#include <string.h>
#include <stdio.h>
-#if _IOLIB == 1
+#if _IOLIB == 1 && !defined(_NO_RAZF)
#define BAM_TRUE_OFFSET
#include "razf.h"
/*! @abstract BAM file handler */
#define BAM_FREAD1 64
#define BAM_FREAD2 128
#define BAM_FSECONDARY 256
+#define BAM_FQCFAIL 512
+#define BAM_FDUP 1024
+
+#define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)
#define BAM_CORE_SIZE sizeof(bam1_core_t)
@field data_len current length of bam1_t::data
@field m_data maximum length of bam1_t::data
@field data all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux
- @field hash hash table for fast retrieval of tag-value pairs; private
@discussion Notes:
bam1_core_t core;
int l_aux, data_len, m_data;
uint8_t *data;
- void *hash;
} bam1_t;
#define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
*/
bam_header_t *sam_header_read2(const char *fn_list);
+ bam_header_t *sam_header_read(tamFile fp);
+ int sam_header_parse(bam_header_t *h);
+
#define sam_write1(header, b) bam_view1(header, b)
/*!
@abstract Free the memory allocated for an alignment.
@param b pointer to an alignment
*/
-#define bam_destroy1(b) do { \
- if ((b)->hash) bam_aux_destroy(b); free((b)->data); free(b); \
+#define bam_destroy1(b) do { \
+ free((b)->data); free(b); \
} while (0)
/*!
- @abstract Print an alignment to the standard output in TAM format.
+ @abstract Format a BAM record in the SAM format
@param header pointer to the header structure
@param b alignment to print
+ @return a pointer to the SAM string
*/
- void bam_view1(const bam_header_t *header, const bam1_t *b);
+ char *bam_format1(const bam_header_t *header, const bam1_t *b);
/*!
@abstract Merge multiple sorted BAM.
/*! @abstract pileup buffer */
typedef struct __bam_plbuf_t bam_plbuf_t;
+ void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask);
+
/*! @typedef
@abstract Type of function to be called by bam_plbuf_push().
@param tid chromosome ID as is defined in the header
*/
int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
- /*!
- @abstract A more convenient interface to bam_plbuf_push()
- @param fp BAM file handler
- @param func user defined function
- @param func_data user provided data
-
- @discussion The file position indicator must be placed right
- before the start of an alignment. See also bam_plbuf_push().
- */
- int bam_pileup_file(bamFile fp, bam_pileup_f func, void *func_data);
-
struct __bam_lplbuf_t;
typedef struct __bam_lplbuf_t bam_lplbuf_t;
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, bam_pileup_f func, void *func_data);
+ int bam_lpileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
struct __bam_index_t;
typedef struct __bam_index_t bam_index_t;
*/
void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
- int32_t bam_aux_geti(bam1_t *b, const char tag[2], int *err);
- float bam_aux_getf(bam1_t *b, const char tag[2], int *err);
- char bam_aux_getc(bam1_t *b, const char tag[2], int *err);
- char *bam_aux_getZH(bam1_t *b, const char tag[2], int *err);
- void bam_aux_destroy(bam1_t *b);
+ void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
+ uint8_t *bam_aux_get(bam1_t *b, const char tag[2]);
+ int32_t bam_aux2i(const uint8_t *s);
+ float bam_aux2f(const uint8_t *s);
+ double bam_aux2d(const uint8_t *s);
+ char bam_aux2A(const uint8_t *s);
+ char *bam_aux2Z(const uint8_t *s);
+
+ /*!
+ @abstract Get the color encoding the previous and current base
+ @param b pointer to an alignment
+ @param i The i-th position, 0-based
+ @return color
+
+ @discussion Returns 0 no color information is found.
+ */
+ char bam_aux_getCSi(bam1_t *b, int i);
+
+ /*!
+ @abstract Get the color quality of the color encoding the previous and current base
+ @param b pointer to an alignment
+ @param i The i-th position, 0-based
+ @return color quality
+
+ @discussion Returns 0 no color information is found.
+ */
+ char bam_aux_getCQi(bam1_t *b, int i);
+
+ /*!
+ @abstract Get the color error profile at the give position
+ @param b pointer to an alignment
+ @return the original color if the color was an error, '-' (dash) otherwise
+
+ @discussion Returns 0 no color information is found.
+ */
+ char bam_aux_getCEi(bam1_t *b, int i);
/*!
@abstract Calculate the rightmost coordinate of an alignment on the
return 0;
}
-static inline void bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
+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
// restore the backup
bdst->m_data = m_data;
bdst->data = data;
+ return bdst;
+}
+
+static inline bam1_t *bam_dup1(const bam1_t *src)
+{
+ bam1_t *b;
+ b = bam_init1();
+ *b = *src;
+ b->m_data = b->data_len;
+ b->data = (uint8_t*)calloc(b->data_len, 1);
+ memcpy(b->data, src->data, b->data_len);
+ return b;
}
#endif
projects / samtools.git / blobdiff