Imported Upstream version 0.1.12a

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index e3f73aaddd03a14343a82084ee060d9c41ba42d4..002297a1229678a256e9045f420b89d5f273b1ea 100644 (file)
--- 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) {