* samtools-0.1.9-9 (r810)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 1dc819a6d8870782dd94eb5d446821c4622d4b94..ad6134b3ee7cdeb179c3a86fd46658b0aef83aef 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -556,7 +556,7 @@ typedef struct {
 static int mplp_func(void *data, bam1_t *b)
 {
        extern int bam_realn(bam1_t *b, const char *ref);
-       extern int bam_prob_realn(bam1_t *b, const char *ref);
+       extern int bam_prob_realn_core(bam1_t *b, const char *ref, int);
        extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
        mplp_aux_t *ma = (mplp_aux_t*)data;
        int ret, skip = 0;
@@ -565,7 +565,7 @@ static int mplp_func(void *data, bam1_t *b)
                ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
                if (ret < 0) break;
                skip = 0;
-               if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn(b, ma->ref);
+               if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, 1);
                if (has_ref && ma->capQ_thres > 10) {
                        int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres);
                        if (q < 0) skip = 1;