X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam.h;h=346c750c8c807c44ea32804eeb1bb93411d0b71a;hp=83c03ada21098eda911caabb0e56db3864599e73;hb=0f906dafb2ad22371a753557562ef95c3034480d;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906 diff --git a/bam.h b/bam.h index 83c03ad..346c750 100644 --- a/bam.h +++ b/bam.h @@ -1,6 +1,6 @@ /* The MIT License - Copyright (c) 2008 Genome Research Ltd (GRL). + Copyright (c) 2008-2010 Genome Research Ltd (GRL). Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the @@ -33,33 +33,21 @@ BAM library provides I/O and various operations on manipulating files in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map) - format. It now supports importing from or exporting to TAM, sorting, + format. It now supports importing from or exporting to SAM, sorting, merging, generating pileup, and quickly retrieval of reads overlapped with a specified region. @copyright Genome Research Ltd. */ +#define BAM_VERSION "0.1.18 (r982:295)" + #include #include #include #include -#define _IOLIB 2 - -#if _IOLIB == 1 && !defined(_NO_RAZF) -#define BAM_TRUE_OFFSET -#include "razf.h" -/*! @abstract BAM file handler */ -typedef RAZF *bamFile; -#define bam_open(fn, mode) razf_open(fn, mode) -#define bam_dopen(fd, mode) razf_dopen(fd, mode) -#define bam_close(fp) razf_close(fp) -#define bam_read(fp, buf, size) razf_read(fp, buf, size) -#define bam_write(fp, buf, size) razf_write(fp, buf, size) -#define bam_tell(fp) razf_tell(fp) -#define bam_seek(fp, pos, dir) razf_seek(fp, pos, dir) -#elif _IOLIB == 2 +#ifndef BAM_LITE #define BAM_VIRTUAL_OFFSET16 #include "bgzf.h" /*! @abstract BAM file handler */ @@ -71,18 +59,15 @@ typedef BGZF *bamFile; #define bam_write(fp, buf, size) bgzf_write(fp, buf, size) #define bam_tell(fp) bgzf_tell(fp) #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) -#elif _IOLIB == 3 -#define BAM_VIRTUAL_OFFSET16 -#include "razf.h" -/*! @abstract BAM file handler */ -typedef RAZF *bamFile; -#define bam_open(fn, mode) razf_open2(fn, mode) -#define bam_dopen(fd, mode) razf_dopen2(fd, mode) -#define bam_close(fp) razf_close(fp) -#define bam_read(fp, buf, size) razf_read(fp, buf, size) -#define bam_write(fp, buf, size) razf_write(fp, buf, size) -#define bam_tell(fp) razf_tell2(fp) -#define bam_seek(fp, pos, dir) razf_seek2(fp, pos, dir) +#else +#define BAM_TRUE_OFFSET +#include +typedef gzFile bamFile; +#define bam_open(fn, mode) gzopen(fn, mode) +#define bam_dopen(fd, mode) gzdopen(fd, mode) +#define bam_close(fp) gzclose(fp) +#define bam_read(fp, buf, size) gzread(fp, buf, size) +/* no bam_write/bam_tell/bam_seek() here */ #endif /*! @typedef @@ -90,6 +75,7 @@ typedef RAZF *bamFile; @field n_targets number of reference sequences @field target_name names of the reference sequences @field target_len lengths of the referene sequences + @field dict header dictionary @field hash hash table for fast name lookup @field rg2lib hash table for @RG-ID -> LB lookup @field l_text length of the plain text in the header @@ -102,8 +88,8 @@ typedef struct { int32_t n_targets; char **target_name; uint32_t *target_len; - void *hash, *rg2lib; - int l_text; + void *dict, *hash, *rg2lib; + size_t l_text, n_text; char *text; } bam_header_t; @@ -130,6 +116,10 @@ typedef struct { /*! @abstract optical or PCR duplicate */ #define BAM_FDUP 1024 +#define BAM_OFDEC 0 +#define BAM_OFHEX 1 +#define BAM_OFSTR 2 + /*! @abstract defautl mask for pileup */ #define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) @@ -144,20 +134,25 @@ typedef struct { /* CIGAR operations. */ -/*! @abstract CIGAR: match */ +/*! @abstract CIGAR: M = match or mismatch*/ #define BAM_CMATCH 0 -/*! @abstract CIGAR: insertion to the reference */ +/*! @abstract CIGAR: I = insertion to the reference */ #define BAM_CINS 1 -/*! @abstract CIGAR: deletion from the reference */ +/*! @abstract CIGAR: D = deletion from the reference */ #define BAM_CDEL 2 -/*! @abstract CIGAR: skip on the reference (e.g. spliced alignment) */ +/*! @abstract CIGAR: N = skip on the reference (e.g. spliced alignment) */ #define BAM_CREF_SKIP 3 -/*! @abstract CIGAR: clip on the read with clipped sequence present in qseq */ +/*! @abstract CIGAR: S = clip on the read with clipped sequence + present in qseq */ #define BAM_CSOFT_CLIP 4 -/*! @abstract CIGAR: clip on the read with clipped sequence trimmed off */ +/*! @abstract CIGAR: H = clip on the read with clipped sequence trimmed off */ #define BAM_CHARD_CLIP 5 -/*! @abstract CIGAR: padding */ +/*! @abstract CIGAR: P = padding */ #define BAM_CPAD 6 +/*! @abstract CIGAR: equals = match */ +#define BAM_CEQUAL 7 +/*! @abstract CIGAR: X = mismatch */ +#define BAM_CDIFF 8 /*! @typedef @abstract Structure for core alignment information. @@ -202,6 +197,8 @@ typedef struct { uint8_t *data; } bam1_t; +typedef struct __bam_iter_t *bam_iter_t; + #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0) #define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0) @@ -240,7 +237,7 @@ typedef struct { @param b pointer to an alignment @return pointer to quality string */ -#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + ((b)->core.l_qseq + 1)/2) +#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1)) /*! @function @abstract Get a base on read @@ -272,6 +269,12 @@ typedef struct { */ extern int bam_is_be; +/*! + @abstract Verbose level between 0 and 3; 0 is supposed to disable all + debugging information, though this may not have been implemented. + */ +extern int bam_verbose; + /*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */ extern unsigned char bam_nt16_table[256]; @@ -284,6 +287,10 @@ extern char bam_nt16_nt4_table[]; extern "C" { #endif + /********************* + * Low-level SAM I/O * + *********************/ + /*! @abstract TAM file handler */ typedef struct __tamFile_t *tamFile; @@ -335,6 +342,7 @@ extern "C" { be destroyed in the first place. */ int sam_header_parse(bam_header_t *h); + int32_t bam_get_tid(const bam_header_t *header, const char *seq_name); /*! @abstract Parse @RG lines a update a header struct @@ -348,12 +356,22 @@ extern "C" { #define sam_write1(header, b) bam_view1(header, b) + + /******************************** + * APIs for string dictionaries * + ********************************/ + int bam_strmap_put(void *strmap, const char *rg, const char *lib); const char *bam_strmap_get(const void *strmap, const char *rg); void *bam_strmap_dup(const void*); void *bam_strmap_init(); void bam_strmap_destroy(void *strmap); + + /********************* + * Low-level BAM I/O * + *********************/ + /*! @abstract Initialize a header structure. @return the pointer to the header structure @@ -436,8 +454,8 @@ extern "C" { @abstract Free the memory allocated for an alignment. @param b pointer to an alignment */ -#define bam_destroy1(b) do { \ - free((b)->data); free(b); \ +#define bam_destroy1(b) do { \ + if (b) { free((b)->data); free(b); } \ } while (0) /*! @@ -448,6 +466,30 @@ extern "C" { */ char *bam_format1(const bam_header_t *header, const bam1_t *b); + char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of); + + /*! + @abstract Check whether a BAM record is plausibly valid + @param header associated header structure, or NULL if unavailable + @param b alignment to validate + @return 0 if the alignment is invalid; non-zero otherwise + + @discussion Simple consistency check of some of the fields of the + alignment record. If the header is provided, several additional checks + are made. Not all fields are checked, so a non-zero result is not a + guarantee that the record is valid. However it is usually good enough + to detect when bam_seek() has been called with a virtual file offset + that is not the offset of an alignment record. + */ + int bam_validate1(const bam_header_t *header, const bam1_t *b); + + const char *bam_get_library(bam_header_t *header, const bam1_t *b); + + + /*************** + * pileup APIs * + ***************/ + /*! @typedef @abstract Structure for one alignment covering the pileup position. @field b pointer to the alignment @@ -466,14 +508,30 @@ extern "C" { bam1_t *b; int32_t qpos; int indel, level; - uint32_t is_del:1, is_head:1, is_tail:1; + uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, aux:28; } bam_pileup1_t; - struct __bam_plbuf_t; - /*! @abstract pileup buffer */ - typedef struct __bam_plbuf_t bam_plbuf_t; + typedef int (*bam_plp_auto_f)(void *data, bam1_t *b); - void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask); + struct __bam_plp_t; + typedef struct __bam_plp_t *bam_plp_t; + + bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data); + int bam_plp_push(bam_plp_t iter, const bam1_t *b); + const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp); + const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp); + void bam_plp_set_mask(bam_plp_t iter, int mask); + void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt); + void bam_plp_reset(bam_plp_t iter); + void bam_plp_destroy(bam_plp_t iter); + + struct __bam_mplp_t; + typedef struct __bam_mplp_t *bam_mplp_t; + + bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data); + void bam_mplp_destroy(bam_mplp_t iter); + void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt); + int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); /*! @typedef @abstract Type of function to be called by bam_plbuf_push(). @@ -486,46 +544,20 @@ extern "C" { */ typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data); - /*! - @abstract Reset a pileup buffer for another pileup process - @param buf the pileup buffer to be reset - */ - void bam_plbuf_reset(bam_plbuf_t *buf); + typedef struct { + bam_plp_t iter; + bam_pileup_f func; + void *data; + } bam_plbuf_t; - /*! - @abstract Initialize a buffer for pileup. - @param func fucntion to be called by bam_pileup_core() - @param data user provided data - @return pointer to the pileup buffer - */ + void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask); + void bam_plbuf_reset(bam_plbuf_t *buf); bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data); - - /*! - @abstract Destroy a pileup buffer. - @param buf pointer to the pileup buffer - */ void bam_plbuf_destroy(bam_plbuf_t *buf); - - /*! - @abstract Push an alignment to the pileup buffer. - @param b alignment to be pushed - @param buf pileup buffer - @see bam_plbuf_init() - @return always 0 currently - - @discussion If all the alignments covering a particular site have - been collected, this function will call the user defined function - as is provided to bam_plbuf_init(). The coordinate of the site and - all the alignments will be transferred to the user defined - function as function parameters. - - When all the alignments are pushed to the buffer, this function - needs to be called with b equal to NULL. This will flush the - buffer. A pileup buffer can only be reused when bam_plbuf_reset() - is called. - */ int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf); + int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data); + struct __bam_lplbuf_t; typedef struct __bam_lplbuf_t bam_lplbuf_t; @@ -540,8 +572,10 @@ extern "C" { /*! @abstract bam_plbuf_push() equivalent with level calculated. */ int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf); - /*! @abstract bam_plbuf_file() equivalent with level calculated. */ - int bam_lpileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data); + + /********************* + * BAM indexing APIs * + *********************/ struct __bam_index_t; typedef struct __bam_index_t bam_index_t; @@ -591,6 +625,10 @@ extern "C" { */ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); + bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end); + int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b); + void bam_iter_destroy(bam_iter_t iter); + /*! @abstract Parse a region in the format: "chr2:100,000-200,000". @discussion bam_header_t::hash will be initialized if empty. @@ -603,6 +641,11 @@ extern "C" { */ int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end); + + /************************** + * APIs for optional tags * + **************************/ + /*! @abstract Retrieve data of a tag @param b pointer to an alignment struct @@ -622,10 +665,15 @@ extern "C" { char bam_aux2A(const uint8_t *s); char *bam_aux2Z(const uint8_t *s); + int bam_aux_del(bam1_t *b, uint8_t *s); void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data); - uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get() + + /***************** + * Miscellaneous * + *****************/ + /*! @abstract Calculate the rightmost coordinate of an alignment on the reference genome. @@ -644,14 +692,6 @@ extern "C" { */ int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar); - typedef struct { - int32_t qbeg, qend; - int32_t tbeg, tend; - int32_t cbeg, cend; - } bam_segreg_t; - - int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg); - #ifdef __cplusplus } #endif @@ -683,8 +723,8 @@ static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc) { uint8_t *data = bdst->data; int m_data = bdst->m_data; // backup data and m_data - if (m_data < bsrc->m_data) { // double the capacity - m_data = bsrc->m_data; kroundup32(m_data); + if (m_data < bsrc->data_len) { // double the capacity + m_data = bsrc->data_len; kroundup32(m_data); data = (uint8_t*)realloc(data, m_data); } memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data @@ -711,4 +751,13 @@ static inline bam1_t *bam_dup1(const bam1_t *src) return b; } +static inline int bam_aux_type2size(int x) +{ + if (x == 'C' || x == 'c' || x == 'A') return 1; + else if (x == 'S' || x == 's') return 2; + else if (x == 'I' || x == 'i' || x == 'f') return 4; + else return 0; +} + + #endif