fixed a silly bug in pileup

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 23602ccd5bcf6dc116632fa1bdb9483993aebf92..dca85181f99bf1c7343650846039153a019e7ea9 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -473,6 +473,7 @@ int bam_pileup(int argc, char *argv[])
                        bam_plp_set_mask(iter, d->mask);
                        while ((ret = samread(fp, b)) >= 0) {
                                int skip = 0;
+                               if ((int)b->core.tid < 0) break;
                                // update d->ref if necessary
                                if (d->fai && (int)b->core.tid != d->tid) {
                                        free(d->ref);