X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_plcmd.c;h=002297a1229678a256e9045f420b89d5f273b1ea;hp=e3f73aaddd03a14343a82084ee060d9c41ba42d4;hb=f2f3968e11eead9ce5601b01890bc2339ff951e9;hpb=6a0c6f060a60789b48e10a72b1381f6e54599302

diff --git a/bam_plcmd.c b/bam_plcmd.c
index e3f73aa..002297a 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -563,9 +563,10 @@ static int mplp_func(void *data, bam1_t *b)
 	mplp_aux_t *ma = (mplp_aux_t*)data;
 	int ret, skip = 0;
 	do {
-		int has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
+		int has_ref;
 		ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
 		if (ret < 0) break;
+		has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
 		skip = 0;
 		if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, 1);
 		if (has_ref && ma->capQ_thres > 10) {