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Move regidx code to htslib #865

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Move regidx code to htslib #865

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23 changes: 7 additions & 16 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ OBJS = main.o vcfindex.o tabix.o \
vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o \
vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \
vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o bin.o hclust.o version.o \
regidx.o smpl_ilist.o csq.o vcfbuf.o \
smpl_ilist.o csq.o vcfbuf.o \
mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \
vcfsort.o \
ccall.o em.o prob1.o kmin.o # the original samtools calling
Expand Down Expand Up @@ -72,7 +72,7 @@ MISC_SCRIPTS = \
misc/plot-roh.py \
misc/run-roh.pl \
misc/vcfutils.pl
TEST_PROGRAMS = test/test-rbuf test/test-regidx
TEST_PROGRAMS = test/test-rbuf

all: $(PROGRAMS) $(TEST_PROGRAMS) plugins

Expand Down Expand Up @@ -183,7 +183,7 @@ tsv2vcf_h = tsv2vcf.h $(htslib_vcf_h)
filter_h = filter.h $(htslib_vcf_h)
gvcf_h = gvcf.h $(bcftools_h)
khash_str2str_h = khash_str2str.h $(htslib_khash_h)
ploidy_h = ploidy.h regidx.h
ploidy_h = ploidy.h $(htslib_regidx_h)
prob1_h = prob1.h $(htslib_vcf_h) $(call_h)
smpl_ilist_h = smpl_ilist.h $(htslib_vcf_h)
vcfbuf_h = vcfbuf.h $(htslib_vcf_h)
Expand All @@ -200,7 +200,7 @@ vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_
vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) hclust.h
vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h) $(htslib_kstring_h) $(htslib_bgzf_h) $(bcftools_h)
vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h)
vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) regidx.h $(bcftools_h) vcmp.h $(htslib_khash_h)
vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(htslib_regidx_h) $(bcftools_h) vcmp.h $(htslib_khash_h)
vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(htslib_khash_str2int_h) $(bcftools_h) rbuf.h
vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_str2int_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h)
vcfroh.o: vcfroh.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(bcftools_h) HMM.h $(smpl_ilist_h) $(filter_h)
Expand All @@ -227,9 +227,8 @@ ploidy.o: ploidy.c $(htslib_khash_str2int_h) $(htslib_kseq_h) $(htslib_hts_h) $(
polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h
peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(htslib_kstring_h)
bin.o: bin.c $(bcftools_h) bin.h
regidx.o: regidx.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) regidx.h
consensus.o: consensus.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) regidx.h $(bcftools_h) rbuf.h $(filter_h)
mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) regidx.h $(bcftools_h) $(bam2bcf_h) $(bam_sample_h) $(gvcf_h)
consensus.o: consensus.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_regidx_h) $(bcftools_h) rbuf.h $(filter_h)
mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) $(bcftools_h) $(bam2bcf_h) $(bam_sample_h) $(gvcf_h)
bam2bcf.o: bam2bcf.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) mw.h
bam2bcf_indel.o: bam2bcf_indel.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h)
bam_sample.o: bam_sample.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(khash_str2str_h) $(bam_sample_h) $(bcftools_h)
Expand All @@ -238,7 +237,7 @@ hclust.o: hclust.c $(htslib_hts_h) $(htslib_kstring_h) $(bcftools_h) hclust.h
HMM.o: HMM.c $(htslib_hts_h) HMM.h
vcfbuf.o: vcfbuf.c $(htslib_vcf_h) $(htslib_vcfutils_h) $(bcftools_h) $(vcfbuf_h) rbuf.h
smpl_ilist.o: smpl_ilist.c $(bcftools_h) $(smpl_ilist_h)
csq.o: csq.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_h) $(htslib_khash_str2int_h) $(htslib_kseq_h) $(htslib_faidx_h) $(bcftools_h) $(filter_h) regidx.h kheap.h $(smpl_ilist_h) rbuf.h
csq.o: csq.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_h) $(htslib_khash_str2int_h) $(htslib_kseq_h) $(htslib_faidx_h) $(bcftools_h) $(filter_h) $(htslib_regidx_h) kheap.h $(smpl_ilist_h) rbuf.h

# test programs

Expand All @@ -247,25 +246,17 @@ csq.o: csq.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(hts
# (regression.sh sets $REF_PATH to a subdirectory itself.)
test-no-plugins: $(PROGRAMS) $(TEST_PROGRAMS) $(BGZIP) $(TABIX)
./test/test-rbuf
./test/test-regidx
REF_PATH=: ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)

test-plugins: $(PROGRAMS) $(TEST_PROGRAMS) $(BGZIP) $(TABIX) plugins
./test/test-rbuf
./test/test-regidx
REF_PATH=: ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)

test/test-rbuf.o: test/test-rbuf.c rbuf.h

test/test-rbuf: test/test-rbuf.o
$(CC) $(LDFLAGS) -o $@ $^ $(ALL_LIBS)

test/test-regidx.o: test/test-regidx.c $(htslib_kstring_h) regidx.h

test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB)
$(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIB) $(ALL_LIBS)


# make docs target depends the a2x asciidoc program
doc/bcftools.1: doc/bcftools.txt
cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
Expand Down
2 changes: 1 addition & 1 deletion consensus.c
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Expand Up @@ -37,7 +37,7 @@
#include <htslib/synced_bcf_reader.h>
#include <htslib/kseq.h>
#include <htslib/bgzf.h>
#include "regidx.h"
#include <htslib/regidx.h>
#include "bcftools.h"
#include "rbuf.h"
#include "filter.h"
Expand Down
2 changes: 1 addition & 1 deletion csq.c
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Expand Up @@ -146,7 +146,7 @@
#include <ctype.h>
#include "bcftools.h"
#include "filter.h"
#include "regidx.h"
#include <htslib/regidx.h>
#include "kheap.h"
#include "smpl_ilist.h"
#include "rbuf.h"
Expand Down
2 changes: 1 addition & 1 deletion mpileup.c
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ DEALINGS IN THE SOFTWARE. */
#include <htslib/kstring.h>
#include <htslib/khash_str2int.h>
#include <assert.h>
#include "regidx.h"
#include <htslib/regidx.h>
#include "bcftools.h"
#include "bam2bcf.h"
#include "bam_sample.h"
Expand Down
2 changes: 1 addition & 1 deletion ploidy.h
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@
#ifndef __PLOIDY_H__
#define __PLOIDY_H__

#include "regidx.h"
#include <htslib/regidx.h>

typedef struct _ploidy_t ploidy_t;

Expand Down
4 changes: 2 additions & 2 deletions plugins/fixploidy.mk
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@@ -1,2 +1,2 @@
plugins/fixploidy.so: plugins/fixploidy.c version.h version.c regidx.h regidx.c ploidy.h ploidy.c
$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) $(LDFLAGS) -o $@ ploidy.c regidx.c version.c $< $(LIBS)
plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c
$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) $(LDFLAGS) -o $@ ploidy.c version.c $< $(LIBS)
2 changes: 1 addition & 1 deletion plugins/mendelian.c
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Expand Up @@ -36,7 +36,7 @@
#include <ctype.h>
#include <unistd.h> // for isatty
#include "bcftools.h"
#include "regidx.h"
#include <htslib/regidx.h>

#define MODE_COUNT 1
#define MODE_LIST_GOOD 2
Expand Down
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