problem while Installing BCFtools/htslib

Question

[always_learning]

Hi All,

I was trying to install bcftools/htslib tools using following commands at http://vcftools.sourceforge.net/htslib.html . I have downloaded latest one from Git Repository already from development branch as mentioned here https://github.com/samtools/bcftools and both bcftools/htslib are updated too.

I am getting below errors while compiling

syed@syed-Precision-M6800:~$ cd bcftools; make; make test
cd ../htslib && make lib-static
make[1]: Entering directory `/home/syed/htslib'
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "0.2.0-rc10-2-gb039db8"' > version.h
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hts.o hts.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o sam.o sam.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/md5.o cram/md5.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/vlen.o cram/vlen.c
cram/vlen.c: In function 'vflen':
cram/vlen.c:121:9: warning: variable 'i' set but not used [-Wunused-but-set-variable]
     int i;
         ^
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/zfio.o cram/zfio.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
make[1]: Leaving directory `/home/syed/htslib'
echo '#define BCFTOOLS_VERSION "0.2.0-rc9-1-g03487c0"' > version.h
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib main.c -o main.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcfindex.c -o vcfindex.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib tabix.c -o tabix.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcfstats.c -o vcfstats.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcfisec.c -o vcfisec.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcfmerge.c -o vcfmerge.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcfquery.c -o vcfquery.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcffilter.c -o vcffilter.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib filter.c -o filter.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcfsom.c -o vcfsom.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcfnorm.c -o vcfnorm.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcfgtcheck.c -o vcfgtcheck.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcfview.c -o vcfview.o
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcfannotate.c -o vcfannotate.o
vcfannotate.c: In function 'init_columns':
vcfannotate.c:642:21: error: too few arguments to function 'bcf_hdr_get_hrec'
                     bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_INFO, str.s);
                     ^
In file included from vcfannotate.c:36:0:
../htslib/htslib/vcf.h:425:17: note: declared here
     bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *key, const char *value, const char *str_class);
                 ^
make: *** [vcfannotate.o] Error 1
gcc -c -g -Wall -Wc++-compat -O2  -I. -I../htslib vcfannotate.c -o vcfannotate.o
vcfannotate.c: In function 'init_columns':
vcfannotate.c:642:21: error: too few arguments to function 'bcf_hdr_get_hrec'
                     bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_INFO, str.s);
                     ^
In file included from vcfannotate.c:36:0:
../htslib/htslib/vcf.h:425:17: note: declared here
     bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *key, const char *value, const char *str_class);
                 ^
make: *** [vcfannotate.o] Error 1

Can you please help me with this errors or some one who faced similar issue already?

Answer 1

[14134125465346445]

I found the same issue. The culprit seems to be vcfannotate, so if you comment out any reference of it in Makefile and main.c, then it compiles successfully. I was using a previous version where the command bcftools isec --complement A.vcf.gz B.vcf.gz C.vcf.gz D.vcf.gz would give me a segfault, but it now works with head master.

Answer 2

[Devon Ryan]

It looks like you caught a broken commit. Unless you have a good reason, just use the current release of samtools/bcftools.