fixed a silly bug in pileup

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 6d42471c007a6b34d5b7b1db3ee535c974564839..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);
@@ -768,7 +769,8 @@ int bam_mpileup(int argc, char *argv[])
        mplp.max_mq = 60;
        mplp.min_baseQ = 13;
        mplp.capQ_thres = 0;
-       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:")) >= 0) {
+       mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
+       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:B")) >= 0) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
@@ -779,6 +781,7 @@ int bam_mpileup(int argc, char *argv[])
                case 'g': mplp.flag |= MPLP_GLF; break;
                case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
                case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
+               case 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break;
                case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
                case 'R': mplp.flag |= MPLP_REALN; break;
                case 'C': mplp.capQ_thres = atoi(optarg); break;
@@ -798,6 +801,7 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
                fprintf(stderr, "         -g          generate BCF output\n");
                fprintf(stderr, "         -u          do not compress BCF output\n");
+               fprintf(stderr, "         -B          disable BAQ computation\n");
                fprintf(stderr, "\n");
                fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
                return 1;