When -B is applied to mpileup, still use paired reads only unless -A is flagged.

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 27f67629337b89385080e1904deb80e4dd313d50..d03bab10af0efe28cbda757b3c7e1a7150bfde1d 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -877,7 +877,7 @@ int bam_mpileup(int argc, char *argv[])
                case 'g': mplp.flag |= MPLP_GLF; break;
                case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
                case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
-               case 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break;
+               case 'B': mplp.flag &= ~MPLP_REALN; break;
                case 'R': mplp.flag |= MPLP_REALN; break;
                case 'D': mplp.flag |= MPLP_FMT_DP; break;
                case 'S': mplp.flag |= MPLP_FMT_SP; break;