Implement -Y for soft clipping of supp. alignments

I tried to base this on bwa-mem and it seems to work for sam alignments.
2026-10-07 04:28:12 +08:00 · 2017-11-09 19:22:36 +01:00
parent a7b38f6900
commit 1cb0bf4bef
3 changed files with 13 additions and 5 deletions
@@ -24,6 +24,7 @@
 #define MM_F_LONG_CIGAR    0x10000
 #define MM_F_INDEPEND_SEG  0x20000
 #define MM_F_SPLICE_FLANK  0x40000
+#define MM_F_SOFTCLIP      0x80000

 #define MM_IDX_MAGIC   "MMI\2"