fixed a bug in bam_plcmd.c

diff --git a/Makefile.mingw b/Makefile.mingw
index 836360f3df3bfdb8587c67ef42c3402eef4ba985..a3f4b9fe6b33f7ec6d706279fdac89ee50f87810 100644 (file)
--- a/Makefile.mingw
+++ b/Makefile.mingw
@@ -6,7 +6,7 @@ KNETFILE_O=     knetfile.o
 LOBJS=         bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
                        bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o \
                        $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-AOBJS=         bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \
+AOBJS=         bam_tview.o bam_plcmd.o sam_view.o      \
                        bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o     \
                        bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o
 BCFOBJS=       bcftools/bcf.o bcftools/fet.o bcftools/bcf2qcall.o bcftools/bcfutils.o \
@@ -43,14 +43,12 @@ bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
 sam.o:sam.h bam.h
 bam_import.o:bam.h kseq.h khash.h razf.h
 bam_pileup.o:bam.h razf.h ksort.h
-bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h bcftools/bcf.h bam2bcf.h
+bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
 bam_lpileup.o:bam.h ksort.h
-bam_tview.o:bam.h faidx.h bam_maqcns.h
-bam_maqcns.o:bam.h ksort.h bam_maqcns.h kaln.h
+bam_tview.o:bam.h faidx.h
 bam_sort.o:bam.h ksort.h razf.h
 bam_md.o:bam.h faidx.h
-glf.o:glf.h
 sam_header.o:sam_header.h khash.h
 bcf.o:bcftools/bcf.h
 bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 17e5806e6c96db00b88533a4e04ce387a08b512e..cbf6ae8c13754be0c441b311eb14dfb9f04452a3 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -179,7 +179,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
        extern void bcf_call_del_rghash(void *rghash);
        mplp_aux_t **data;
-       int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth, max_indel_depth;
+       int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth;
        const bam_pileup1_t **plp;
        bam_mplp_t iter;
        bam_header_t *h = 0;
@@ -276,6 +276,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        }
        if (tid0 >= 0 && conf->fai) { // region is set
                ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
+               ref_tid = tid0;
                for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
        } else ref_tid = -1, ref = 0;
        iter = bam_mplp_init(n, mplp_func, (void**)data);