converted padded SAM to unpadded SAM

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 346c750c8c807c44ea32804eeb1bb93411d0b71a..376e3246318f84cb28166f3052ad0b0aa96d375a 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -154,6 +154,13 @@ typedef struct {
 /*! @abstract CIGAR: X = mismatch */
 #define BAM_CDIFF        8
 
+#define BAM_CIGAR_STR "MIDNSHP=X"
+
+#define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
+#define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)
+#define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])
+#define bam_cigar_gen(o, l) ((o)<<BAM_CIGAR_SHIFT|(l))
+
 /*! @typedef
   @abstract Structure for core alignment information.
   @field  tid     chromosome ID, defined by bam_header_t