Fix a bug in --indels-v2.0

which caused an endless loop when CIGAR operator 'H' or 'P' was encountered.

Likely addresses one of the issues raised by #1930

Author: pd3

NEWS

@@ -61,6 +61,11 @@ Changes affecting specific commands:
     - Revamped line matching code to fix problems in gVCF merging where split gVCF blocks
       would not update genotypes (#1891, #1164).
 
+* bcftool mpileup
+
+    - Fix a bug in --indels-v2.0 which caused an endless loop when CIGAR operator 'H' or 'P'
+      was encountered
+
 * bcftools norm
 
     - The `-m, --multiallelics +` mode now preserves phasing (#1893)

cigar_state.h

@@ -107,6 +107,12 @@ static inline int cstate_seek_fwd(cigar_state_t *cs, hts_pos_t *pos_ptr, int tri
             cs->icig++;
             continue;
         }
+        if ( op==BAM_CHARD_CLIP || op==BAM_CPAD )
+        {
+            cs->icig++;
+            continue;
+        }
+        error("FIXME: not ready for CIGAR operator %d\n",op);
     }
     // the read starts after pos
     if ( trim_left )
@@ -175,6 +181,12 @@ static inline int cstate_seek_op_fwd(cigar_state_t *cs, hts_pos_t pos, int seek_
             cs->icig++;
             continue;
         }
+        if ( op==BAM_CHARD_CLIP || op==BAM_CPAD )
+        {
+            cs->icig++;
+            continue;
+        }
+        error("FIXME: not ready for CIGAR operator %d\n",op);
     }
     return cs->icig < cs->ncig ? -1 : -2;
 }