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New upstream release (no new copyright holder nor license statement).
[samtools.git]
/
bam.h
diff --git
a/bam.h
b/bam.h
index bc8e3f19edf59a1aa4ef9aaa6a57e44b08b60af6..246b020d679a07f073cfbae8dc40a8d57b501d25 100644
(file)
--- a/
bam.h
+++ b/
bam.h
@@
-33,14
+33,14
@@
BAM library provides I/O and various operations on manipulating files
in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map)
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
T
AM, sorting,
+ format. It now supports importing from or exporting to
S
AM, sorting,
merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
@copyright Genome Research Ltd.
*/
merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
@copyright Genome Research Ltd.
*/
-#define BAM_VERSION "0.1.1
4 (r933:170
)"
+#define BAM_VERSION "0.1.1
7 (r973:277
)"
#include <stdint.h>
#include <stdlib.h>
#include <stdint.h>
#include <stdlib.h>
@@
-264,6
+264,12
@@
typedef struct __bam_iter_t *bam_iter_t;
*/
extern int bam_is_be;
*/
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];
/*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
extern unsigned char bam_nt16_table[256];
@@
-740,4
+746,13
@@
static inline bam1_t *bam_dup1(const bam1_t *src)
return b;
}
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
#endif