The following packages will be installed: bcftools Fetching README... 0%100%100%100%100%100%Done Fetching bcftools.SlackBuild... 0%100%100%100%100%100%Done Fetching bcftools.info... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done bcftools-1.15.1/ bcftools-1.15.1/AUTHORS bcftools-1.15.1/HMM.c bcftools-1.15.1/HMM.h bcftools-1.15.1/INSTALL bcftools-1.15.1/LICENSE bcftools-1.15.1/Makefile bcftools-1.15.1/NEWS bcftools-1.15.1/README bcftools-1.15.1/abuf.c bcftools-1.15.1/abuf.h bcftools-1.15.1/bam2bcf.c bcftools-1.15.1/bam2bcf.h bcftools-1.15.1/bam2bcf_indel.c bcftools-1.15.1/bam_sample.c bcftools-1.15.1/bam_sample.h bcftools-1.15.1/bcftools.h bcftools-1.15.1/bin.c bcftools-1.15.1/bin.h bcftools-1.15.1/call.h bcftools-1.15.1/ccall.c bcftools-1.15.1/cols.c bcftools-1.15.1/cols.h bcftools-1.15.1/config.mk.in bcftools-1.15.1/configure.ac bcftools-1.15.1/consensus.c bcftools-1.15.1/convert.c bcftools-1.15.1/convert.h bcftools-1.15.1/csq.c bcftools-1.15.1/dbuf.h bcftools-1.15.1/dist.c bcftools-1.15.1/dist.h bcftools-1.15.1/doc/ bcftools-1.15.1/doc/bcftools.1 bcftools-1.15.1/doc/bcftools.html bcftools-1.15.1/doc/bcftools.txt bcftools-1.15.1/doc/docbook-xsl.css bcftools-1.15.1/em.c bcftools-1.15.1/extsort.c bcftools-1.15.1/extsort.h bcftools-1.15.1/filter.c bcftools-1.15.1/filter.h bcftools-1.15.1/gvcf.c bcftools-1.15.1/gvcf.h bcftools-1.15.1/hclust.c bcftools-1.15.1/hclust.h bcftools-1.15.1/hex.h bcftools-1.15.1/install-sh bcftools-1.15.1/khash_str2str.h bcftools-1.15.1/kheap.h bcftools-1.15.1/kmin.c bcftools-1.15.1/kmin.h bcftools-1.15.1/m4/ bcftools-1.15.1/m4/ax_with_htslib.m4 bcftools-1.15.1/m4/hts_prog_cc_warnings.m4 bcftools-1.15.1/main.c bcftools-1.15.1/mcall.c bcftools-1.15.1/misc/ bcftools-1.15.1/misc/color-chrs.pl bcftools-1.15.1/misc/demo-flt.pl bcftools-1.15.1/misc/fix-broken-GATK-Double-vs-Integer bcftools-1.15.1/misc/gff2gff.py bcftools-1.15.1/misc/guess-ploidy.py bcftools-1.15.1/misc/plot-roh.py bcftools-1.15.1/misc/plot-vcfstats bcftools-1.15.1/misc/run-roh.pl bcftools-1.15.1/misc/vcfutils.pl bcftools-1.15.1/mpileup.c bcftools-1.15.1/mw.h bcftools-1.15.1/peakfit.c bcftools-1.15.1/peakfit.h bcftools-1.15.1/ploidy.c bcftools-1.15.1/ploidy.h bcftools-1.15.1/plugins/ bcftools-1.15.1/plugins/GTisec.c bcftools-1.15.1/plugins/GTisec.mk bcftools-1.15.1/plugins/GTsubset.c bcftools-1.15.1/plugins/GTsubset.mk bcftools-1.15.1/plugins/ad-bias.c bcftools-1.15.1/plugins/ad-bias.mk bcftools-1.15.1/plugins/add-variantkey.c bcftools-1.15.1/plugins/af-dist.c bcftools-1.15.1/plugins/af-dist.mk bcftools-1.15.1/plugins/allele-length.c bcftools-1.15.1/plugins/check-ploidy.c bcftools-1.15.1/plugins/check-sparsity.c bcftools-1.15.1/plugins/color-chrs.c bcftools-1.15.1/plugins/color-chrs.mk bcftools-1.15.1/plugins/contrast.c bcftools-1.15.1/plugins/counts.c bcftools-1.15.1/plugins/dosage.c bcftools-1.15.1/plugins/fill-AN-AC.c bcftools-1.15.1/plugins/fill-from-fasta.c bcftools-1.15.1/plugins/fill-from-fasta.mk bcftools-1.15.1/plugins/fill-tags.c bcftools-1.15.1/plugins/fixploidy.c bcftools-1.15.1/plugins/fixploidy.mk bcftools-1.15.1/plugins/fixref.c bcftools-1.15.1/plugins/frameshifts.c bcftools-1.15.1/plugins/guess-ploidy.c bcftools-1.15.1/plugins/gvcfz.c bcftools-1.15.1/plugins/impute-info.c bcftools-1.15.1/plugins/indel-stats.c bcftools-1.15.1/plugins/isecGT.c bcftools-1.15.1/plugins/isecGT.mk bcftools-1.15.1/plugins/mendelian.c bcftools-1.15.1/plugins/missing2ref.c bcftools-1.15.1/plugins/parental-origin.c bcftools-1.15.1/plugins/prune.c bcftools-1.15.1/plugins/remove-overlaps.c bcftools-1.15.1/plugins/scatter.c bcftools-1.15.1/plugins/setGT.c bcftools-1.15.1/plugins/smpl-stats.c bcftools-1.15.1/plugins/split-vep.c bcftools-1.15.1/plugins/split.c bcftools-1.15.1/plugins/tag2tag.c bcftools-1.15.1/plugins/trio-dnm2.c bcftools-1.15.1/plugins/trio-stats.c bcftools-1.15.1/plugins/trio-switch-rate.c bcftools-1.15.1/plugins/variantkey-hex.c bcftools-1.15.1/polysomy.c bcftools-1.15.1/prob1.c bcftools-1.15.1/prob1.h bcftools-1.15.1/rbuf.h bcftools-1.15.1/regidx.c bcftools-1.15.1/regidx.h bcftools-1.15.1/reheader.c bcftools-1.15.1/smpl_ilist.c bcftools-1.15.1/smpl_ilist.h bcftools-1.15.1/str_finder.c bcftools-1.15.1/str_finder.h bcftools-1.15.1/tabix.c bcftools-1.15.1/test/ bcftools-1.15.1/test/23andme.fa bcftools-1.15.1/test/aa.2.out bcftools-1.15.1/test/aa.fa bcftools-1.15.1/test/aa.hdr bcftools-1.15.1/test/aa.out bcftools-1.15.1/test/aa.vcf bcftools-1.15.1/test/ad-bias.2.out bcftools-1.15.1/test/ad-bias.2.vcf bcftools-1.15.1/test/ad-bias.out bcftools-1.15.1/test/ad-bias.samples bcftools-1.15.1/test/ad-bias.vcf bcftools-1.15.1/test/af-dist.out bcftools-1.15.1/test/af-dist.vcf bcftools-1.15.1/test/annotate.hdr bcftools-1.15.1/test/annotate.id.1.out bcftools-1.15.1/test/annotate.id.2.out bcftools-1.15.1/test/annotate.id.vcf bcftools-1.15.1/test/annotate.missing-append.1.out bcftools-1.15.1/test/annotate.missing-append.tab bcftools-1.15.1/test/annotate.missing-append.vcf bcftools-1.15.1/test/annotate.missing.1.out bcftools-1.15.1/test/annotate.missing.2.out bcftools-1.15.1/test/annotate.missing.3.out bcftools-1.15.1/test/annotate.missing.4.out bcftools-1.15.1/test/annotate.missing.5.out bcftools-1.15.1/test/annotate.missing.6.out bcftools-1.15.1/test/annotate.missing.tab bcftools-1.15.1/test/annotate.missing.vcf bcftools-1.15.1/test/annotate.multi.1.out bcftools-1.15.1/test/annotate.multi.tab bcftools-1.15.1/test/annotate.multi.vcf bcftools-1.15.1/test/annotate.olap.1.out bcftools-1.15.1/test/annotate.olap.2.out bcftools-1.15.1/test/annotate.olap.vcf bcftools-1.15.1/test/annotate.out bcftools-1.15.1/test/annotate.tab bcftools-1.15.1/test/annotate.vcf bcftools-1.15.1/test/annotate10.hdr bcftools-1.15.1/test/annotate10.out bcftools-1.15.1/test/annotate10.vcf bcftools-1.15.1/test/annotate11.out bcftools-1.15.1/test/annotate11.vcf bcftools-1.15.1/test/annotate12.out bcftools-1.15.1/test/annotate12.vcf bcftools-1.15.1/test/annotate13.hdr bcftools-1.15.1/test/annotate13.out bcftools-1.15.1/test/annotate13.vcf bcftools-1.15.1/test/annotate14.out bcftools-1.15.1/test/annotate14.vcf bcftools-1.15.1/test/annotate15.hdr bcftools-1.15.1/test/annotate15.out bcftools-1.15.1/test/annotate15.tab bcftools-1.15.1/test/annotate15.vcf bcftools-1.15.1/test/annotate16.out bcftools-1.15.1/test/annotate16.vcf bcftools-1.15.1/test/annotate17.1.out bcftools-1.15.1/test/annotate17.1.tab bcftools-1.15.1/test/annotate17.1.vcf bcftools-1.15.1/test/annotate17.2.out bcftools-1.15.1/test/annotate17.2.vcf bcftools-1.15.1/test/annotate17.3.out bcftools-1.15.1/test/annotate17.3.tab bcftools-1.15.1/test/annotate17.3.vcf bcftools-1.15.1/test/annotate17.out bcftools-1.15.1/test/annotate18.1.out bcftools-1.15.1/test/annotate18.1.tab bcftools-1.15.1/test/annotate18.1.vcf bcftools-1.15.1/test/annotate18.2.out bcftools-1.15.1/test/annotate18.2.tab bcftools-1.15.1/test/annotate18.2.vcf bcftools-1.15.1/test/annotate18.out bcftools-1.15.1/test/annotate19.1.out bcftools-1.15.1/test/annotate19.2.out bcftools-1.15.1/test/annotate19.dst.vcf bcftools-1.15.1/test/annotate19.out bcftools-1.15.1/test/annotate19.src.vcf bcftools-1.15.1/test/annotate2.out bcftools-1.15.1/test/annotate2.tab bcftools-1.15.1/test/annotate2.vcf bcftools-1.15.1/test/annotate20.1.out bcftools-1.15.1/test/annotate20.2.out bcftools-1.15.1/test/annotate20.3.out bcftools-1.15.1/test/annotate20.dst.vcf bcftools-1.15.1/test/annotate20.out bcftools-1.15.1/test/annotate20.src.vcf bcftools-1.15.1/test/annotate21.out bcftools-1.15.1/test/annotate21.txt bcftools-1.15.1/test/annotate21.vcf bcftools-1.15.1/test/annotate22.out bcftools-1.15.1/test/annotate22.vcf bcftools-1.15.1/test/annotate23.out bcftools-1.15.1/test/annotate23.tab bcftools-1.15.1/test/annotate23.vcf bcftools-1.15.1/test/annotate24.1.out bcftools-1.15.1/test/annotate24.dst.vcf bcftools-1.15.1/test/annotate24.out bcftools-1.15.1/test/annotate24.src.vcf bcftools-1.15.1/test/annotate25.1.out bcftools-1.15.1/test/annotate25.out bcftools-1.15.1/test/annotate25.tab bcftools-1.15.1/test/annotate25.vcf bcftools-1.15.1/test/annotate26.1.out bcftools-1.15.1/test/annotate26.out bcftools-1.15.1/test/annotate26.tab bcftools-1.15.1/test/annotate26.vcf bcftools-1.15.1/test/annotate27.out bcftools-1.15.1/test/annotate28.out bcftools-1.15.1/test/annotate29.out bcftools-1.15.1/test/annotate3.out bcftools-1.15.1/test/annotate3.vcf bcftools-1.15.1/test/annotate30.out bcftools-1.15.1/test/annotate31.out bcftools-1.15.1/test/annotate4.hdr bcftools-1.15.1/test/annotate4.out bcftools-1.15.1/test/annotate4.vcf bcftools-1.15.1/test/annotate5.out bcftools-1.15.1/test/annotate6.out bcftools-1.15.1/test/annotate7.out bcftools-1.15.1/test/annotate8.out bcftools-1.15.1/test/annotate9.out bcftools-1.15.1/test/annotate9.vcf bcftools-1.15.1/test/annots.id.vcf bcftools-1.15.1/test/annots.olap.tab bcftools-1.15.1/test/annots.vcf bcftools-1.15.1/test/annots10.tab bcftools-1.15.1/test/annots11.tab bcftools-1.15.1/test/annots11.vcf bcftools-1.15.1/test/annots12.vcf bcftools-1.15.1/test/annots13.tab bcftools-1.15.1/test/annots2.vcf bcftools-1.15.1/test/annots4.tab bcftools-1.15.1/test/annots4.vcf bcftools-1.15.1/test/annots9.tab bcftools-1.15.1/test/annots9.vcf bcftools-1.15.1/test/atomize.split.1.1.out bcftools-1.15.1/test/atomize.split.1.2.out bcftools-1.15.1/test/atomize.split.1.vcf bcftools-1.15.1/test/atomize.split.2.1.out bcftools-1.15.1/test/atomize.split.2.2.out bcftools-1.15.1/test/atomize.split.2.vcf bcftools-1.15.1/test/atomize.split.3.1.out bcftools-1.15.1/test/atomize.split.3.vcf bcftools-1.15.1/test/call-G.1.out bcftools-1.15.1/test/call-G.2.1.out bcftools-1.15.1/test/call-G.2.out bcftools-1.15.1/test/call-G.2.vcf bcftools-1.15.1/test/call-G.vcf bcftools-1.15.1/test/call.af-fixation.1.out bcftools-1.15.1/test/call.af-fixation.2.out bcftools-1.15.1/test/call.af-fixation.3.out bcftools-1.15.1/test/call.af-fixation.txt bcftools-1.15.1/test/call.af-fixation.vcf bcftools-1.15.1/test/check.chk bcftools-1.15.1/test/check.gs.chrom.gen bcftools-1.15.1/test/check.gs.chrom.samples bcftools-1.15.1/test/check.gs.vcfids.gen bcftools-1.15.1/test/check.gs.vcfids.samples bcftools-1.15.1/test/check.gs.vcfids_chrom.gen bcftools-1.15.1/test/check.gs.vcfids_chrom.samples bcftools-1.15.1/test/check.vcf bcftools-1.15.1/test/check_merge.chk bcftools-1.15.1/test/checkploidy.2.out bcftools-1.15.1/test/checkploidy.2.vcf bcftools-1.15.1/test/checkploidy.3.out bcftools-1.15.1/test/checkploidy.out bcftools-1.15.1/test/checkploidy.vcf bcftools-1.15.1/test/concat.1.a.vcf bcftools-1.15.1/test/concat.1.b.vcf bcftools-1.15.1/test/concat.1.bcf.out bcftools-1.15.1/test/concat.1.vcf.out bcftools-1.15.1/test/concat.2.a.vcf bcftools-1.15.1/test/concat.2.b.vcf bcftools-1.15.1/test/concat.2.bcf.out bcftools-1.15.1/test/concat.2.vcf.out bcftools-1.15.1/test/concat.3.0.vcf bcftools-1.15.1/test/concat.3.a.vcf bcftools-1.15.1/test/concat.3.b.vcf bcftools-1.15.1/test/concat.3.bcf.out bcftools-1.15.1/test/concat.3.c.vcf bcftools-1.15.1/test/concat.3.d.vcf bcftools-1.15.1/test/concat.3.e.vcf bcftools-1.15.1/test/concat.3.f.vcf bcftools-1.15.1/test/concat.3.vcf.out bcftools-1.15.1/test/concat.4.a.vcf bcftools-1.15.1/test/concat.4.b.vcf bcftools-1.15.1/test/concat.4.bcf.out bcftools-1.15.1/test/concat.4.vcf.out bcftools-1.15.1/test/concat.5.1.out bcftools-1.15.1/test/concat.5.2.out bcftools-1.15.1/test/concat.5.a.vcf bcftools-1.15.1/test/concat.5.b.vcf bcftools-1.15.1/test/concat.5.c.vcf bcftools-1.15.1/test/concat.5.out bcftools-1.15.1/test/consensus.1.chain bcftools-1.15.1/test/consensus.1.out bcftools-1.15.1/test/consensus.10.vcf bcftools-1.15.1/test/consensus.11.1.out bcftools-1.15.1/test/consensus.11.2.out bcftools-1.15.1/test/consensus.11.fa bcftools-1.15.1/test/consensus.11.vcf bcftools-1.15.1/test/consensus.12.fa bcftools-1.15.1/test/consensus.12.out bcftools-1.15.1/test/consensus.12.vcf bcftools-1.15.1/test/consensus.13.fa bcftools-1.15.1/test/consensus.13.out bcftools-1.15.1/test/consensus.13.vcf bcftools-1.15.1/test/consensus.14.fa bcftools-1.15.1/test/consensus.14.out bcftools-1.15.1/test/consensus.14.vcf bcftools-1.15.1/test/consensus.15.fa bcftools-1.15.1/test/consensus.15.out bcftools-1.15.1/test/consensus.15.vcf bcftools-1.15.1/test/consensus.16.out bcftools-1.15.1/test/consensus.16.vcf bcftools-1.15.1/test/consensus.17.bed bcftools-1.15.1/test/consensus.17.out bcftools-1.15.1/test/consensus.17.vcf bcftools-1.15.1/test/consensus.18.fa bcftools-1.15.1/test/consensus.18.out bcftools-1.15.1/test/consensus.18.vcf bcftools-1.15.1/test/consensus.19.fa bcftools-1.15.1/test/consensus.19.vcf bcftools-1.15.1/test/consensus.2.chain bcftools-1.15.1/test/consensus.2.out bcftools-1.15.1/test/consensus.3.chain bcftools-1.15.1/test/consensus.3.out bcftools-1.15.1/test/consensus.4.chain bcftools-1.15.1/test/consensus.4.out bcftools-1.15.1/test/consensus.5.out 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bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.txt-l bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.vcf bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.txt bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.txt-l bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.vcf bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.txt bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.txt-l bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.vcf bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.txt bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.txt-l bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.vcf bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.txt bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.txt-l bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.vcf bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.txt bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.txt-l bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.vcf bcftools-1.15.1/test/csq/ENST00000357367/ bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.fa bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.fa.fai bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.gff bcftools-1.15.1/test/csq/ENST00000357367/stop-retained.txt bcftools-1.15.1/test/csq/ENST00000357367/stop-retained.vcf bcftools-1.15.1/test/csq/ENST00000368801.2/ bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.fa bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.fa.fai bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.gff bcftools-1.15.1/test/csq/ENST00000368801.2/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000368801.2/start-lost.txt bcftools-1.15.1/test/csq/ENST00000368801.2/start-lost.vcf bcftools-1.15.1/test/csq/ENST00000368801/ bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.fa bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.fa.fai bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.gff bcftools-1.15.1/test/csq/ENST00000368801/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000368801/compound-lost.txt bcftools-1.15.1/test/csq/ENST00000368801/compound-lost.vcf bcftools-1.15.1/test/csq/ENST00000373833/ bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa.fai bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.gff bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.txt bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.txt-l bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.vcf bcftools-1.15.1/test/csq/ENST00000375992/ bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.fa bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.fa.fai bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.gff bcftools-1.15.1/test/csq/ENST00000375992/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.txt bcftools-1.15.1/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf bcftools-1.15.1/test/csq/ENST00000378322/ bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa.fai bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.gff bcftools-1.15.1/test/csq/ENST00000378322/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000378322/ascii-art.txt-l bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.txt bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.txt-l bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.vcf bcftools-1.15.1/test/csq/ENST00000379416/ bcftools-1.15.1/test/csq/ENST00000379416/ENST00000379416.fa bcftools-1.15.1/test/csq/ENST00000379416/ENST00000379416.fa.fai bcftools-1.15.1/test/csq/ENST00000379416/ENST00000379416.gff bcftools-1.15.1/test/csq/ENST00000379416/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000379416/compound.cmd bcftools-1.15.1/test/csq/ENST00000379416/compound.cmd.out bcftools-1.15.1/test/csq/ENST00000379416/compound.del-snp.vcf bcftools-1.15.1/test/csq/ENST00000379416/compound.ins-del.vcf bcftools-1.15.1/test/csq/ENST00000379416/compound.ins-ins.vcf bcftools-1.15.1/test/csq/ENST00000379416/compound.ins-snp.vcf bcftools-1.15.1/test/csq/ENST00000379416/single.vcf bcftools-1.15.1/test/csq/ENST00000381157/ bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.fa bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.fa.fai bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.gff bcftools-1.15.1/test/csq/ENST00000381157/haploid-diploid.txt bcftools-1.15.1/test/csq/ENST00000381157/haploid-diploid.vcf bcftools-1.15.1/test/csq/ENST00000382647/ bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.fa bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.fa.fai bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.gff bcftools-1.15.1/test/csq/ENST00000382647/synon-splice-region-insert.txt bcftools-1.15.1/test/csq/ENST00000382647/synon-splice-region-insert.vcf bcftools-1.15.1/test/csq/ENST00000390520/ bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.fa bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.fa.fai bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.gff bcftools-1.15.1/test/csq/ENST00000390520/deletion-overlap.txt bcftools-1.15.1/test/csq/ENST00000390520/deletion-overlap.vcf bcftools-1.15.1/test/csq/ENST00000400151/ bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.fa bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.fa.fai bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.gff bcftools-1.15.1/test/csq/ENST00000400151/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000400151/long-del.txt bcftools-1.15.1/test/csq/ENST00000400151/long-del.vcf bcftools-1.15.1/test/csq/ENST00000409523/ bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.fa bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.fa.fai bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.gff bcftools-1.15.1/test/csq/ENST00000409523/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000409523/long-overlapping-del.txt bcftools-1.15.1/test/csq/ENST00000409523/long-overlapping-del.vcf bcftools-1.15.1/test/csq/ENST00000410009/ bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.fa bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.fa.fai bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.gff bcftools-1.15.1/test/csq/ENST00000410009/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000410009/frameshift.1.cmd bcftools-1.15.1/test/csq/ENST00000410009/frameshift.1.cmd.out bcftools-1.15.1/test/csq/ENST00000410009/frameshift.2.cmd bcftools-1.15.1/test/csq/ENST00000410009/frameshift.2.cmd.out bcftools-1.15.1/test/csq/ENST00000410009/frameshift.3.cmd bcftools-1.15.1/test/csq/ENST00000410009/frameshift.3.cmd.out bcftools-1.15.1/test/csq/ENST00000410009/frameshift.txt bcftools-1.15.1/test/csq/ENST00000410009/frameshift.vcf bcftools-1.15.1/test/csq/ENST00000413103/ bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.fa bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.fa.fai bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.gff bcftools-1.15.1/test/csq/ENST00000413103/long-deletion.txt bcftools-1.15.1/test/csq/ENST00000413103/long-deletion.vcf bcftools-1.15.1/test/csq/ENST00000420190/ bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.fa bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.fa.fai bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.gff bcftools-1.15.1/test/csq/ENST00000420190/abort-in-csq-push.txt bcftools-1.15.1/test/csq/ENST00000420190/abort-in-csq-push.vcf bcftools-1.15.1/test/csq/ENST00000420670/ bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa.fai bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.gff bcftools-1.15.1/test/csq/ENST00000420670/segfault.txt bcftools-1.15.1/test/csq/ENST00000420670/segfault.vcf bcftools-1.15.1/test/csq/ENST00000420670/start-stop-lost.txt bcftools-1.15.1/test/csq/ENST00000420670/start-stop-lost.vcf bcftools-1.15.1/test/csq/ENST00000422159/ bcftools-1.15.1/test/csq/ENST00000422159/ENST00000422159.fa bcftools-1.15.1/test/csq/ENST00000422159/ENST00000422159.fa.fai bcftools-1.15.1/test/csq/ENST00000422159/ENST00000422159.gff bcftools-1.15.1/test/csq/ENST00000422159/multiallelic.vcf bcftools-1.15.1/test/csq/ENST00000422159/short.gff bcftools-1.15.1/test/csq/ENST00000422159/test.cmd bcftools-1.15.1/test/csq/ENST00000422159/test.cmd.out bcftools-1.15.1/test/csq/ENST00000423372/ bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa.fai bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff bcftools-1.15.1/test/csq/ENST00000423372/insert3.txt bcftools-1.15.1/test/csq/ENST00000423372/insert3.txt-l bcftools-1.15.1/test/csq/ENST00000423372/insert3.vcf bcftools-1.15.1/test/csq/ENST00000423372/snps.txt bcftools-1.15.1/test/csq/ENST00000423372/snps.txt-l bcftools-1.15.1/test/csq/ENST00000423372/snps.vcf bcftools-1.15.1/test/csq/ENST00000436063/ bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.fa bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.fa.fai bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.gff bcftools-1.15.1/test/csq/ENST00000436063/insert-before-utr.txt bcftools-1.15.1/test/csq/ENST00000436063/insert-before-utr.vcf bcftools-1.15.1/test/csq/ENST00000448695/ bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.fa bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.fa.fai bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.gff bcftools-1.15.1/test/csq/ENST00000448695/syn-and-splice-reg.txt bcftools-1.15.1/test/csq/ENST00000448695/syn-and-splice-reg.vcf bcftools-1.15.1/test/csq/ENST00000479739/ bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa.fai bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.gff bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.txt bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.txt-l bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.vcf bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa.fai bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/valgrind.txt bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf bcftools-1.15.1/test/csq/ENST00000518414/ bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.fa bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.fa.fai bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.gff bcftools-1.15.1/test/csq/ENST00000518414/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000518414/incorrect-inframe-del.txt bcftools-1.15.1/test/csq/ENST00000518414/incorrect-inframe-del.vcf bcftools-1.15.1/test/csq/ENST00000519442/ bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.fa bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.fa.fai bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.gff bcftools-1.15.1/test/csq/ENST00000519442/synon-splice-region-del.txt bcftools-1.15.1/test/csq/ENST00000519442/synon-splice-region-del.vcf bcftools-1.15.1/test/csq/ENST00000520795/ bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa.fai bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.gff bcftools-1.15.1/test/csq/ENST00000520795/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000520795/ascii-art.txt-l bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.txt bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.txt-l bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.vcf bcftools-1.15.1/test/csq/ENST00000520868/ bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.fa bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.fa.fai bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.gff bcftools-1.15.1/test/csq/ENST00000520868/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000520868/long-deletion.txt bcftools-1.15.1/test/csq/ENST00000520868/long-deletion.vcf bcftools-1.15.1/test/csq/ENST00000528237/ bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.fa bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.fa.fai bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.gff bcftools-1.15.1/test/csq/ENST00000528237/retained-stop-incomplete-cds.txt bcftools-1.15.1/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf bcftools-1.15.1/test/csq/ENST00000536784/ bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa.fai bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.gff bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.txt bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.txt-l bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.vcf bcftools-1.15.1/test/csq/ENST00000542803/ bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa.fai bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.gff bcftools-1.15.1/test/csq/ENST00000542803/splice-region.txt bcftools-1.15.1/test/csq/ENST00000542803/splice-region.txt-l bcftools-1.15.1/test/csq/ENST00000542803/splice-region.vcf bcftools-1.15.1/test/csq/ENST00000543077/ bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa.fai bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.gff bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.txt bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.txt-l bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.vcf bcftools-1.15.1/test/csq/ENST00000545279/ bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.fa bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.fa.fai bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.gff bcftools-1.15.1/test/csq/ENST00000545279/splice-region-insert.txt bcftools-1.15.1/test/csq/ENST00000545279/splice-region-insert.vcf bcftools-1.15.1/test/csq/ENST00000557788/ bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.fa bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.fa.fai bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.gff bcftools-1.15.1/test/csq/ENST00000557788/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000557788/long-overlap-del.txt bcftools-1.15.1/test/csq/ENST00000557788/long-overlap-del.vcf bcftools-1.15.1/test/csq/ENST00000573314/ bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa.fai bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.gff bcftools-1.15.1/test/csq/ENST00000573314/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000573314/ascii-art.txt-l bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.txt bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf bcftools-1.15.1/test/csq/ENST00000580206/ bcftools-1.15.1/test/csq/ENST00000580206/ENST00000580206.fa bcftools-1.15.1/test/csq/ENST00000580206/ENST00000580206.fa.fai bcftools-1.15.1/test/csq/ENST00000580206/ENST00000580206.gff bcftools-1.15.1/test/csq/ENST00000580206/ascii-art.txt bcftools-1.15.1/test/csq/ENST00000580206/compound.del-ins.vcf bcftools-1.15.1/test/csq/ENST00000580206/compound.del-snv.vcf bcftools-1.15.1/test/csq/ENST00000580206/compound.ins-snv.vcf bcftools-1.15.1/test/csq/ENST00000580206/short.gff bcftools-1.15.1/test/csq/ENST00000580206/single.del-ins.vcf bcftools-1.15.1/test/csq/ENST00000580206/single.del-snv.vcf bcftools-1.15.1/test/csq/ENST00000580206/single.ins-snv.vcf bcftools-1.15.1/test/csq/ENST00000580206/test.cmd bcftools-1.15.1/test/csq/ENST00000580206/test.cmd.out bcftools-1.15.1/test/csq/ENST00000593942/ bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.fa bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.fa.fai bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.gff bcftools-1.15.1/test/csq/ENST00000593942/last-codon-deletion.txt 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bcftools-1.15.1/htslib-1.15.1/test/tabix/bed_file.Y.100200.out bcftools-1.15.1/htslib-1.15.1/test/tabix/bed_file.bed bcftools-1.15.1/htslib-1.15.1/test/tabix/bed_file.separate.out bcftools-1.15.1/htslib-1.15.1/test/tabix/gff_file.X.2934832.2935190.out bcftools-1.15.1/htslib-1.15.1/test/tabix/gff_file.gff bcftools-1.15.1/htslib-1.15.1/test/tabix/large_chr.20.1.2147483647.out bcftools-1.15.1/htslib-1.15.1/test/tabix/large_chr.vcf bcftools-1.15.1/htslib-1.15.1/test/tabix/tabix.tst bcftools-1.15.1/htslib-1.15.1/test/tabix/test-tabix.sh bcftools-1.15.1/htslib-1.15.1/test/tabix/vcf_file.1.3000151.out bcftools-1.15.1/htslib-1.15.1/test/tabix/vcf_file.2.3199812.out bcftools-1.15.1/htslib-1.15.1/test/tabix/vcf_file.bcf bcftools-1.15.1/htslib-1.15.1/test/tabix/vcf_file.vcf bcftools-1.15.1/htslib-1.15.1/test/test-bcf-sr.c bcftools-1.15.1/htslib-1.15.1/test/test-bcf-sr.pl bcftools-1.15.1/htslib-1.15.1/test/test-bcf-translate.c bcftools-1.15.1/htslib-1.15.1/test/test-bcf-translate.out bcftools-1.15.1/htslib-1.15.1/test/test-logging.pl bcftools-1.15.1/htslib-1.15.1/test/test-parse-reg.c bcftools-1.15.1/htslib-1.15.1/test/test-regidx.c bcftools-1.15.1/htslib-1.15.1/test/test-vcf-api.c bcftools-1.15.1/htslib-1.15.1/test/test-vcf-api.out bcftools-1.15.1/htslib-1.15.1/test/test-vcf-hdr-in.vcf bcftools-1.15.1/htslib-1.15.1/test/test-vcf-hdr.out bcftools-1.15.1/htslib-1.15.1/test/test-vcf-sweep.c bcftools-1.15.1/htslib-1.15.1/test/test-vcf-sweep.out bcftools-1.15.1/htslib-1.15.1/test/test.pl bcftools-1.15.1/htslib-1.15.1/test/test_bgzf.c bcftools-1.15.1/htslib-1.15.1/test/test_expr.c bcftools-1.15.1/htslib-1.15.1/test/test_index.c bcftools-1.15.1/htslib-1.15.1/test/test_introspection.c bcftools-1.15.1/htslib-1.15.1/test/test_kfunc.c bcftools-1.15.1/htslib-1.15.1/test/test_kstring.c bcftools-1.15.1/htslib-1.15.1/test/test_mod.c bcftools-1.15.1/htslib-1.15.1/test/test_realn.c bcftools-1.15.1/htslib-1.15.1/test/test_str2int.c bcftools-1.15.1/htslib-1.15.1/test/test_view.c bcftools-1.15.1/htslib-1.15.1/test/thrash_threads1.c bcftools-1.15.1/htslib-1.15.1/test/thrash_threads2.c bcftools-1.15.1/htslib-1.15.1/test/thrash_threads3.c bcftools-1.15.1/htslib-1.15.1/test/thrash_threads4.c bcftools-1.15.1/htslib-1.15.1/test/thrash_threads5.c bcftools-1.15.1/htslib-1.15.1/test/thrash_threads6.c bcftools-1.15.1/htslib-1.15.1/test/thrash_threads7.c bcftools-1.15.1/htslib-1.15.1/test/thread_pool.md bcftools-1.15.1/htslib-1.15.1/test/vcf_meta_meta.vcf bcftools-1.15.1/htslib-1.15.1/test/with-shlib.sh bcftools-1.15.1/htslib-1.15.1/test/xx#MD.sam bcftools-1.15.1/htslib-1.15.1/test/xx#MD2.sam bcftools-1.15.1/htslib-1.15.1/test/xx#blank.sam bcftools-1.15.1/htslib-1.15.1/test/xx#large_aux.sam bcftools-1.15.1/htslib-1.15.1/test/xx#large_aux2.sam bcftools-1.15.1/htslib-1.15.1/test/xx#large_aux_java.cram bcftools-1.15.1/htslib-1.15.1/test/xx#minimal.sam bcftools-1.15.1/htslib-1.15.1/test/xx#pair.sam bcftools-1.15.1/htslib-1.15.1/test/xx#repeated.sam bcftools-1.15.1/htslib-1.15.1/test/xx#rg.sam bcftools-1.15.1/htslib-1.15.1/test/xx#tlen.sam bcftools-1.15.1/htslib-1.15.1/test/xx#tlen2.sam bcftools-1.15.1/htslib-1.15.1/test/xx#triplet.sam bcftools-1.15.1/htslib-1.15.1/test/xx#unsorted.sam bcftools-1.15.1/htslib-1.15.1/test/xx.fa bcftools-1.15.1/htslib-1.15.1/test/xx.fa.fai bcftools-1.15.1/htslib-1.15.1/textutils.c bcftools-1.15.1/htslib-1.15.1/textutils_internal.h bcftools-1.15.1/htslib-1.15.1/thread_pool.c bcftools-1.15.1/htslib-1.15.1/thread_pool_internal.h bcftools-1.15.1/htslib-1.15.1/vcf.5 bcftools-1.15.1/htslib-1.15.1/vcf.c bcftools-1.15.1/htslib-1.15.1/vcf_sweep.c bcftools-1.15.1/htslib-1.15.1/vcfutils.c bcftools-1.15.1/htslib-1.15.1/version.sh bcftools-1.15.1/htslib-1.15.1/config.h.in bcftools-1.15.1/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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h echo '#define BCFTOOLS_VERSION "1.15.1"' > version.h gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o main.o main.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfindex.o vcfindex.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o tabix.o tabix.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfstats.o vcfstats.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfisec.o vcfisec.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfmerge.o vcfmerge.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfquery.o vcfquery.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcffilter.o vcffilter.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o filter.o filter.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfsom.o vcfsom.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfnorm.o vcfnorm.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfview.o vcfview.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfannotate.o vcfannotate.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfroh.o vcfroh.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfconcat.o vcfconcat.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfcall.o vcfcall.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o mcall.o mcall.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcmp.o vcmp.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o gvcf.o gvcf.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o reheader.o reheader.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o convert.o convert.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfconvert.o vcfconvert.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfcnv.o vcfcnv.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfhead.o vcfhead.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o HMM.o HMM.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o consensus.o consensus.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o ploidy.o ploidy.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o bin.o bin.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o hclust.o hclust.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o version.o version.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o regidx.o regidx.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o csq.o csq.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfbuf.o vcfbuf.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o mpileup.o mpileup.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o bam2bcf.o bam2bcf.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o bam_sample.o bam_sample.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o vcfsort.o vcfsort.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o cols.o cols.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o extsort.o extsort.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o dist.o dist.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o abuf.o abuf.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o ccall.o ccall.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o em.o em.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o prob1.o prob1.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o kmin.o kmin.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o str_finder.o str_finder.c gcc -Wall -O2 -march=i586 -mtune=i686 -I. -DPLUGINPATH='"/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -rdynamic -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o vcfplugin.o -lhts -lm -lz -ldl -lpthread gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o test/test-rbuf.o test/test-rbuf.c gcc -o test/test-rbuf test/test-rbuf.o -lz -ldl gcc -Wall -O2 -march=i586 -mtune=i686 -I. -c -o test/test-regidx.o test/test-regidx.c gcc -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/GTisec.so version.c plugins/GTisec.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/allele-length.so version.c plugins/allele-length.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/contrast.so version.c plugins/contrast.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/counts.so version.c plugins/counts.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/dosage.so version.c plugins/dosage.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/fixref.so version.c plugins/fixref.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/gvcfz.so version.c plugins/gvcfz.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/impute-info.so version.c plugins/impute-info.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/indel-stats.so version.c plugins/indel-stats.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/mendelian.so version.c plugins/mendelian.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/parental-origin.so version.c plugins/parental-origin.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/prune.so version.c plugins/prune.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/scatter.so version.c plugins/scatter.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/setGT.so version.c plugins/setGT.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/split-vep.so version.c plugins/split-vep.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/split.so version.c plugins/split.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/trio-stats.so version.c plugins/trio-stats.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl gcc -fPIC -shared -Wall -O2 -march=i586 -mtune=i686 -I. -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c -ldl mkdir -p -m 755 /usr/src/slapt-src/academic/bcftools/package-bcftools/usr/bin /usr/src/slapt-src/academic/bcftools/package-bcftools/usr/man/man1 /usr/src/slapt-src/academic/bcftools/package-bcftools/usr/libexec/bcftools install -p bcftools /usr/src/slapt-src/academic/bcftools/package-bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /usr/src/slapt-src/academic/bcftools/package-bcftools/usr/bin install -p -m 644 doc/bcftools.1 /usr/src/slapt-src/academic/bcftools/package-bcftools/usr/man/man1 install -p plugins/*.so /usr/src/slapt-src/academic/bcftools/package-bcftools/usr/libexec/bcftools Slackware package maker, version 3.14159265. Searching for symbolic links: No symbolic links were found, so we won't make an installation script. You can make your own later in ./install/doinst.sh and rebuild the package if you like. 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/academic/bcftools/bcftools-1.15.1-i586-1salix15.0.txz ./ install/ install/slack-desc usr/ usr/bin/ usr/bin/bcftools usr/bin/color-chrs.pl usr/bin/gff2gff.py usr/bin/guess-ploidy.py usr/bin/plot-roh.py usr/bin/plot-vcfstats usr/bin/run-roh.pl usr/bin/vcfutils.pl usr/doc/ usr/doc/bcftools-1.15.1/ usr/doc/bcftools-1.15.1/AUTHORS usr/doc/bcftools-1.15.1/INSTALL usr/doc/bcftools-1.15.1/LICENSE usr/doc/bcftools-1.15.1/NEWS usr/doc/bcftools-1.15.1/README usr/doc/bcftools-1.15.1/bcftools.SlackBuild usr/libexec/ usr/libexec/bcftools/ usr/libexec/bcftools/GTisec.so usr/libexec/bcftools/GTsubset.so usr/libexec/bcftools/ad-bias.so usr/libexec/bcftools/add-variantkey.so usr/libexec/bcftools/af-dist.so usr/libexec/bcftools/allele-length.so usr/libexec/bcftools/check-ploidy.so usr/libexec/bcftools/check-sparsity.so usr/libexec/bcftools/color-chrs.so usr/libexec/bcftools/contrast.so usr/libexec/bcftools/counts.so usr/libexec/bcftools/dosage.so usr/libexec/bcftools/fill-AN-AC.so usr/libexec/bcftools/fill-from-fasta.so usr/libexec/bcftools/fill-tags.so usr/libexec/bcftools/fixploidy.so usr/libexec/bcftools/fixref.so usr/libexec/bcftools/frameshifts.so usr/libexec/bcftools/guess-ploidy.so usr/libexec/bcftools/gvcfz.so usr/libexec/bcftools/impute-info.so usr/libexec/bcftools/indel-stats.so usr/libexec/bcftools/isecGT.so usr/libexec/bcftools/mendelian.so usr/libexec/bcftools/missing2ref.so usr/libexec/bcftools/parental-origin.so usr/libexec/bcftools/prune.so usr/libexec/bcftools/remove-overlaps.so usr/libexec/bcftools/scatter.so usr/libexec/bcftools/setGT.so usr/libexec/bcftools/smpl-stats.so usr/libexec/bcftools/split-vep.so usr/libexec/bcftools/split.so usr/libexec/bcftools/tag2tag.so usr/libexec/bcftools/trio-dnm2.so usr/libexec/bcftools/trio-stats.so usr/libexec/bcftools/trio-switch-rate.so usr/libexec/bcftools/variantkey-hex.so usr/man/ usr/man/man1/ usr/man/man1/bcftools.1.gz Slackware package /usr/src/slapt-src/academic/bcftools/bcftools-1.15.1-i586-1salix15.0.txz created. Installing package bcftools-1.15.1-i586-1salix15.0... | bcftools (BCF calling tools) | | bcftools contains all the "vcf..." commands which previously lived in | the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and | the samtools BCF calling from bcftools subdirectory of the previous | samtools. BCFtools are meant as a faster replacement for most of the | perl VCFtools commands. Bcftools comes with its own hstlib sources. | | Homepage: http://www.htslib.org | | | |