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Pysam wants several functions not included in the library
[samtools.git]
/
bam.h
diff --git
a/bam.h
b/bam.h
index 246b020d679a07f073cfbae8dc40a8d57b501d25..346c750c8c807c44ea32804eeb1bb93411d0b71a 100644
(file)
--- a/
bam.h
+++ b/
bam.h
@@
-40,7
+40,7
@@
@copyright Genome Research Ltd.
*/
@copyright Genome Research Ltd.
*/
-#define BAM_VERSION "0.1.1
7 (r973:277
)"
+#define BAM_VERSION "0.1.1
8 (r982:295
)"
#include <stdint.h>
#include <stdlib.h>
#include <stdint.h>
#include <stdlib.h>
@@
-134,20
+134,25
@@
typedef struct {
/*
CIGAR operations.
*/
/*
CIGAR operations.
*/
-/*! @abstract CIGAR:
match
*/
+/*! @abstract CIGAR:
M = match or mismatch
*/
#define BAM_CMATCH 0
#define BAM_CMATCH 0
-/*! @abstract CIGAR: insertion to the reference */
+/*! @abstract CIGAR:
I =
insertion to the reference */
#define BAM_CINS 1
#define BAM_CINS 1
-/*! @abstract CIGAR: deletion from the reference */
+/*! @abstract CIGAR:
D =
deletion from the reference */
#define BAM_CDEL 2
#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
#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
#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
#define BAM_CHARD_CLIP 5
-/*! @abstract CIGAR: padding */
+/*! @abstract CIGAR:
P =
padding */
#define BAM_CPAD 6
#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.
/*! @typedef
@abstract Structure for core alignment information.