Imported Upstream version 0.1.7~dfsg

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 83c03ada21098eda911caabb0e56db3864599e73..291b30314f75d3d882b1d5dc9960e7b709a50c02 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -45,21 +45,7 @@
 #include <string.h>
 #include <stdio.h>
 
-#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 +57,15 @@ 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 <zlib.h>
+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 +73,7 @@ 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
@@ -102,7 +86,7 @@ typedef struct {
        int32_t n_targets;
        char **target_name;
        uint32_t *target_len;
-       void *hash, *rg2lib;
+       void *dict, *hash, *rg2lib;
        int l_text;
        char *text;
 } bam_header_t;
@@ -130,6 +114,10 @@ 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)
 
@@ -436,8 +424,8 @@ 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 +436,10 @@ 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);
+
+       const char *bam_get_library(bam_header_t *header, const bam1_t *b);
+
        /*! @typedef
          @abstract Structure for one alignment covering the pileup position.
          @field  b      pointer to the alignment
@@ -526,6 +518,8 @@ extern "C" {
         */
        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;
 
@@ -540,9 +534,6 @@ 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);
-
        struct __bam_index_t;
        typedef struct __bam_index_t bam_index_t;
 
@@ -622,8 +613,8 @@ 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()
 
        /*!  
@@ -644,14 +635,6 @@ 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