makefile requires -lhts flag

[hanbin973]

Dear shapeit developers,

Due to the lack of releases, I had to manually compile the program from source. I found that running make causes the following error:

g++ -std=c++20 -O3 obj/main.o obj/haplotype_segment_single.o obj/haplotype_segment_double.o obj/compute_job.o obj/variant.o obj/hmm_parameters.o obj/genotype_mendel.o obj/genotype_sweep.o obj/genotype_prune.o obj/genotype_managment.o obj/genotype_build.o obj/genotype_reader_scaning.o obj/genotype_reader_managment.o obj/genotype_reader_reading.o obj/graph_writer.o obj/gmap_reader.o obj/haplotype_writer.o obj/pedigree_reader.o obj/haploid_reader.o obj/window_set.o obj/variant_map.o obj/genotype_set.o obj/ibd2_tracks.o obj/bitmatrix.o obj/conditioning_set_selection.o obj/conditioning_set_solve.o obj/conditioning_set_managment.o obj/haplotype_set.o obj/genotype_builder.o obj/phaser_initialise.o obj/phaser_finalise.o obj/phaser_management.o obj/phaser_parameters.o obj/phaser_algorithm.o -o bin/phase_common  /home/hanbin/.local/lib/libboost_iostreams.a /home/hanbin/.local/lib/libboost_program_options.a -lz -lpthread -lbz2 -llzma -lcurl -lcrypto -ldeflate
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/genotype_reader_scaning.o: in function `xcf_reader::addFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) [clone .isra.0]':
genotype_reader_scaning.cpp:(.text+0x2b21): undefined reference to `bcf_sr_add_reader'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text+0x2f1e): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text+0x324d): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text+0x3284): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text+0x32c3): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/genotype_reader_scaning.o: in function `genotype_reader::scanGenotypes()':
genotype_reader_scaning.cpp:(.text+0x5811): undefined reference to `bcf_sr_init'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text+0x5954): undefined reference to `bcf_sr_init'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text+0x5994): undefined reference to `bcf_sr_set_regions'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text+0x59b4): undefined reference to `bcf_sr_set_targets'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text+0x5ad6): undefined reference to `bcf_sr_set_threads'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text+0x5af6): undefined reference to `bcf_sr_set_threads'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text+0x5cd5): undefined reference to `bcf_sr_destroy'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/genotype_reader_scaning.o: in function `xcf_reader::nextRecord()':
genotype_reader_scaning.cpp:(.text._ZN10xcf_reader10nextRecordEv[_ZN10xcf_reader10nextRecordEv]+0x19): undefined reference to `bcf_sr_next_line'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text._ZN10xcf_reader10nextRecordEv[_ZN10xcf_reader10nextRecordEv]+0x542): undefined reference to `bcf_get_info_values'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text._ZN10xcf_reader10nextRecordEv[_ZN10xcf_reader10nextRecordEv]+0x57e): undefined reference to `bcf_get_info_values'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_scaning.cpp:(.text._ZN10xcf_reader10nextRecordEv[_ZN10xcf_reader10nextRecordEv]+0x785): undefined reference to `bcf_get_info_values'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/genotype_reader_reading.o: in function `xcf_reader::readRecord(unsigned int, char**, char**, int*) [clone .constprop.0]':
genotype_reader_reading.cpp:(.text+0xde): undefined reference to `bcf_get_format_values'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/genotype_reader_reading.o: in function `xcf_reader::addFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) [clone .isra.0]':
genotype_reader_reading.cpp:(.text+0x33e1): undefined reference to `bcf_sr_add_reader'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text+0x37de): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text+0x3b0d): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text+0x3b44): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text+0x3b83): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/genotype_reader_reading.o: in function `genotype_reader::readGenotypes()':
genotype_reader_reading.cpp:(.text+0x60df): undefined reference to `bcf_sr_init'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text+0x7089): undefined reference to `bcf_sr_init'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text+0x70d8): undefined reference to `bcf_sr_set_regions'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text+0x70f8): undefined reference to `bcf_sr_set_targets'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text+0x745b): undefined reference to `bcf_sr_set_threads'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text+0x7480): undefined reference to `bcf_sr_set_threads'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text+0x7e3e): undefined reference to `bcf_get_format_values'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text+0x816a): undefined reference to `bcf_sr_destroy'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/genotype_reader_reading.o: in function `xcf_reader::readRecord(unsigned int, char**, char**, int*)':
genotype_reader_reading.cpp:(.text._ZN10xcf_reader10readRecordEjPPcS1_Pi[_ZN10xcf_reader10readRecordEjPPcS1_Pi]+0x150): undefined reference to `bcf_get_format_values'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: genotype_reader_reading.cpp:(.text._ZN10xcf_reader10readRecordEjPPcS1_Pi[_ZN10xcf_reader10readRecordEjPPcS1_Pi]+0x191): undefined reference to `bcf_get_format_values'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/haplotype_writer.o: in function `haplotype_writer::writeHaplotypes(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
haplotype_writer.cpp:(.text+0x2058): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x207c): undefined reference to `bcf_update_id'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x21ef): undefined reference to `bcf_update_alleles_str'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x221c): undefined reference to `bcf_update_info'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x2249): undefined reference to `bcf_update_info'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x23a4): undefined reference to `bcf_update_format'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x23be): undefined reference to `bcf_write'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x23d2): undefined reference to `bcf_clear'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x262d): undefined reference to `bcf_update_format'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x2647): undefined reference to `bcf_write'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x275f): undefined reference to `bcf_update_info'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x27de): undefined reference to `bcf_update_info'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x287e): undefined reference to `bcf_destroy'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x288a): undefined reference to `bcf_hdr_destroy'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x2896): undefined reference to `hts_close'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text+0x38fc): undefined reference to `bcf_idx_save'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/haplotype_writer.o: in function `xcf_writer::writeHeader_initialize(bcf_hdr_t const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool)':
haplotype_writer.cpp:(.text._ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb[_ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb]+0x80): undefined reference to `bcf_hdr_init'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb[_ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb]+0x499): undefined reference to `bcf_hdr_append'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb[_ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb]+0x505): undefined reference to `bcf_hdr_append'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb[_ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb]+0xb3c): undefined reference to `bcf_hdr_append'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb[_ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb]+0xc04): undefined reference to `bcf_hdr_append'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb[_ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb]+0xc14): undefined reference to `bcf_hdr_append'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/haplotype_writer.o:haplotype_writer.cpp:(.text._ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb[_ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb]+0xc2e): more undefined references to `bcf_hdr_append' follow
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/haplotype_writer.o: in function `xcf_writer::writeHeader_initialize(bcf_hdr_t const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool)':
haplotype_writer.cpp:(.text._ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb[_ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb]+0xc6d): undefined reference to `bcf_hdr_subset'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb[_ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb]+0xc82): undefined reference to `bcf_hdr_add_sample'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb[_ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb]+0xc92): undefined reference to `bcf_hdr_remove'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb[_ZN10xcf_writer22writeHeader_initializeEPK9bcf_hdr_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb]+0xc59): undefined reference to `bcf_hdr_append'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/haplotype_writer.o: in function `xcf_writer::xcf_writer(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, unsigned int, bool)':
haplotype_writer.cpp:(.text._ZN10xcf_writerC2ENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEbjb[_ZN10xcf_writerC5ENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEbjb]+0x31f): undefined reference to `bcf_init'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writerC2ENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEbjb[_ZN10xcf_writerC5ENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEbjb]+0x346): undefined reference to `hts_open'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: obj/haplotype_writer.o: in function `xcf_writer::writeHeader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool)':
haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x19f): undefined reference to `bcf_sr_init'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x254): undefined reference to `bcf_sr_add_reader'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x2f4): undefined reference to `bcf_sr_set_threads'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x66c): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x9b5): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x9f0): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0xa33): undefined reference to `bcf_hdr_id2int'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x1171): undefined reference to `bcf_hdr_add_sample'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x11a2): undefined reference to `bcf_hdr_add_sample'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x11b4): undefined reference to `bcf_hdr_write'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x11de): undefined reference to `bcf_idx_init'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x11f4): undefined reference to `bcf_clear'
/home/hanbin/micromamba/envs/shapeit/bin/../libexec/gcc/x86_64-conda-linux-gnu/15.2.0/ld: haplotype_writer.cpp:(.text._ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b[_ZN10xcf_writer11writeHeaderENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_b]+0x12b5): undefined reference to `bcf_sr_destroy'

This was fixed after adding -lhts to the [common](https://github.com/odelaneau/shapeit/tree/main/common) /makefile_common.mk's line 23.

Thanks.