The following packages will be installed: htslib Fetching README... 0%100%100%100%100%100%Done Fetching htslib.SlackBuild... 0%100%100%100%100%100%Done Fetching htslib.info... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done htslib-1.15.1/ htslib-1.15.1/INSTALL htslib-1.15.1/LICENSE htslib-1.15.1/Makefile htslib-1.15.1/NEWS htslib-1.15.1/README htslib-1.15.1/README.large_positions.md htslib-1.15.1/bcf_sr_sort.c htslib-1.15.1/bcf_sr_sort.h htslib-1.15.1/bgzf.c htslib-1.15.1/bgzip.1 htslib-1.15.1/bgzip.c htslib-1.15.1/builddir_vars.mk.in htslib-1.15.1/config.mk.in htslib-1.15.1/configure.ac htslib-1.15.1/cram/ htslib-1.15.1/cram/cram.h htslib-1.15.1/cram/cram_codecs.c htslib-1.15.1/cram/cram_codecs.h htslib-1.15.1/cram/cram_decode.c htslib-1.15.1/cram/cram_decode.h htslib-1.15.1/cram/cram_encode.c htslib-1.15.1/cram/cram_encode.h htslib-1.15.1/cram/cram_external.c htslib-1.15.1/cram/cram_index.c htslib-1.15.1/cram/cram_index.h htslib-1.15.1/cram/cram_io.c htslib-1.15.1/cram/cram_io.h htslib-1.15.1/cram/cram_samtools.h htslib-1.15.1/cram/cram_stats.c htslib-1.15.1/cram/cram_stats.h htslib-1.15.1/cram/cram_structs.h htslib-1.15.1/cram/mFILE.c htslib-1.15.1/cram/mFILE.h htslib-1.15.1/cram/misc.h htslib-1.15.1/cram/open_trace_file.c htslib-1.15.1/cram/open_trace_file.h htslib-1.15.1/cram/os.h htslib-1.15.1/cram/pooled_alloc.c htslib-1.15.1/cram/pooled_alloc.h htslib-1.15.1/cram/string_alloc.c htslib-1.15.1/cram/string_alloc.h htslib-1.15.1/errmod.c htslib-1.15.1/faidx.5 htslib-1.15.1/faidx.c htslib-1.15.1/header.c htslib-1.15.1/header.h htslib-1.15.1/hfile.c htslib-1.15.1/hfile_gcs.c htslib-1.15.1/hfile_internal.h htslib-1.15.1/hfile_libcurl.c htslib-1.15.1/hfile_s3.c htslib-1.15.1/hfile_s3_write.c htslib-1.15.1/hts.c htslib-1.15.1/hts_expr.c htslib-1.15.1/hts_internal.h htslib-1.15.1/hts_os.c htslib-1.15.1/htscodecs/ htslib-1.15.1/htscodecs/LICENSE.md htslib-1.15.1/htscodecs/MAINTAINERS.md htslib-1.15.1/htscodecs/NEWS htslib-1.15.1/htscodecs/htscodecs/ htslib-1.15.1/htscodecs/htscodecs/arith_dynamic.c htslib-1.15.1/htscodecs/htscodecs/arith_dynamic.h htslib-1.15.1/htscodecs/htscodecs/c_range_coder.h htslib-1.15.1/htscodecs/htscodecs/c_simple_model.h htslib-1.15.1/htscodecs/htscodecs/fqzcomp_qual.c htslib-1.15.1/htscodecs/htscodecs/fqzcomp_qual.h htslib-1.15.1/htscodecs/htscodecs/htscodecs.c htslib-1.15.1/htscodecs/htscodecs/htscodecs.h htslib-1.15.1/htscodecs/htscodecs/htscodecs_endian.h htslib-1.15.1/htscodecs/htscodecs/pack.c htslib-1.15.1/htscodecs/htscodecs/pack.h htslib-1.15.1/htscodecs/htscodecs/pooled_alloc.h htslib-1.15.1/htscodecs/htscodecs/rANS_byte.h htslib-1.15.1/htscodecs/htscodecs/rANS_static.c htslib-1.15.1/htscodecs/htscodecs/rANS_static.h htslib-1.15.1/htscodecs/htscodecs/rANS_static4x16.h htslib-1.15.1/htscodecs/htscodecs/rANS_static4x16pr.c htslib-1.15.1/htscodecs/htscodecs/rANS_word.h htslib-1.15.1/htscodecs/htscodecs/rle.c htslib-1.15.1/htscodecs/htscodecs/rle.h htslib-1.15.1/htscodecs/htscodecs/tokenise_name3.c htslib-1.15.1/htscodecs/htscodecs/tokenise_name3.h htslib-1.15.1/htscodecs/htscodecs/utils.h htslib-1.15.1/htscodecs/htscodecs/varint.h htslib-1.15.1/htscodecs/htscodecs/varint2.h htslib-1.15.1/htscodecs/htscodecs/version.h htslib-1.15.1/htscodecs/tests/ htslib-1.15.1/htscodecs/tests/arith.test htslib-1.15.1/htscodecs/tests/arith_dynamic_fuzz.c htslib-1.15.1/htscodecs/tests/arith_dynamic_test.c htslib-1.15.1/htscodecs/tests/dat/ htslib-1.15.1/htscodecs/tests/dat/arith/ htslib-1.15.1/htscodecs/tests/dat/arith/q4.0 htslib-1.15.1/htscodecs/tests/dat/arith/q4.1 htslib-1.15.1/htscodecs/tests/dat/arith/q4.128 htslib-1.15.1/htscodecs/tests/dat/arith/q4.129 htslib-1.15.1/htscodecs/tests/dat/arith/q4.192 htslib-1.15.1/htscodecs/tests/dat/arith/q4.193 htslib-1.15.1/htscodecs/tests/dat/arith/q4.64 htslib-1.15.1/htscodecs/tests/dat/arith/q4.65 htslib-1.15.1/htscodecs/tests/dat/arith/q4.8 htslib-1.15.1/htscodecs/tests/dat/arith/q4.9 htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.0 htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.1 htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.64 htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.65 htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.8 htslib-1.15.1/htscodecs/tests/dat/arith/q40+dir.9 htslib-1.15.1/htscodecs/tests/dat/arith/q8.0 htslib-1.15.1/htscodecs/tests/dat/arith/q8.1 htslib-1.15.1/htscodecs/tests/dat/arith/q8.128 htslib-1.15.1/htscodecs/tests/dat/arith/q8.129 htslib-1.15.1/htscodecs/tests/dat/arith/q8.192 htslib-1.15.1/htscodecs/tests/dat/arith/q8.193 htslib-1.15.1/htscodecs/tests/dat/arith/q8.64 htslib-1.15.1/htscodecs/tests/dat/arith/q8.65 htslib-1.15.1/htscodecs/tests/dat/arith/qvar.0 htslib-1.15.1/htscodecs/tests/dat/arith/qvar.1 htslib-1.15.1/htscodecs/tests/dat/arith/qvar.64 htslib-1.15.1/htscodecs/tests/dat/arith/qvar.65 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/ htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q4.0 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q4.1 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q4.2 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q4.3 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q40+dir.0 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q40+dir.1 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q40+dir.2 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q40+dir.3 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q8.0 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q8.1 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q8.2 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/q8.3 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/qvar.0 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/qvar.1 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/qvar.2 htslib-1.15.1/htscodecs/tests/dat/fqzcomp/qvar.3 htslib-1.15.1/htscodecs/tests/dat/q4 htslib-1.15.1/htscodecs/tests/dat/q40+dir htslib-1.15.1/htscodecs/tests/dat/q8 htslib-1.15.1/htscodecs/tests/dat/qvar htslib-1.15.1/htscodecs/tests/dat/r4x16/ htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.0 htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.1 htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.128 htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.129 htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.192 htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.193 htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.64 htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.65 htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.8 htslib-1.15.1/htscodecs/tests/dat/r4x16/q4.9 htslib-1.15.1/htscodecs/tests/dat/r4x16/q40+dir.0 htslib-1.15.1/htscodecs/tests/dat/r4x16/q40+dir.1 htslib-1.15.1/htscodecs/tests/dat/r4x16/q40+dir.8 htslib-1.15.1/htscodecs/tests/dat/r4x16/q40+dir.9 htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.0 htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.1 htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.128 htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.129 htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.192 htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.193 htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.64 htslib-1.15.1/htscodecs/tests/dat/r4x16/q8.65 htslib-1.15.1/htscodecs/tests/dat/r4x16/qvar.0 htslib-1.15.1/htscodecs/tests/dat/r4x16/qvar.1 htslib-1.15.1/htscodecs/tests/dat/r4x8/ htslib-1.15.1/htscodecs/tests/dat/r4x8/q4.0 htslib-1.15.1/htscodecs/tests/dat/r4x8/q4.1 htslib-1.15.1/htscodecs/tests/dat/r4x8/q40+dir.0 htslib-1.15.1/htscodecs/tests/dat/r4x8/q40+dir.1 htslib-1.15.1/htscodecs/tests/dat/r4x8/q8.0 htslib-1.15.1/htscodecs/tests/dat/r4x8/q8.1 htslib-1.15.1/htscodecs/tests/dat/r4x8/qvar.0 htslib-1.15.1/htscodecs/tests/dat/r4x8/qvar.1 htslib-1.15.1/htscodecs/tests/fqzcomp.test htslib-1.15.1/htscodecs/tests/fqzcomp_qual_fuzz.c htslib-1.15.1/htscodecs/tests/fqzcomp_qual_test.c htslib-1.15.1/htscodecs/tests/names/ htslib-1.15.1/htscodecs/tests/names/01.names htslib-1.15.1/htscodecs/tests/names/02.names htslib-1.15.1/htscodecs/tests/names/03.names htslib-1.15.1/htscodecs/tests/names/05.names htslib-1.15.1/htscodecs/tests/names/08.names htslib-1.15.1/htscodecs/tests/names/09.names htslib-1.15.1/htscodecs/tests/names/10.names htslib-1.15.1/htscodecs/tests/names/20.names htslib-1.15.1/htscodecs/tests/names/nv.names htslib-1.15.1/htscodecs/tests/names/nv2.names htslib-1.15.1/htscodecs/tests/names/rr.names htslib-1.15.1/htscodecs/tests/names/tok3/ htslib-1.15.1/htscodecs/tests/names/tok3/01.names.1 htslib-1.15.1/htscodecs/tests/names/tok3/01.names.11 htslib-1.15.1/htscodecs/tests/names/tok3/01.names.13 htslib-1.15.1/htscodecs/tests/names/tok3/01.names.15 htslib-1.15.1/htscodecs/tests/names/tok3/01.names.17 htslib-1.15.1/htscodecs/tests/names/tok3/01.names.19 htslib-1.15.1/htscodecs/tests/names/tok3/01.names.3 htslib-1.15.1/htscodecs/tests/names/tok3/01.names.5 htslib-1.15.1/htscodecs/tests/names/tok3/01.names.7 htslib-1.15.1/htscodecs/tests/names/tok3/01.names.9 htslib-1.15.1/htscodecs/tests/names/tok3/02.names.1 htslib-1.15.1/htscodecs/tests/names/tok3/02.names.11 htslib-1.15.1/htscodecs/tests/names/tok3/02.names.13 htslib-1.15.1/htscodecs/tests/names/tok3/02.names.15 htslib-1.15.1/htscodecs/tests/names/tok3/02.names.17 htslib-1.15.1/htscodecs/tests/names/tok3/02.names.19 htslib-1.15.1/htscodecs/tests/names/tok3/02.names.3 htslib-1.15.1/htscodecs/tests/names/tok3/02.names.5 htslib-1.15.1/htscodecs/tests/names/tok3/02.names.7 htslib-1.15.1/htscodecs/tests/names/tok3/02.names.9 htslib-1.15.1/htscodecs/tests/names/tok3/03.names.1 htslib-1.15.1/htscodecs/tests/names/tok3/03.names.11 htslib-1.15.1/htscodecs/tests/names/tok3/03.names.13 htslib-1.15.1/htscodecs/tests/names/tok3/03.names.15 htslib-1.15.1/htscodecs/tests/names/tok3/03.names.17 htslib-1.15.1/htscodecs/tests/names/tok3/03.names.19 htslib-1.15.1/htscodecs/tests/names/tok3/03.names.3 htslib-1.15.1/htscodecs/tests/names/tok3/03.names.5 htslib-1.15.1/htscodecs/tests/names/tok3/03.names.7 htslib-1.15.1/htscodecs/tests/names/tok3/03.names.9 htslib-1.15.1/htscodecs/tests/names/tok3/05.names.1 htslib-1.15.1/htscodecs/tests/names/tok3/05.names.11 htslib-1.15.1/htscodecs/tests/names/tok3/05.names.13 htslib-1.15.1/htscodecs/tests/names/tok3/05.names.15 htslib-1.15.1/htscodecs/tests/names/tok3/05.names.17 htslib-1.15.1/htscodecs/tests/names/tok3/05.names.19 htslib-1.15.1/htscodecs/tests/names/tok3/05.names.3 htslib-1.15.1/htscodecs/tests/names/tok3/05.names.5 htslib-1.15.1/htscodecs/tests/names/tok3/05.names.7 htslib-1.15.1/htscodecs/tests/names/tok3/05.names.9 htslib-1.15.1/htscodecs/tests/names/tok3/08.names.1 htslib-1.15.1/htscodecs/tests/names/tok3/08.names.11 htslib-1.15.1/htscodecs/tests/names/tok3/08.names.13 htslib-1.15.1/htscodecs/tests/names/tok3/08.names.15 htslib-1.15.1/htscodecs/tests/names/tok3/08.names.17 htslib-1.15.1/htscodecs/tests/names/tok3/08.names.19 htslib-1.15.1/htscodecs/tests/names/tok3/08.names.3 htslib-1.15.1/htscodecs/tests/names/tok3/08.names.5 htslib-1.15.1/htscodecs/tests/names/tok3/08.names.7 htslib-1.15.1/htscodecs/tests/names/tok3/08.names.9 htslib-1.15.1/htscodecs/tests/names/tok3/09.names.1 htslib-1.15.1/htscodecs/tests/names/tok3/09.names.11 htslib-1.15.1/htscodecs/tests/names/tok3/09.names.13 htslib-1.15.1/htscodecs/tests/names/tok3/09.names.15 htslib-1.15.1/htscodecs/tests/names/tok3/09.names.17 htslib-1.15.1/htscodecs/tests/names/tok3/09.names.19 htslib-1.15.1/htscodecs/tests/names/tok3/09.names.3 htslib-1.15.1/htscodecs/tests/names/tok3/09.names.5 htslib-1.15.1/htscodecs/tests/names/tok3/09.names.7 htslib-1.15.1/htscodecs/tests/names/tok3/09.names.9 htslib-1.15.1/htscodecs/tests/names/tok3/10.names.1 htslib-1.15.1/htscodecs/tests/names/tok3/10.names.11 htslib-1.15.1/htscodecs/tests/names/tok3/10.names.13 htslib-1.15.1/htscodecs/tests/names/tok3/10.names.15 htslib-1.15.1/htscodecs/tests/names/tok3/10.names.17 htslib-1.15.1/htscodecs/tests/names/tok3/10.names.19 htslib-1.15.1/htscodecs/tests/names/tok3/10.names.3 htslib-1.15.1/htscodecs/tests/names/tok3/10.names.5 htslib-1.15.1/htscodecs/tests/names/tok3/10.names.7 htslib-1.15.1/htscodecs/tests/names/tok3/10.names.9 htslib-1.15.1/htscodecs/tests/names/tok3/20.names.1 htslib-1.15.1/htscodecs/tests/names/tok3/20.names.11 htslib-1.15.1/htscodecs/tests/names/tok3/20.names.13 htslib-1.15.1/htscodecs/tests/names/tok3/20.names.15 htslib-1.15.1/htscodecs/tests/names/tok3/20.names.17 htslib-1.15.1/htscodecs/tests/names/tok3/20.names.19 htslib-1.15.1/htscodecs/tests/names/tok3/20.names.3 htslib-1.15.1/htscodecs/tests/names/tok3/20.names.5 htslib-1.15.1/htscodecs/tests/names/tok3/20.names.7 htslib-1.15.1/htscodecs/tests/names/tok3/20.names.9 htslib-1.15.1/htscodecs/tests/names/tok3/nv.names.1 htslib-1.15.1/htscodecs/tests/names/tok3/nv.names.11 htslib-1.15.1/htscodecs/tests/names/tok3/nv.names.13 htslib-1.15.1/htscodecs/tests/names/tok3/nv.names.15 htslib-1.15.1/htscodecs/tests/names/tok3/nv.names.17 htslib-1.15.1/htscodecs/tests/names/tok3/nv.names.19 htslib-1.15.1/htscodecs/tests/names/tok3/nv.names.3 htslib-1.15.1/htscodecs/tests/names/tok3/nv.names.5 htslib-1.15.1/htscodecs/tests/names/tok3/nv.names.7 htslib-1.15.1/htscodecs/tests/names/tok3/nv.names.9 htslib-1.15.1/htscodecs/tests/names/tok3/nv2.names.1 htslib-1.15.1/htscodecs/tests/names/tok3/nv2.names.11 htslib-1.15.1/htscodecs/tests/names/tok3/nv2.names.13 htslib-1.15.1/htscodecs/tests/names/tok3/nv2.names.15 htslib-1.15.1/htscodecs/tests/names/tok3/nv2.names.17 htslib-1.15.1/htscodecs/tests/names/tok3/nv2.names.19 htslib-1.15.1/htscodecs/tests/names/tok3/nv2.names.3 htslib-1.15.1/htscodecs/tests/names/tok3/nv2.names.5 htslib-1.15.1/htscodecs/tests/names/tok3/nv2.names.7 htslib-1.15.1/htscodecs/tests/names/tok3/nv2.names.9 htslib-1.15.1/htscodecs/tests/names/tok3/rr.names.1 htslib-1.15.1/htscodecs/tests/names/tok3/rr.names.11 htslib-1.15.1/htscodecs/tests/names/tok3/rr.names.13 htslib-1.15.1/htscodecs/tests/names/tok3/rr.names.15 htslib-1.15.1/htscodecs/tests/names/tok3/rr.names.17 htslib-1.15.1/htscodecs/tests/names/tok3/rr.names.19 htslib-1.15.1/htscodecs/tests/names/tok3/rr.names.3 htslib-1.15.1/htscodecs/tests/names/tok3/rr.names.5 htslib-1.15.1/htscodecs/tests/names/tok3/rr.names.7 htslib-1.15.1/htscodecs/tests/names/tok3/rr.names.9 htslib-1.15.1/htscodecs/tests/rANS_static4x16pr_fuzz.c htslib-1.15.1/htscodecs/tests/rANS_static4x16pr_test.c htslib-1.15.1/htscodecs/tests/rANS_static_fuzz.c htslib-1.15.1/htscodecs/tests/rANS_static_test.c htslib-1.15.1/htscodecs/tests/rans4x16.test htslib-1.15.1/htscodecs/tests/rans4x8.test htslib-1.15.1/htscodecs/tests/tok3.test htslib-1.15.1/htscodecs/tests/tokenise_name3_fuzz.c htslib-1.15.1/htscodecs/tests/tokenise_name3_test.c htslib-1.15.1/htscodecs/tests/varint_test.c htslib-1.15.1/htscodecs_bundled.mk htslib-1.15.1/htscodecs_external.mk htslib-1.15.1/htsfile.1 htslib-1.15.1/htsfile.c htslib-1.15.1/htslib-s3-plugin.7 htslib-1.15.1/htslib.mk htslib-1.15.1/htslib.pc.in htslib-1.15.1/htslib/ htslib-1.15.1/htslib/bgzf.h htslib-1.15.1/htslib/cram.h htslib-1.15.1/htslib/faidx.h htslib-1.15.1/htslib/hfile.h htslib-1.15.1/htslib/hts.h htslib-1.15.1/htslib/hts_defs.h htslib-1.15.1/htslib/hts_endian.h htslib-1.15.1/htslib/hts_expr.h htslib-1.15.1/htslib/hts_log.h htslib-1.15.1/htslib/hts_os.h htslib-1.15.1/htslib/kbitset.h htslib-1.15.1/htslib/kfunc.h htslib-1.15.1/htslib/khash.h htslib-1.15.1/htslib/khash_str2int.h htslib-1.15.1/htslib/klist.h htslib-1.15.1/htslib/knetfile.h htslib-1.15.1/htslib/kroundup.h htslib-1.15.1/htslib/kseq.h htslib-1.15.1/htslib/ksort.h htslib-1.15.1/htslib/kstring.h htslib-1.15.1/htslib/regidx.h htslib-1.15.1/htslib/sam.h htslib-1.15.1/htslib/synced_bcf_reader.h htslib-1.15.1/htslib/tbx.h htslib-1.15.1/htslib/thread_pool.h htslib-1.15.1/htslib/vcf.h htslib-1.15.1/htslib/vcf_sweep.h htslib-1.15.1/htslib/vcfutils.h htslib-1.15.1/htslib_vars.mk htslib-1.15.1/kfunc.c htslib-1.15.1/kstring.c htslib-1.15.1/m4/ htslib-1.15.1/m4/hts_hide_dynamic_syms.m4 htslib-1.15.1/m4/hts_prog_cc_warnings.m4 htslib-1.15.1/m4/pkg.m4 htslib-1.15.1/md5.c htslib-1.15.1/multipart.c htslib-1.15.1/os/ htslib-1.15.1/os/lzma_stub.h htslib-1.15.1/os/rand.c htslib-1.15.1/plugin.c htslib-1.15.1/probaln.c htslib-1.15.1/realn.c htslib-1.15.1/regidx.c htslib-1.15.1/region.c htslib-1.15.1/sam.5 htslib-1.15.1/sam.c htslib-1.15.1/sam_internal.h htslib-1.15.1/synced_bcf_reader.c htslib-1.15.1/tabix.1 htslib-1.15.1/tabix.c htslib-1.15.1/tbx.c htslib-1.15.1/test/ htslib-1.15.1/test/auxf#values.sam htslib-1.15.1/test/auxf#values_java.cram htslib-1.15.1/test/auxf.fa htslib-1.15.1/test/auxf.fa.fai htslib-1.15.1/test/base_mods/ htslib-1.15.1/test/base_mods/MM-chebi.out htslib-1.15.1/test/base_mods/MM-chebi.sam htslib-1.15.1/test/base_mods/MM-double.out htslib-1.15.1/test/base_mods/MM-double.sam htslib-1.15.1/test/base_mods/MM-multi.out htslib-1.15.1/test/base_mods/MM-multi.sam htslib-1.15.1/test/base_mods/MM-orient.sam htslib-1.15.1/test/base_mods/MM-pileup.out htslib-1.15.1/test/base_mods/MM-pileup.sam htslib-1.15.1/test/base_mods/MM-pileup2.out htslib-1.15.1/test/base_mods/MM-pileup2.sam htslib-1.15.1/test/base_mods/base-mods.sh htslib-1.15.1/test/base_mods/base-mods.tst htslib-1.15.1/test/bcf-sr/ htslib-1.15.1/test/bcf-sr/merge.noidx.a.vcf htslib-1.15.1/test/bcf-sr/merge.noidx.abc.expected.out htslib-1.15.1/test/bcf-sr/merge.noidx.b.vcf htslib-1.15.1/test/bcf-sr/merge.noidx.c.vcf htslib-1.15.1/test/bcf-sr/merge.noidx.hdr_order.vcf htslib-1.15.1/test/bcf-sr/merge.noidx.rec_order.vcf htslib-1.15.1/test/bgziptest.txt htslib-1.15.1/test/bgziptest.txt.gz htslib-1.15.1/test/bgziptest.txt.gz.gzi htslib-1.15.1/test/c1#bounds.sam htslib-1.15.1/test/c1#clip.sam htslib-1.15.1/test/c1#noseq.sam htslib-1.15.1/test/c1#pad1.sam htslib-1.15.1/test/c1#pad2.sam htslib-1.15.1/test/c1#pad3.sam htslib-1.15.1/test/c1#unknown.sam htslib-1.15.1/test/c1.fa htslib-1.15.1/test/c1.fa.fai htslib-1.15.1/test/c2#pad.sam htslib-1.15.1/test/c2.fa htslib-1.15.1/test/c2.fa.fai htslib-1.15.1/test/ce#1.sam htslib-1.15.1/test/ce#1000.sam htslib-1.15.1/test/ce#2.sam htslib-1.15.1/test/ce#5.sam htslib-1.15.1/test/ce#5b.sam htslib-1.15.1/test/ce#5b_java.cram htslib-1.15.1/test/ce#large_seq.sam htslib-1.15.1/test/ce#supp.sam htslib-1.15.1/test/ce#tag_depadded.sam htslib-1.15.1/test/ce#tag_padded.sam htslib-1.15.1/test/ce#unmap.sam htslib-1.15.1/test/ce#unmap1.sam htslib-1.15.1/test/ce#unmap2.sam htslib-1.15.1/test/ce.fa htslib-1.15.1/test/ce.fa.fai htslib-1.15.1/test/colons.bam htslib-1.15.1/test/colons.bam.bai htslib-1.15.1/test/compare_sam.pl htslib-1.15.1/test/cross_validate.sh htslib-1.15.1/test/emptyfile htslib-1.15.1/test/faidx.fa htslib-1.15.1/test/fastq/ htslib-1.15.1/test/fastq/fastq.tst htslib-1.15.1/test/fastq/filter_casava-q.sam htslib-1.15.1/test/fastq/filter_casava.fa htslib-1.15.1/test/fastq/filter_casava.fq htslib-1.15.1/test/fastq/filter_casava.sam htslib-1.15.1/test/fastq/inter_aux-q.sam htslib-1.15.1/test/fastq/inter_aux.sam htslib-1.15.1/test/fastq/inter_casava-q.sam htslib-1.15.1/test/fastq/inter_casava.sam htslib-1.15.1/test/fastq/inter_casavaOX-q.sam htslib-1.15.1/test/fastq/inter_casavaOX.sam 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htslib-1.15.1/test/index2.sam htslib-1.15.1/test/index_dos.sam htslib-1.15.1/test/longrefs/ htslib-1.15.1/test/longrefs/index.expected1.vcf htslib-1.15.1/test/longrefs/index.expected2.vcf htslib-1.15.1/test/longrefs/index.vcf htslib-1.15.1/test/longrefs/longref.sam htslib-1.15.1/test/longrefs/longref_itr.expected.sam htslib-1.15.1/test/longrefs/longref_multi.expected.sam htslib-1.15.1/test/maintainer/ htslib-1.15.1/test/maintainer/check_copyright.pl htslib-1.15.1/test/maintainer/check_spaces.pl htslib-1.15.1/test/md#1.sam htslib-1.15.1/test/md.fa htslib-1.15.1/test/md.fa.fai htslib-1.15.1/test/mpileup/ htslib-1.15.1/test/mpileup/c1#pad1.out htslib-1.15.1/test/mpileup/c1#pad1.sam htslib-1.15.1/test/mpileup/c1#pad2.out htslib-1.15.1/test/mpileup/c1#pad2.sam htslib-1.15.1/test/mpileup/c1#pad3.out htslib-1.15.1/test/mpileup/c1#pad3.sam htslib-1.15.1/test/mpileup/mp_D.out htslib-1.15.1/test/mpileup/mp_D.sam htslib-1.15.1/test/mpileup/mp_DI.out htslib-1.15.1/test/mpileup/mp_DI.sam htslib-1.15.1/test/mpileup/mp_I.out htslib-1.15.1/test/mpileup/mp_I.sam htslib-1.15.1/test/mpileup/mp_ID.out htslib-1.15.1/test/mpileup/mp_ID.sam htslib-1.15.1/test/mpileup/mp_N.out htslib-1.15.1/test/mpileup/mp_N.sam htslib-1.15.1/test/mpileup/mp_N2.out htslib-1.15.1/test/mpileup/mp_N2.sam htslib-1.15.1/test/mpileup/mp_P.out htslib-1.15.1/test/mpileup/mp_P.sam htslib-1.15.1/test/mpileup/mpileup.tst htslib-1.15.1/test/mpileup/small.bam htslib-1.15.1/test/mpileup/small.out htslib-1.15.1/test/mpileup/test-pileup.sh htslib-1.15.1/test/no_hdr_sq_1.bam htslib-1.15.1/test/no_hdr_sq_1.bam.csi htslib-1.15.1/test/no_hdr_sq_1.expected.sam htslib-1.15.1/test/noroundtrip-out.vcf htslib-1.15.1/test/noroundtrip.vcf htslib-1.15.1/test/pileup.c htslib-1.15.1/test/pileup_mod.c htslib-1.15.1/test/plugins-dlhts.c htslib-1.15.1/test/range.bam htslib-1.15.1/test/range.bam.bai htslib-1.15.1/test/range.cram htslib-1.15.1/test/range.cram.crai htslib-1.15.1/test/range.out htslib-1.15.1/test/realn01.fa 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htslib-1.15.1/test/sam_filter/string5.out htslib-1.15.1/test/sam_filter/string6.out htslib-1.15.1/test/sam_filter/string7.out htslib-1.15.1/test/simple_test_driver.sh htslib-1.15.1/test/tabix.out htslib-1.15.1/test/tabix/ htslib-1.15.1/test/tabix/bed_file.Y.100200.out htslib-1.15.1/test/tabix/bed_file.bed htslib-1.15.1/test/tabix/bed_file.separate.out htslib-1.15.1/test/tabix/gff_file.X.2934832.2935190.out htslib-1.15.1/test/tabix/gff_file.gff htslib-1.15.1/test/tabix/large_chr.20.1.2147483647.out htslib-1.15.1/test/tabix/large_chr.vcf htslib-1.15.1/test/tabix/tabix.tst htslib-1.15.1/test/tabix/test-tabix.sh htslib-1.15.1/test/tabix/vcf_file.1.3000151.out htslib-1.15.1/test/tabix/vcf_file.2.3199812.out htslib-1.15.1/test/tabix/vcf_file.bcf htslib-1.15.1/test/tabix/vcf_file.vcf htslib-1.15.1/test/test-bcf-sr.c htslib-1.15.1/test/test-bcf-sr.pl htslib-1.15.1/test/test-bcf-translate.c htslib-1.15.1/test/test-bcf-translate.out htslib-1.15.1/test/test-logging.pl htslib-1.15.1/test/test-parse-reg.c htslib-1.15.1/test/test-regidx.c htslib-1.15.1/test/test-vcf-api.c htslib-1.15.1/test/test-vcf-api.out htslib-1.15.1/test/test-vcf-hdr-in.vcf htslib-1.15.1/test/test-vcf-hdr.out htslib-1.15.1/test/test-vcf-sweep.c htslib-1.15.1/test/test-vcf-sweep.out htslib-1.15.1/test/test.pl htslib-1.15.1/test/test_bgzf.c htslib-1.15.1/test/test_expr.c htslib-1.15.1/test/test_index.c htslib-1.15.1/test/test_introspection.c htslib-1.15.1/test/test_kfunc.c htslib-1.15.1/test/test_kstring.c htslib-1.15.1/test/test_mod.c htslib-1.15.1/test/test_realn.c htslib-1.15.1/test/test_str2int.c htslib-1.15.1/test/test_view.c htslib-1.15.1/test/thrash_threads1.c htslib-1.15.1/test/thrash_threads2.c htslib-1.15.1/test/thrash_threads3.c htslib-1.15.1/test/thrash_threads4.c htslib-1.15.1/test/thrash_threads5.c htslib-1.15.1/test/thrash_threads6.c htslib-1.15.1/test/thrash_threads7.c htslib-1.15.1/test/thread_pool.md htslib-1.15.1/test/vcf_meta_meta.vcf htslib-1.15.1/test/with-shlib.sh htslib-1.15.1/test/xx#MD.sam htslib-1.15.1/test/xx#MD2.sam htslib-1.15.1/test/xx#blank.sam htslib-1.15.1/test/xx#large_aux.sam htslib-1.15.1/test/xx#large_aux2.sam htslib-1.15.1/test/xx#large_aux_java.cram htslib-1.15.1/test/xx#minimal.sam htslib-1.15.1/test/xx#pair.sam htslib-1.15.1/test/xx#repeated.sam htslib-1.15.1/test/xx#rg.sam htslib-1.15.1/test/xx#tlen.sam htslib-1.15.1/test/xx#tlen2.sam htslib-1.15.1/test/xx#triplet.sam htslib-1.15.1/test/xx#unsorted.sam htslib-1.15.1/test/xx.fa htslib-1.15.1/test/xx.fa.fai htslib-1.15.1/textutils.c htslib-1.15.1/textutils_internal.h htslib-1.15.1/thread_pool.c htslib-1.15.1/thread_pool_internal.h htslib-1.15.1/vcf.5 htslib-1.15.1/vcf.c htslib-1.15.1/vcf_sweep.c htslib-1.15.1/vcfutils.c htslib-1.15.1/version.sh htslib-1.15.1/config.h.in htslib-1.15.1/configure checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for 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(cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing dlsym... -ldl checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o kfunc.o kfunc.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o kstring.o kstring.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o bgzf.o bgzf.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o errmod.o errmod.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o faidx.o faidx.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o header.o header.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h echo '#define HTS_CPPFLAGS ""' >> config_vars.h echo '#define HTS_CFLAGS "-Wall -O2 -fPIC -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LDFLAGS "-fvisibility=hidden -rdynamic"' >> config_vars.h echo '#define HTS_LIBS "-llzma -lbz2 -lz -lm -ldl "' >> config_vars.h gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o hts.o hts.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o hts_os.o hts_os.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o md5.o md5.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o multipart.o multipart.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o probaln.o probaln.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o realn.o realn.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o regidx.o regidx.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o region.o region.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o sam.o sam.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o tbx.o tbx.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o textutils.o textutils.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o vcf.o vcf.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/libexec/htslib\" -c -o plugin.o plugin.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o plugin.o ranlib libhts.a gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o header.pico header.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o region.pico region.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c gcc -shared -Wl,-soname,libhts.so.3 -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico plugin.pico -llzma -lbz2 -lz -lm -ldl -lpthread ln -sf libhts.so libhts.so.3 gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o bgzip.o bgzip.c gcc -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htsfile.o htsfile.c gcc -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o tabix.o tabix.c gcc -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c gcc -shared -Wl,-E -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -ldl -lcurl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c gcc -shared -Wl,-E -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c gcc -shared -Wl,-E -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -ldl -lcrypto -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -fpic -c -o hfile_s3_write.pico hfile_s3_write.c gcc -shared -Wl,-E -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -llzma -lbz2 -lz -lm -ldl -lcrypto -lcurl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c gcc -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm -ldl gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c gcc -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c gcc -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c gcc -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c gcc -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm -ldl gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/sam.o test/sam.c gcc -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c gcc -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c gcc -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c gcc -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c gcc -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c gcc -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c gcc -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c gcc -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c gcc -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c gcc -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c gcc -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -ldl -lpthread sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc mkdir -p -m 755 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/bin /usr/src/slapt-src/libraries/htslib/package-htslib/usr/include /usr/src/slapt-src/libraries/htslib/package-htslib/usr/include/htslib /usr/src/slapt-src/libraries/htslib/package-htslib/usr/lib64 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/man/man1 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/man/man5 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/man/man7 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/libexec/htslib; fi install -p -m 644 libhts.so /usr/src/slapt-src/libraries/htslib/package-htslib/usr/lib64/libhts.so.1.15.1 ln -sf libhts.so.1.15.1 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/lib64/libhts.so ln -sf libhts.so.1.15.1 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/lib64/libhts.so.3 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.15.1#g' htslib.pc.tmp > /usr/src/slapt-src/libraries/htslib/package-htslib/usr/lib64/pkgconfig/htslib.pc chmod 644 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/lib64/pkgconfig/htslib.pc install -p bgzip htsfile tabix /usr/src/slapt-src/libraries/htslib/package-htslib/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /usr/src/slapt-src/libraries/htslib/package-htslib/usr/libexec/htslib; fi install -p -m 644 htslib/*.h /usr/src/slapt-src/libraries/htslib/package-htslib/usr/include/htslib install -p -m 644 libhts.a /usr/src/slapt-src/libraries/htslib/package-htslib/usr/lib64/libhts.a install -p -m 644 bgzip.1 htsfile.1 tabix.1 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/man/man5 install -p -m 644 htslib-s3-plugin.7 /usr/src/slapt-src/libraries/htslib/package-htslib/usr/man/man7 Slackware package maker, version 3.14159265. Searching for symbolic links: usr/lib64/libhts.so libhts.so.1.15.1 usr/lib64/libhts.so.3 libhts.so.1.15.1 Making symbolic link creation script: ( cd usr/lib64 ; rm -rf libhts.so ) ( cd usr/lib64 ; ln -sf libhts.so.1.15.1 libhts.so ) ( cd usr/lib64 ; rm -rf libhts.so.3 ) ( cd usr/lib64 ; ln -sf libhts.so.1.15.1 libhts.so.3 ) It is recommended that you make these lines your new installation script. Would you like to make this stuff the install script for this package and remove the symbolic links ([y]es, [n]o)? y Removing symbolic links: removed './usr/lib64/libhts.so' removed './usr/lib64/libhts.so.3' Creating your new ./install/doinst.sh... This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/libraries/htslib/htslib-1.15.1-x86_64-1salix15.0.txz ./ install/ install/doinst.sh install/slack-desc usr/ usr/bin/ usr/bin/bgzip usr/bin/htsfile usr/bin/tabix usr/doc/ usr/doc/htslib-1.15.1/ usr/doc/htslib-1.15.1/INSTALL usr/doc/htslib-1.15.1/LICENSE usr/doc/htslib-1.15.1/NEWS usr/doc/htslib-1.15.1/README usr/doc/htslib-1.15.1/htslib.SlackBuild usr/include/ usr/include/htslib/ usr/include/htslib/bgzf.h usr/include/htslib/cram.h usr/include/htslib/faidx.h usr/include/htslib/hfile.h usr/include/htslib/hts.h usr/include/htslib/hts_defs.h usr/include/htslib/hts_endian.h usr/include/htslib/hts_expr.h usr/include/htslib/hts_log.h usr/include/htslib/hts_os.h usr/include/htslib/kbitset.h usr/include/htslib/kfunc.h usr/include/htslib/khash.h usr/include/htslib/khash_str2int.h usr/include/htslib/klist.h usr/include/htslib/knetfile.h usr/include/htslib/kroundup.h usr/include/htslib/kseq.h usr/include/htslib/ksort.h usr/include/htslib/kstring.h usr/include/htslib/regidx.h usr/include/htslib/sam.h usr/include/htslib/synced_bcf_reader.h usr/include/htslib/tbx.h usr/include/htslib/thread_pool.h usr/include/htslib/vcf.h usr/include/htslib/vcf_sweep.h usr/include/htslib/vcfutils.h usr/lib64/ usr/lib64/libhts.a usr/lib64/libhts.so.1.15.1 usr/lib64/pkgconfig/ usr/lib64/pkgconfig/htslib.pc usr/libexec/ usr/libexec/htslib/ usr/libexec/htslib/hfile_gcs.so usr/libexec/htslib/hfile_libcurl.so usr/libexec/htslib/hfile_s3.so usr/libexec/htslib/hfile_s3_write.so usr/man/ usr/man/man1/ usr/man/man1/bgzip.1.gz usr/man/man1/htsfile.1.gz usr/man/man1/tabix.1.gz usr/man/man5/ usr/man/man5/faidx.5.gz usr/man/man5/sam.5.gz usr/man/man5/vcf.5.gz usr/man/man7/ usr/man/man7/htslib-s3-plugin.7.gz Slackware package /usr/src/slapt-src/libraries/htslib/htslib-1.15.1-x86_64-1salix15.0.txz created. Installing package htslib-1.15.1-x86_64-1salix15.0... | htslib (High Troughput Sequencing Library) | | HTSlib is an implementation of a unified C library for accessing | common file formats, such as SAM, CRAM and VCF, used for high- | throughput sequencing data, and is the core library used by samtools | and bcftools. It is known to be compatible with gcc, g++ and clang. | HTSlib also provides the bgzip, htsfile, and tabix utilities. | | Homepage: http://www.htslib.org | | | |