data, src->data, b->data_len);