The following packages will be installed:
 htslib 
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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
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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
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htslib-1.15.1/htscodecs/tests/dat/arith/q4.9
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htslib-1.15.1/htscodecs/tests/dat/arith/q8.1
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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/
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htslib-1.15.1/htscodecs/tests/names/tok3/01.names.11
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htslib-1.15.1/htscodecs/tests/rANS_static4x16pr_fuzz.c
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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
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htslib-1.15.1/htslib/
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htslib-1.15.1/htslib/cram.h
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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
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htslib-1.15.1/m4/
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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/
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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
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htslib-1.15.1/sam_internal.h
htslib-1.15.1/synced_bcf_reader.c
htslib-1.15.1/tabix.1
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htslib-1.15.1/tbx.c
htslib-1.15.1/test/
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htslib-1.15.1/test/auxf#values_java.cram
htslib-1.15.1/test/auxf.fa
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htslib-1.15.1/test/base_mods/
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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
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htslib-1.15.1/test/base_mods/MM-orient.sam
htslib-1.15.1/test/base_mods/MM-pileup.out
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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
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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
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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
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htslib-1.15.1/test/c2#pad.sam
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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
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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/
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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
htslib-1.15.1/test/fastq/inter_noaux-q.sam
htslib-1.15.1/test/fastq/inter_noaux.sam
htslib-1.15.1/test/fastq/interleaved.fa
htslib-1.15.1/test/fastq/interleaved.fq
htslib-1.15.1/test/fastq/interleaved_casava.fa
htslib-1.15.1/test/fastq/interleaved_casava.fq
htslib-1.15.1/test/fastq/minimal-q.sam
htslib-1.15.1/test/fastq/minimal.fa
htslib-1.15.1/test/fastq/minimal.fq
htslib-1.15.1/test/fastq/minimal.sam
htslib-1.15.1/test/fastq/multiline-q.sam
htslib-1.15.1/test/fastq/multiline.fa
htslib-1.15.1/test/fastq/multiline.fq
htslib-1.15.1/test/fastq/multiline.sam
htslib-1.15.1/test/fastq/name2-q.sam
htslib-1.15.1/test/fastq/name2.fa
htslib-1.15.1/test/fastq/name2.fq
htslib-1.15.1/test/fastq/name2.sam
htslib-1.15.1/test/fastq/r1-q.sam
htslib-1.15.1/test/fastq/r1.fa
htslib-1.15.1/test/fastq/r1.fq
htslib-1.15.1/test/fastq/r1.sam
htslib-1.15.1/test/fastq/r2-q.sam
htslib-1.15.1/test/fastq/r2.fa
htslib-1.15.1/test/fastq/r2.fq
htslib-1.15.1/test/fastq/r2.sam
htslib-1.15.1/test/fastq/single.fa
htslib-1.15.1/test/fastq/single.fq
htslib-1.15.1/test/fastq/single_aux-q.sam
htslib-1.15.1/test/fastq/single_aux.sam
htslib-1.15.1/test/fastq/single_noaux-q.sam
htslib-1.15.1/test/fastq/single_noaux.sam
htslib-1.15.1/test/fastq/test-fastq.sh
htslib-1.15.1/test/fastqs.fq
htslib-1.15.1/test/fastqs_README.txt
htslib-1.15.1/test/fieldarith.c
htslib-1.15.1/test/fieldarith.sam
htslib-1.15.1/test/formatcols.vcf
htslib-1.15.1/test/formatmissing-out.vcf
htslib-1.15.1/test/formatmissing.vcf
htslib-1.15.1/test/fuzz/
htslib-1.15.1/test/fuzz/hts_open_fuzzer.c
htslib-1.15.1/test/header_syms.pl
htslib-1.15.1/test/hfile.c
htslib-1.15.1/test/hts_endian.c
htslib-1.15.1/test/index.bam.bai
htslib-1.15.1/test/index.bam.csi
htslib-1.15.1/test/index.bcf.csi
htslib-1.15.1/test/index.cram.crai
htslib-1.15.1/test/index.sam
htslib-1.15.1/test/index.sam.gz.bai
htslib-1.15.1/test/index.sam.gz.csi
htslib-1.15.1/test/index.vcf
htslib-1.15.1/test/index.vcf.gz.csi
htslib-1.15.1/test/index.vcf.gz.tbi
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/
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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
htslib-1.15.1/test/realn01.fa.fai
htslib-1.15.1/test/realn01.sam
htslib-1.15.1/test/realn01_exp-a.sam
htslib-1.15.1/test/realn01_exp-e.sam
htslib-1.15.1/test/realn01_exp.sam
htslib-1.15.1/test/realn02-r.sam
htslib-1.15.1/test/realn02.fa
htslib-1.15.1/test/realn02.fa.fai
htslib-1.15.1/test/realn02.sam
htslib-1.15.1/test/realn02_exp-a.sam
htslib-1.15.1/test/realn02_exp-e.sam
htslib-1.15.1/test/realn02_exp.sam
htslib-1.15.1/test/sam.c
htslib-1.15.1/test/sam_filter/
htslib-1.15.1/test/sam_filter/filter.sh
htslib-1.15.1/test/sam_filter/filter.tst
htslib-1.15.1/test/sam_filter/func1.out
htslib-1.15.1/test/sam_filter/func2.out
htslib-1.15.1/test/sam_filter/func3.out
htslib-1.15.1/test/sam_filter/func4.out
htslib-1.15.1/test/sam_filter/int1.out
htslib-1.15.1/test/sam_filter/int2.out
htslib-1.15.1/test/sam_filter/int3.out
htslib-1.15.1/test/sam_filter/string1.out
htslib-1.15.1/test/sam_filter/string2.out
htslib-1.15.1/test/sam_filter/string3.out
htslib-1.15.1/test/sam_filter/string4.out
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
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checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
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checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
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checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
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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
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checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
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checking for unistd.h... yes
checking for stdlib.h... (cached) yes
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checking for sys/param.h... yes
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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
| 
| 
| 
|