@copyright Genome Research Ltd.
*/
-#define BAM_VERSION "0.1.17 (r973:277)"
+#define BAM_VERSION "0.1.18 (r982:295)"
#include <stdint.h>
#include <stdlib.h>
/*
CIGAR operations.
*/
-/*! @abstract CIGAR: match */
+/*! @abstract CIGAR: M = match or mismatch*/
#define BAM_CMATCH 0
-/*! @abstract CIGAR: insertion to the reference */
+/*! @abstract CIGAR: I = insertion to the reference */
#define BAM_CINS 1
-/*! @abstract CIGAR: deletion from the reference */
+/*! @abstract CIGAR: D = deletion from the reference */
#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
-/*! @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
-/*! @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
-/*! @abstract CIGAR: padding */
+/*! @abstract CIGAR: P = padding */
#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.