From ef04d5264880651d082138b99f6a63e8659457dc Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 7 Jul 2011 03:46:12 +0000 Subject: [PATCH] fixed a bug in bam_plcmd.c --- Makefile.mingw | 8 +++----- bam_plcmd.c | 3 ++- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/Makefile.mingw b/Makefile.mingw index 836360f..a3f4b9f 100644 --- 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 17e5806..cbf6ae8 100644 --- 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); -- 2.39.2