* samtools-0.1.5-5 (r395)

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 6316c9b438320dc5df8751f5c1a73ed6c185b6e4..64867f10733f6889c1a0e0fa7a61e8e2802c2407 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -41,26 +41,11 @@
  */
 
 #include <stdint.h>
-#include <assert.h>
 #include <stdlib.h>
 #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 */
@@ -72,18 +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
@@ -527,6 +509,8 @@ 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;
 
@@ -541,9 +525,6 @@ 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;
 
@@ -600,8 +581,9 @@ extern "C" {
          @param  ref_id  the returned chromosome ID
          @param  begin   the returned start coordinate
          @param  end     the returned end coordinate
+         @return         0 on success; -1 on failure
         */
-       void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
+       int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
 
        /*!
          @abstract       Retrieve data of a tag
@@ -624,7 +606,7 @@ extern "C" {
 
        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()
+       uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
 
        /*!  
          @abstract Calculate the rightmost coordinate of an alignment on the