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 #define sam_write1(header, b) bam_view1(header, b)
321 @abstract Initialize a header structure.
322 @return the pointer to the header structure
324 @discussion This function also modifies the global variable
327 bam_header_t *bam_header_init();
330 @abstract Destroy a header structure.
331 @param header pointer to the header
333 void bam_header_destroy(bam_header_t *header);
336 @abstract Read a header structure from BAM.
337 @param fp BAM file handler, opened by bam_open()
338 @return pointer to the header structure
340 @discussion The file position indicator must be placed at the
341 beginning of the file. Upon success, the position indicator will
342 be set at the start of the first alignment.
344 bam_header_t *bam_header_read(bamFile fp);
347 @abstract Write a header structure to BAM.
348 @param fp BAM file handler
349 @param header pointer to the header structure
350 @return always 0 currently
352 int bam_header_write(bamFile fp, const bam_header_t *header);
355 @abstract Read an alignment from BAM.
356 @param fp BAM file handler
357 @param b read alignment; all members are updated.
358 @return number of bytes read from the file
360 @discussion The file position indicator must be
361 placed right before an alignment. Upon success, this function
362 will set the position indicator to the start of the next
363 alignment. This function is not affected by the machine
366 int bam_read1(bamFile fp, bam1_t *b);
369 @abstract Write an alignment to BAM.
370 @param fp BAM file handler
371 @param c pointer to the bam1_core_t structure
372 @param data_len total length of variable size data related to
374 @param data pointer to the concatenated data
375 @return number of bytes written to the file
377 @discussion This function is not affected by the machine
380 int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);
383 @abstract Write an alignment to BAM.
384 @param fp BAM file handler
385 @param b alignment to write
386 @return number of bytes written to the file
388 @abstract It is equivalent to:
389 bam_write1_core(fp, &b->core, b->data_len, b->data)
391 int bam_write1(bamFile fp, const bam1_t *b);
394 @abstract Initiate a pointer to bam1_t struct
396 #define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
399 @abstract Free the memory allocated for an alignment.
400 @param b pointer to an alignment
402 #define bam_destroy1(b) do { \
403 free((b)->data); free(b); \
407 @abstract Format a BAM record in the SAM format
408 @param header pointer to the header structure
409 @param b alignment to print
410 @return a pointer to the SAM string
412 char *bam_format1(const bam_header_t *header, const bam1_t *b);
415 @abstract Merge multiple sorted BAM.
416 @param is_by_qname whether to sort by query name
417 @param out output BAM file name
418 @param n number of files to be merged
419 @param fn names of files to be merged
421 @discussion Padding information may NOT correctly maintained. This
422 function is NOT thread safe.
424 void bam_merge_core(int is_by_qname, const char *out, int n, char * const *fn);
427 @abstract Sort an unsorted BAM file based on the chromosome order
428 and the leftmost position of an alignment
430 @param is_by_qname whether to sort by query name
431 @param fn name of the file to be sorted
432 @param prefix prefix of the output and the temporary files; upon
433 sucessess, prefix.bam will be written.
434 @param max_mem approxiate maximum memory (very inaccurate)
436 @discussion It may create multiple temporary subalignment files
437 and then merge them by calling bam_merge_core(). This function is
440 void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem);
443 @abstract Structure for one alignment covering the pileup position.
444 @field b pointer to the alignment
445 @field qpos position of the read base at the pileup site, 0-based
446 @field indel indel length; 0 for no indel, positive for ins and negative for del
447 @field is_del 1 iff the base on the padded read is a deletion
448 @field level the level of the read in the "viewer" mode
450 @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
451 difference between the two functions is that the former does not
452 set bam_pileup1_t::level, while the later does. Level helps the
453 implementation of alignment viewers, but calculating this has some
460 uint32_t is_del:1, is_head:1, is_tail:1;
463 struct __bam_plbuf_t;
464 /*! @abstract pileup buffer */
465 typedef struct __bam_plbuf_t bam_plbuf_t;
467 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask);
470 @abstract Type of function to be called by bam_plbuf_push().
471 @param tid chromosome ID as is defined in the header
472 @param pos start coordinate of the alignment, 0-based
473 @param n number of elements in pl array
474 @param pl array of alignments
475 @param data user provided data
476 @discussion See also bam_plbuf_push(), bam_plbuf_init() and bam_pileup1_t.
478 typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
480 void bam_plbuf_reset(bam_plbuf_t *buf);
483 @abstract Initialize a buffer for pileup.
484 @param func fucntion to be called by bam_pileup_core()
485 @param data user provided data
486 @return pointer to the pileup buffer
488 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data);
491 @abstract Destroy a pileup buffer.
492 @param buf pointer to the pileup buffer
494 void bam_plbuf_destroy(bam_plbuf_t *buf);
497 @abstract Push an alignment to the pileup buffer.
498 @param b alignment to be pushed
499 @param buf pileup buffer
500 @see bam_plbuf_init()
501 @return always 0 currently
503 @discussion If all the alignments covering a particular site have
504 been collected, this function will call the user defined function
505 as is provided to bam_plbuf_init(). The coordinate of the site the
506 all the alignments will be transferred to the user defined
507 function as function parameters.
509 When all the alignments are pushed to the buffer, this function
510 needs to be called with b equal to NULL. This will flush the
511 buffer. A pileup buffer cannot be reused.
513 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
515 struct __bam_lplbuf_t;
516 typedef struct __bam_lplbuf_t bam_lplbuf_t;
518 void bam_lplbuf_reset(bam_lplbuf_t *buf);
520 /*! @abstract bam_plbuf_init() equivalent with level calculated. */
521 bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data);
523 /*! @abstract bam_plbuf_destroy() equivalent with level calculated. */
524 void bam_lplbuf_destroy(bam_lplbuf_t *tv);
526 /*! @abstract bam_plbuf_push() equivalent with level calculated. */
527 int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);
529 /*! @abstract bam_plbuf_file() equivalent with level calculated. */
530 int bam_lpileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
532 struct __bam_index_t;
533 typedef struct __bam_index_t bam_index_t;
536 @abstract Build index for a BAM file.
537 @discussion Index file "fn.bai" will be created.
538 @param fn name of the BAM file
539 @return always 0 currently
541 int bam_index_build(const char *fn);
544 @abstract Load index from file "fn.bai".
545 @param fn name of the BAM file (NOT the index file)
546 @return pointer to the index structure
548 bam_index_t *bam_index_load(const char *fn);
551 @abstract Destroy an index structure.
552 @param idx pointer to the index structure
554 void bam_index_destroy(bam_index_t *idx);
557 @abstract Type of function to be called by bam_fetch().
558 @param b the alignment
559 @param data user provided data
561 typedef int (*bam_fetch_f)(const bam1_t *b, void *data);
564 @abstract Retrieve the alignments that are overlapped with the
567 @discussion A user defined function will be called for each
568 retrieved alignment ordered by its start position.
570 @param fp BAM file handler
571 @param idx pointer to the alignment index
572 @param tid chromosome ID as is defined in the header
573 @param beg start coordinate, 0-based
574 @param end end coordinate, 0-based
575 @param data user provided data (will be transferred to func)
576 @param func user defined function
578 int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
581 @abstract Parse a region in the format: "chr2:100,000-200,000".
582 @discussion bam_header_t::hash will be initialized if empty.
583 @param header pointer to the header structure
584 @param str string to be parsed
585 @param ref_id the returned chromosome ID
586 @param begin the returned start coordinate
587 @param end the returned end coordinate
589 void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
591 void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
592 uint8_t *bam_aux_get(bam1_t *b, const char tag[2]);
593 int32_t bam_aux2i(const uint8_t *s);
594 float bam_aux2f(const uint8_t *s);
595 double bam_aux2d(const uint8_t *s);
596 char bam_aux2A(const uint8_t *s);
597 char *bam_aux2Z(const uint8_t *s);
600 @abstract Get the color encoding the previous and current base
601 @param b pointer to an alignment
602 @param i The i-th position, 0-based
605 @discussion Returns 0 no color information is found.
607 char bam_aux_getCSi(bam1_t *b, int i);
610 @abstract Get the color quality of the color encoding the previous and current base
611 @param b pointer to an alignment
612 @param i The i-th position, 0-based
613 @return color quality
615 @discussion Returns 0 no color information is found.
617 char bam_aux_getCQi(bam1_t *b, int i);
620 @abstract Get the color error profile at the give position
621 @param b pointer to an alignment
622 @return the original color if the color was an error, '-' (dash) otherwise
624 @discussion Returns 0 no color information is found.
626 char bam_aux_getCEi(bam1_t *b, int i);
629 @abstract Calculate the rightmost coordinate of an alignment on the
632 @param c pointer to the bam1_core_t structure
633 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
634 @return the rightmost coordinate, 0-based
636 uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar);
639 @abstract Calculate the length of the query sequence from CIGAR.
640 @param c pointer to the bam1_core_t structure
641 @param cigar the corresponding CIGAR array (from bam1_t::cigar)
642 @return length of the query sequence
644 int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar);
646 int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg);
653 @abstract Calculate the minimum bin that contains a region [beg,end).
654 @param beg start of the region, 0-based
655 @param end end of the region, 0-based
658 static inline int bam_reg2bin(uint32_t beg, uint32_t end)
661 if (beg>>14 == end>>14) return 4681 + (beg>>14);
662 if (beg>>17 == end>>17) return 585 + (beg>>17);
663 if (beg>>20 == end>>20) return 73 + (beg>>20);
664 if (beg>>23 == end>>23) return 9 + (beg>>23);
665 if (beg>>26 == end>>26) return 1 + (beg>>26);
669 static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
671 uint8_t *data = bdst->data;
672 int m_data = bdst->m_data; // backup data and m_data
673 if (m_data < bsrc->m_data) { // double the capacity
674 m_data = bsrc->m_data; kroundup32(m_data);
675 data = (uint8_t*)realloc(data, m_data);
677 memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
678 *bdst = *bsrc; // copy the rest
679 // restore the backup
680 bdst->m_data = m_data;
685 static inline bam1_t *bam_dup1(const bam1_t *src)
690 b->m_data = b->data_len;
691 b->data = (uint8_t*)calloc(b->data_len, 1);
692 memcpy(b->data, src->data, b->data_len);