fixed a bug in realignment

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 1205e10b845288f25dbd240b3b612ae79d2f8b8a..cdbf67d861cf5e90418422057901dfab0bf0ee6b 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -490,7 +490,8 @@ static int mplp_func(void *data, bam1_t *b)
                cond = 0;
                ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
                if (ret < 0) break;
-               if (b->core.qual < ma->min_mq) cond = 1; 
+               if (b->core.flag&BAM_FUNMAP) cond = 1;
+               else if (b->core.qual < ma->min_mq) cond = 1; 
                else if ((ma->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) cond = 1;
                if (ma->ref && !cond && (ma->flag&MPLP_REALN)) bam_realn(b, ma->ref);
        } while (cond);