r235: optionally output tag cs in PAF

cs encodes the query, the reference sequence and CIGAR.
2026-10-07 21:08:12 +08:00 · 2017-07-31 12:06:49 -04:00
parent 46de0fbdad
commit 4c0713ee14
5 changed files with 72 additions and 7 deletions
@@ -12,6 +12,8 @@
 #define MM_F_CIGAR     0x04
 #define MM_F_OUT_SAM   0x08
 #define MM_F_NO_QUAL   0x10
+#define MM_F_OUT_CG    0x20
+#define MM_F_OUT_CS    0x40

 #define MM_IDX_MAGIC   "MMI\2"