Resolve merge conflicts

Author: pd3

Makefile

@@ -41,7 +41,7 @@ OBJS     = main.o vcfindex.o tabix.o \
            vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o \
            regidx.o smpl_ilist.o csq.o vcfbuf.o \
            mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o \
-	   read_consensus.o bam_sample.o \
+           read_consensus.o bam_sample.o \
            vcfsort.o cols.o extsort.o dist.o abuf.o \
            ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o
 PLUGIN_OBJS = vcfplugin.o
@@ -235,7 +235,6 @@ vcfbuf_h = vcfbuf.h $(htslib_vcf_h)
 abuf_h = abuf.h $(htslib_vcf_h)
 dbuf_h = dbuf.h $(htslib_vcf_h)
 bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h)
-edlib.h = edlib.h
 bam_sample_h = bam_sample.h $(htslib_sam_h)
 cigar_state_h = cigar_state.h $(htslib_hts_h) $(htslib_sam_h)
 read_consensus_h = read_consensus.h $(htslib_hts_h) $(htslib_sam_h)
@@ -249,11 +248,11 @@ vcfcall.o: vcfcall.c $(htslib_vcf_h) $(htslib_kfunc_h) $(htslib_synced_bcf_reade
 vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_thread_pool_h) $(htslib_hts_endian_h) $(bcftools_h)
 vcfconvert.o: vcfconvert.c $(htslib_faidx_h) $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_kseq_h) $(htslib_hts_endian_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h)
 vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h regidx.h
-vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_kbitset_h) $(htslib_hts_os_h) $(htslib_bgzf_h) $(bcftools_h) extsort.h filter.h
+vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_kbitset_h) $(htslib_hts_os_h) $(htslib_bgzf_h) $(bcftools_h) extsort.h $(filter_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) $(htslib_hts_os_h) $(htslib_hts_defs_h) $(bcftools_h) $(filter_h)
-vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(htslib_kbitset_h) $(htslib_hts_endian_h) $(bcftools_h) regidx.h vcmp.h $(htslib_khash_h) $(htslib_kbitset_h)
-vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(htslib_khash_str2int_h) $(bcftools_h) rbuf.h abuf.h gff.h regidx.h
+vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_hts_os_h) $(bcftools_h) $(filter_h)
+vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(htslib_kbitset_h) $(htslib_hts_endian_h) $(bcftools_h) regidx.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 abuf.h gff.h regidx.h $(filter_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) $(smpl_ilist_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)
 vcfcnv.o: vcfcnv.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(htslib_khash_str2int_h) $(htslib_hts_defs_h) $(bcftools_h) HMM.h rbuf.h
@@ -287,14 +286,15 @@ mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(hts
 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) $(str_finder_h)
 bam2bcf_iaux.o: bam2bcf_iaux.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bcftools_h) $(bam2bcf_h) $(htslib_ksort_h) $(read_consensus_h) $(cigar_state_h)
-bam2bcf_edlib.o: bam2bcf_edlib.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bcftools_h) $(bam2bcf_h) $(htslib_ksort_h) $(read_consensus_h) $(cigar_state_h) $(edlib.h)
+bam2bcf_edlib.o: bam2bcf_edlib.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(str_finder_h) $(htslib_ksort_h) edlib.h
 read_consensus.o: read_consensus.c $(read_consensus_h) $(cigar_state_h) $(bcftools_h) kheap.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)
 version.o: version.h version.c
 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) $(htslib_hts_os_h) $(bcftools_h) $(vcfbuf_h) rbuf.h
+vcfbuf.o: vcfbuf.c $(htslib_vcf_h) $(htslib_vcfutils_h) $(htslib_hts_os_h) $(htslib_kbitset_h) $(bcftools_h) $(vcfbuf_h) rbuf.h
 abuf.o: abuf.c $(htslib_vcf_h) $(bcftools_h) rbuf.h abuf.h
+edlib.o: edlib.c edlib.h
 extsort.o: extsort.c $(bcftools_h) extsort.h kheap.h
 smpl_ilist.o: smpl_ilist.c $(bcftools_h) $(smpl_ilist_h)
 gff.o: gff.c $(htslib_hts_h) $(htslib_khash_h)  $(htslib_khash_str2int_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(bcftools_h) gff.h regidx.h

csq.c

@@ -149,6 +149,7 @@
 #include <errno.h>
 #include <unistd.h>
 #include <ctype.h>
+#include <strings.h>
 #include "bcftools.h"
 #include "filter.h"
 #include "regidx.h"

gff.c

@@ -29,6 +29,7 @@
 #include <assert.h>
 #include <inttypes.h>
 #include <string.h>
+#include <strings.h>
 #include <htslib/hts.h>
 #include <htslib/khash.h>
 #include <htslib/khash_str2int.h>

plugins/tag2tag.c

@@ -24,6 +24,7 @@ DEALINGS IN THE SOFTWARE.  */
 
 #include <stdio.h>
 #include <stdlib.h>
+#include <strings.h>
 #include <getopt.h>
 #include <math.h>
 #include <inttypes.h>