The following packages will be installed: bedtools Fetching README... 0%100%100%100%100%100%Done Fetching bedtools.SlackBuild... 0%100%100%100%100%100%Done Fetching bedtools.info... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done bedtools2/ bedtools2/obj/ bedtools2/tutorial/ bedtools2/LICENSE bedtools2/test/ bedtools2/bin/ bedtools2/Makefile bedtools2/docs/ bedtools2/README.md bedtools2/genomes/ bedtools2/.gitignore bedtools2/scripts/ bedtools2/.github/ bedtools2/data/ bedtools2/src/ bedtools2/src/spacingFile/ bedtools2/src/sortBed/ bedtools2/src/split/ bedtools2/src/bedToBam/ bedtools2/src/complementFile/ bedtools2/src/expand/ bedtools2/src/fisher/ bedtools2/src/linksBed/ bedtools2/src/pairToPair/ bedtools2/src/bedtools.cpp bedtools2/src/mapFile/ bedtools2/src/slopBed/ bedtools2/src/annotateBed/ bedtools2/src/randomBed/ bedtools2/src/getOverlap/ bedtools2/src/reldist/ bedtools2/src/nucBed/ bedtools2/src/bedToIgv/ bedtools2/src/regressTest/ bedtools2/src/maskFastaFromBed/ bedtools2/src/genomeCoverageBed/ bedtools2/src/utils/ bedtools2/src/windowBed/ bedtools2/src/jaccard/ bedtools2/src/groupBy/ bedtools2/src/bamToFastq/ bedtools2/src/htsutil.cpp bedtools2/src/fastaFromBed/ bedtools2/src/nekSandbox1/ bedtools2/src/unionBedGraphs/ bedtools2/src/bed12ToBed6/ bedtools2/src/subtractFile/ bedtools2/src/bedpeToBam/ bedtools2/src/windowMaker/ bedtools2/src/coverageFile/ bedtools2/src/summaryFile/ bedtools2/src/multiIntersectBed/ bedtools2/src/intersectFile/ bedtools2/src/closestFile/ bedtools2/src/shuffleBed/ bedtools2/src/flankBed/ bedtools2/src/tagBam/ bedtools2/src/multiBamCov/ bedtools2/src/sampleFile/ bedtools2/src/clusterBed/ bedtools2/src/shiftBed/ bedtools2/src/mergeFile/ bedtools2/src/bamToBed/ bedtools2/src/pairToBed/ bedtools2/src/pairToBed/pairToBed.h bedtools2/src/pairToBed/pairToBedMain.cpp bedtools2/src/pairToBed/Makefile.frag bedtools2/src/pairToBed/pairToBed.cpp bedtools2/src/bamToBed/bamToBed.cpp bedtools2/src/bamToBed/Makefile.frag bedtools2/src/mergeFile/mergeFile.cpp bedtools2/src/mergeFile/Makefile.frag bedtools2/src/mergeFile/mergeHelp.cpp bedtools2/src/mergeFile/mergeFile.h bedtools2/src/shiftBed/shiftBed.cpp bedtools2/src/shiftBed/shiftBedMain.cpp bedtools2/src/shiftBed/Makefile.frag bedtools2/src/shiftBed/shiftBed.h bedtools2/src/clusterBed/clusterBed.h bedtools2/src/clusterBed/clusterBed.cpp bedtools2/src/clusterBed/clusterMain.cpp bedtools2/src/clusterBed/Makefile.frag bedtools2/src/sampleFile/sampleFile.cpp bedtools2/src/sampleFile/sampleFile.h bedtools2/src/sampleFile/Makefile.frag bedtools2/src/sampleFile/sampleHelp.cpp bedtools2/src/multiBamCov/multiBamCov.cpp bedtools2/src/multiBamCov/Makefile.frag bedtools2/src/multiBamCov/multiBamCov.h bedtools2/src/multiBamCov/multiBamCovMain.cpp bedtools2/src/tagBam/tagBam.cpp bedtools2/src/tagBam/tagBamMain.cpp bedtools2/src/tagBam/tagBam.h bedtools2/src/tagBam/Makefile.frag bedtools2/src/flankBed/flankBed.cpp 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bedtools2/src/unionBedGraphs/unionBedGraphs.h bedtools2/src/nekSandbox1/FormatGuess.h bedtools2/src/nekSandbox1/Makefile bedtools2/src/nekSandbox1/nekSandboxMain.cpp bedtools2/src/fastaFromBed/fastaFromBedMain.cpp bedtools2/src/fastaFromBed/fastaFromBed.cpp bedtools2/src/fastaFromBed/fastaFromBed.h bedtools2/src/fastaFromBed/Makefile.frag bedtools2/src/bamToFastq/bamToFastq.h bedtools2/src/bamToFastq/bamToFastq.cpp bedtools2/src/bamToFastq/bamToFastqMain.cpp bedtools2/src/bamToFastq/Makefile.frag bedtools2/src/groupBy/groupBy.cpp bedtools2/src/groupBy/groupBy.h bedtools2/src/groupBy/Makefile.frag bedtools2/src/groupBy/groupByHelp.cpp bedtools2/src/jaccard/jaccard.cpp bedtools2/src/jaccard/Makefile.frag bedtools2/src/jaccard/jaccardHelp.cpp bedtools2/src/jaccard/jaccard.h bedtools2/src/windowBed/windowBed.cpp bedtools2/src/windowBed/windowBed.h bedtools2/src/windowBed/windowMain.cpp bedtools2/src/windowBed/Makefile.frag bedtools2/src/utils/tabFile/ bedtools2/src/utils/htslib/ 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bedtools2/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp bedtools2/src/utils/FileRecordTools/FileReaders/FileReader.cpp bedtools2/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp bedtools2/src/utils/FileRecordTools/FileReaders/Makefile.frag bedtools2/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h bedtools2/src/utils/FileRecordTools/FileReaders/FileReader.h bedtools2/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h bedtools2/src/utils/FileRecordTools/Records/BedGraphInterval.cpp bedtools2/src/utils/FileRecordTools/Records/RecordMgr.cpp bedtools2/src/utils/FileRecordTools/Records/RecordList.cpp bedtools2/src/utils/FileRecordTools/Records/Bed12Interval.h bedtools2/src/utils/FileRecordTools/Records/GffRecord.h bedtools2/src/utils/FileRecordTools/Records/Bed4Interval.h bedtools2/src/utils/FileRecordTools/Records/BedGraphInterval.h bedtools2/src/utils/FileRecordTools/Records/RecordList.h bedtools2/src/utils/FileRecordTools/Records/BamRecord.cpp bedtools2/src/utils/FileRecordTools/Records/RecordKeyVector.cpp bedtools2/src/utils/FileRecordTools/Records/PlusFields.h bedtools2/src/utils/FileRecordTools/Records/StrandQueue.cpp bedtools2/src/utils/FileRecordTools/Records/Bed5Interval.h bedtools2/src/utils/FileRecordTools/Records/Record.h bedtools2/src/utils/FileRecordTools/Records/GffRecord.cpp bedtools2/src/utils/FileRecordTools/Records/Bed4Interval.cpp bedtools2/src/utils/FileRecordTools/Records/VcfRecord.h bedtools2/src/utils/FileRecordTools/Records/Bed3Interval.h bedtools2/src/utils/FileRecordTools/Records/RecordKeyList.h bedtools2/src/utils/FileRecordTools/Records/VcfRecord.cpp bedtools2/src/utils/FileRecordTools/Records/EmptyRecord.h bedtools2/src/utils/FileRecordTools/Records/Bed3Interval.cpp bedtools2/src/utils/FileRecordTools/Records/RecordKeyVector.h bedtools2/src/utils/FileRecordTools/Records/Bed6Interval.h bedtools2/src/utils/FileRecordTools/Records/BlockMgr.h bedtools2/src/utils/FileRecordTools/Records/RecordMgr.h bedtools2/src/utils/FileRecordTools/Records/Bed6Interval.cpp bedtools2/src/utils/FileRecordTools/Records/GffPlusRecord.h bedtools2/src/utils/FileRecordTools/Records/GffPlusRecord.cpp bedtools2/src/utils/FileRecordTools/Records/BedPlusInterval.cpp bedtools2/src/utils/FileRecordTools/Records/Makefile.frag bedtools2/src/utils/FileRecordTools/Records/StrandQueue.h bedtools2/src/utils/FileRecordTools/Records/Record.cpp bedtools2/src/utils/FileRecordTools/Records/Bed5Interval.cpp bedtools2/src/utils/FileRecordTools/Records/NoPosPlusRecord.h bedtools2/src/utils/FileRecordTools/Records/Bed12Interval.cpp bedtools2/src/utils/FileRecordTools/Records/BlockMgr.cpp bedtools2/src/utils/FileRecordTools/Records/RecordKeyList.cpp bedtools2/src/utils/FileRecordTools/Records/PlusFields.cpp bedtools2/src/utils/FileRecordTools/Records/BamRecord.h bedtools2/src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp bedtools2/src/utils/FileRecordTools/Records/EmptyRecord.cpp bedtools2/src/utils/FileRecordTools/Records/BedPlusInterval.h bedtools2/src/utils/chromsweep/chromsweep.cpp bedtools2/src/utils/chromsweep/Makefile.frag bedtools2/src/utils/chromsweep/chromsweep.h bedtools2/src/utils/bedFilePE/bedFilePE.cpp bedtools2/src/utils/bedFilePE/Makefile.frag bedtools2/src/utils/bedFilePE/bedFilePE.h bedtools2/src/utils/lineFileUtilities/lineFileUtilities.h bedtools2/src/utils/ToolBase/ToolBase.cpp bedtools2/src/utils/ToolBase/Makefile.frag bedtools2/src/utils/ToolBase/ToolBase.h bedtools2/src/utils/version/version.h bedtools2/src/utils/version/version.cpp bedtools2/src/utils/version/version_release.txt bedtools2/src/utils/version/Makefile.frag bedtools2/src/utils/GenomeFile/NewGenomeFile.cpp bedtools2/src/utils/GenomeFile/NewGenomeFile.h bedtools2/src/utils/GenomeFile/GenomeFile.cpp bedtools2/src/utils/GenomeFile/Makefile.frag bedtools2/src/utils/GenomeFile/GenomeFile.h bedtools2/src/utils/BamTools-Ancillary/BamAncillary.h bedtools2/src/utils/BamTools-Ancillary/BamAncillary.cpp bedtools2/src/utils/BamTools-Ancillary/Makefile.frag bedtools2/src/utils/KeyListOps/KeyListOps.h bedtools2/src/utils/KeyListOps/KeyListOps.cpp bedtools2/src/utils/KeyListOps/KeyListOpsMethods.cpp bedtools2/src/utils/KeyListOps/Makefile.frag bedtools2/src/utils/KeyListOps/KeyListOpsMethods.h bedtools2/src/utils/fileType/fileType.cpp bedtools2/src/utils/fileType/FileRecordTypeChecker.h bedtools2/src/utils/fileType/FileRecordTypeChecker.cpp bedtools2/src/utils/fileType/Makefile.frag bedtools2/src/utils/fileType/fileType.h bedtools2/src/utils/gzstream/gzstream.C bedtools2/src/utils/gzstream/README bedtools2/src/utils/gzstream/COPYING.LIB bedtools2/src/utils/gzstream/Makefile.frag bedtools2/src/utils/gzstream/version.txt bedtools2/src/utils/gzstream/gzstream.h bedtools2/src/utils/Fasta/Fasta.h bedtools2/src/utils/Fasta/split.cpp bedtools2/src/utils/Fasta/Fasta.cpp bedtools2/src/utils/Fasta/LargeFileSupport.h bedtools2/src/utils/Fasta/Makefile.frag bedtools2/src/utils/Fasta/split.h bedtools2/src/utils/sequenceUtilities/sequenceUtils.h bedtools2/src/utils/sequenceUtilities/Makefile.frag bedtools2/src/utils/sequenceUtilities/sequenceUtils.cpp bedtools2/src/utils/bedGraphFile/bedGraphFile.h bedtools2/src/utils/bedGraphFile/Makefile.frag bedtools2/src/utils/bedGraphFile/bedGraphFile.cpp bedtools2/src/utils/Point/Point.h bedtools2/src/utils/driver/BedtoolsDriver.h bedtools2/src/utils/driver/BedtoolsDriver.cpp bedtools2/src/utils/driver/Makefile.frag bedtools2/src/utils/general/QuickString.cpp bedtools2/src/utils/general/ParseTools.cpp bedtools2/src/utils/general/CommonHelp.h bedtools2/src/utils/general/FreeList.h bedtools2/src/utils/general/CompressionTools.cpp bedtools2/src/utils/general/Random.cpp bedtools2/src/utils/general/BedtoolsTypes.h bedtools2/src/utils/general/ErrorMsg.h bedtools2/src/utils/general/PushBackStreamBuf.h 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bedtools2/test/shift/test-shift.sh bedtools2/test/shift/issue_807.bed bedtools2/test/shift/a.bed bedtools2/test/shift/b.bed bedtools2/test/shift/tiny.genome bedtools2/test/shift/huge.genome bedtools2/test/shift/issue_807.genomesize bedtools2/test/reldist/issue_711.a.bed bedtools2/test/reldist/issue_711.b.bed bedtools2/test/reldist/test-reldist.sh bedtools2/test/slop/a.bed bedtools2/test/slop/tiny.genome bedtools2/test/slop/test-slop.sh bedtools2/test/general/hg19.fa.fai bedtools2/test/general/empty.bed bedtools2/test/general/a.chromheader.bed bedtools2/test/general/test-general.sh bedtools2/test/general/non-empty.bed.gz bedtools2/test/general/t.bed bedtools2/test/general/a.trackheader.bed bedtools2/test/merge/bamCol8Mean.txt bedtools2/test/merge/mergeBugTest.bed bedtools2/test/merge/expFormat.bed bedtools2/test/merge/bamCol9Mean.txt bedtools2/test/merge/unsorted.bed bedtools2/test/merge/bug254_d.bed bedtools2/test/merge/bug254_e.bed bedtools2/test/merge/bamCol6Collapse.txt bedtools2/test/merge/bamCol3Collapse.txt bedtools2/test/merge/vcfSVtest.vcf bedtools2/test/merge/bug254_c.bed bedtools2/test/merge/bamCol11Collapse.txt bedtools2/test/merge/a.full.bed bedtools2/test/merge/a.bed bedtools2/test/merge/test-merge.sh bedtools2/test/merge/precisionTest.bed bedtools2/test/merge/b.bed bedtools2/test/merge/a.names.bed bedtools2/test/merge/testA.vcf bedtools2/test/merge/bamCol1Collapse.txt bedtools2/test/merge/precisionTest2.bed bedtools2/test/merge/bamCol10Collapse.txt bedtools2/test/merge/bamCol5Mean.txt bedtools2/test/merge/a.gff bedtools2/test/merge/bamCol7Collapse.txt bedtools2/test/merge/bamCol4Mean.txt bedtools2/test/merge/a.full.bam bedtools2/test/merge/mixedStrands.bed bedtools2/test/merge/fullFields.bam bedtools2/test/subtract/test-subtract.sh bedtools2/test/subtract/a.bed bedtools2/test/subtract/c.bed bedtools2/test/subtract/b.bed bedtools2/test/subtract/b2.bed bedtools2/test/subtract/d.bed bedtools2/test/sort/names.txt bedtools2/test/sort/a.bed bedtools2/test/sort/test-sort.sh bedtools2/test/sort/b.bed bedtools2/test/intersect/two_blocks.sam bedtools2/test/intersect/a_with_bothUnmapped.bam bedtools2/test/intersect/gdc.gff bedtools2/test/intersect/bug223_sv1_b.vcf bedtools2/test/intersect/bed3.bed bedtools2/test/intersect/bug150_a.bed bedtools2/test/intersect/test_ref.fa.fai bedtools2/test/intersect/x.bam bedtools2/test/intersect/exons.issue750.bed bedtools2/test/intersect/performanceTest.sh bedtools2/test/intersect/bed6.strand.bed bedtools2/test/intersect/queryUnmappedMateMappedCoordsInvalid.bam bedtools2/test/intersect/bug223_sv1_a.vcf bedtools2/test/intersect/bug150_b.bed bedtools2/test/intersect/headerOnly.vcf bedtools2/test/intersect/gdc_one.bed bedtools2/test/intersect/bed6.strand2.bed bedtools2/test/intersect/null_b.bed bedtools2/test/intersect/a_withLargeHeader.bed bedtools2/test/intersect/human.hg19.vSort.genome bedtools2/test/intersect/gdc.bam bedtools2/test/intersect/bed4.bed bedtools2/test/intersect/chromOrderB.bed bedtools2/test/intersect/bedplus.bed bedtools2/test/intersect/test_ref.fa bedtools2/test/intersect/bed5.bed bedtools2/test/intersect/oneRecordNoNewline.bed bedtools2/test/intersect/aWithHeaderVsB.txt bedtools2/test/intersect/null_c.bed bedtools2/test/intersect/j1.bed bedtools2/test/intersect/b.issue311.vcf bedtools2/test/intersect/null_a.bed bedtools2/test/intersect/oneUnmapped.bam bedtools2/test/intersect/chromOrderA.bed bedtools2/test/intersect/bed6.bed bedtools2/test/intersect/issue_773_b.bed bedtools2/test/intersect/new_test-intersect.sh bedtools2/test/intersect/chromsOutOfOrder.bed bedtools2/test/intersect/jim.bed bedtools2/test/intersect/three_blocks_nomatch.bed bedtools2/test/intersect/b_vcfSVtest.vcf bedtools2/test/intersect/bug223_f.vcf bedtools2/test/intersect/a.issue311.bed bedtools2/test/intersect/three_blocks.sam bedtools2/test/intersect/gdc_exp bedtools2/test/intersect/bug44_b.bed bedtools2/test/intersect/bug223_d.vcf bedtools2/test/intersect/bug223_e.vcf bedtools2/test/intersect/a_testZeroLen.bed bedtools2/test/intersect/a_bgzipped.bed.gz bedtools2/test/intersect/x.bed bedtools2/test/intersect/a_withLargeHeader_bgzipped.bed.gz bedtools2/test/intersect/dosLineChar_a.bed bedtools2/test/intersect/bug44_a.vcf.gz bedtools2/test/intersect/b.cram bedtools2/test/intersect/y.bed bedtools2/test/intersect/test-intersect.sh bedtools2/test/intersect/a_vcfSVtest.vcf bedtools2/test/intersect/blocks.bed12 bedtools2/test/intersect/recordsOutOfOrder.bed bedtools2/test/intersect/a.bed bedtools2/test/intersect/jim.vcf bedtools2/test/intersect/c.bed bedtools2/test/intersect/three_blocks_match.bam bedtools2/test/intersect/dosLineCharWithExtraTab_b.bed bedtools2/test/intersect/a.cram bedtools2/test/intersect/b.bed bedtools2/test/intersect/two_blocks_partial.bam.bai bedtools2/test/intersect/foo bedtools2/test/intersect/split.issue750.bam bedtools2/test/intersect/mapped_and_unmapped.sam bedtools2/test/intersect/two_blocks_partial.bam bedtools2/test/intersect/e.bed bedtools2/test/intersect/a_withLargeHeader_gzipped.bed.gz bedtools2/test/intersect/svlen.vcf bedtools2/test/intersect/d.bed bedtools2/test/intersect/splitBug155_a.bed bedtools2/test/intersect/multi_intersect/ bedtools2/test/intersect/notexthdr.bam bedtools2/test/intersect/large_b.bed bedtools2/test/intersect/nonamecheck_a.bed bedtools2/test/intersect/issue_773_y.bed bedtools2/test/intersect/sortAndNaming/ bedtools2/test/intersect/split.issue750.sam bedtools2/test/intersect/a_gzipped.bed.gz bedtools2/test/intersect/splitBug155_b.bed bedtools2/test/intersect/bug167_strandSweep.bed bedtools2/test/intersect/large_a.bed bedtools2/test/intersect/nonamecheck_b.bed bedtools2/test/intersect/b.issue311.gff bedtools2/test/intersect/two_blocks_partial.bed bedtools2/test/intersect/three_blocks_match.bed bedtools2/test/intersect/human.hg19.genome bedtools2/test/intersect/bug187_a.bed bedtools2/test/intersect/strand_with_star.b.bed bedtools2/test/intersect/b_testZeroLen.bed bedtools2/test/intersect/one_block.sam bedtools2/test/intersect/bug187_b.bed bedtools2/test/intersect/three_blocks_match_1bp.bed bedtools2/test/intersect/strand_with_star.a.bed bedtools2/test/intersect/aVSb.bam bedtools2/test/intersect/a.bam bedtools2/test/intersect/sortAndNaming/num_all.bed bedtools2/test/intersect/sortAndNaming/diffs.txt bedtools2/test/intersect/sortAndNaming/db1_noChr.bed bedtools2/test/intersect/sortAndNaming/alpha_all.bed bedtools2/test/intersect/sortAndNaming/test-sort-and-naming.sh bedtools2/test/intersect/sortAndNaming/exp1 bedtools2/test/intersect/sortAndNaming/q1_gls.bed bedtools2/test/intersect/sortAndNaming/db1_num.bed bedtools2/test/intersect/sortAndNaming/db2_numBackwards.bed bedtools2/test/intersect/sortAndNaming/num_missing.bed bedtools2/test/intersect/sortAndNaming/q1_num.bed bedtools2/test/intersect/sortAndNaming/db2_num.bed bedtools2/test/intersect/sortAndNaming/db1_leadingZero.txt bedtools2/test/intersect/sortAndNaming/sq1.bed bedtools2/test/intersect/sortAndNaming/db1_gls.bed bedtools2/test/intersect/sortAndNaming/alpha_missing.bed bedtools2/test/intersect/sortAndNaming/bigTests/ bedtools2/test/intersect/sortAndNaming/sdb1.bed bedtools2/test/intersect/sortAndNaming/db3_numBackwards.bed bedtools2/test/intersect/sortAndNaming/q1a_num.bed bedtools2/test/intersect/sortAndNaming/bigTests/curr5v5.txt bedtools2/test/intersect/sortAndNaming/bigTests/2.21_500Kvs500K.txt bedtools2/test/intersect/sortAndNaming/bigTests/q500K.bed bedtools2/test/intersect/sortAndNaming/bigTests/dbchr1.bed bedtools2/test/intersect/sortAndNaming/bigTests/2.21_chr1.txt bedtools2/test/intersect/sortAndNaming/bigTests/diffs.txt bedtools2/test/intersect/sortAndNaming/bigTests/curr500Kvs500K.txt bedtools2/test/intersect/sortAndNaming/bigTests/qchr1.bed bedtools2/test/intersect/sortAndNaming/bigTests/2.21_5v5.txt bedtools2/test/intersect/sortAndNaming/bigTests/currChr1.txt bedtools2/test/intersect/sortAndNaming/bigTests/db500K.bed bedtools2/test/intersect/multi_intersect/query3.bed bedtools2/test/intersect/multi_intersect/query2.bed bedtools2/test/intersect/multi_intersect/d8.bed bedtools2/test/intersect/multi_intersect/d9.bed bedtools2/test/intersect/multi_intersect/query.bed bedtools2/test/intersect/multi_intersect/g.bed bedtools2/test/intersect/multi_intersect/test-multi_intersect.sh bedtools2/test/intersect/multi_intersect/d4.bed bedtools2/test/intersect/multi_intersect/d5.bed bedtools2/test/intersect/multi_intersect/d7.bed bedtools2/test/intersect/multi_intersect/d6.bed bedtools2/test/intersect/multi_intersect/d2.bed bedtools2/test/intersect/multi_intersect/d3.bed bedtools2/test/intersect/multi_intersect/d1.bed bedtools2/test/complement/test-complement.sh bedtools2/test/complement/issue_503.genome bedtools2/test/complement/issue_503.bed bedtools2/test/fisher/test-fisher.sh bedtools2/test/fisher/sim.py bedtools2/test/fisher/plot.py bedtools2/test/fisher/cmp.sh bedtools2/test/fisher/dm6.fai bedtools2/test/fisher/t.60.genome bedtools2/test/fisher/get.sh bedtools2/test/fisher/README.md bedtools2/test/fisher/a.bed bedtools2/test/fisher/b.bed bedtools2/test/fisher/tumor.gff bedtools2/test/fisher/t.500.genome bedtools2/test/fisher/a_merge.bed bedtools2/test/fisher/shuf.sh bedtools2/test/fisher/test.bed bedtools2/test/shuffle/incl.sizedif.bed bedtools2/test/shuffle/test-shuffle.sh bedtools2/test/shuffle/excl.bed bedtools2/test/shuffle/simrep.bed bedtools2/test/shuffle/incl.bed bedtools2/test/expand/expand.txt bedtools2/test/expand/test-expand.sh bedtools2/test/cluster/in.bed bedtools2/test/cluster/test-cluster.sh bedtools2/test/bedtobam/test-bedtobam.sh bedtools2/test/bedtobam/chrsize.tmp bedtools2/test/split/test-split.sh bedtools2/test/split/randData.bed bedtools2/tutorial/answers.md bedtools2/tutorial/template.class.html bedtools2/tutorial/answers.html bedtools2/tutorial/bootstrap.css bedtools2/tutorial/Makefile bedtools2/tutorial/bedtools.html bedtools2/tutorial/bedtools.md bedtools2/tutorial/template.html Building BEDTools: ========================================================= CXXFLAGS is [-g -Wall -O2 -std=c++11 -O2 -march=i586 -mtune=i686] DETECTED_VERSION = v2.30.0 CURRENT_VERSION = Updating version file. * compiling src/bedtools.cpp * compiling src/annotateBed/annotateMain.cpp * compiling src/annotateBed/annotateBed.cpp * compiling src/bamToBed/bamToBed.cpp src/bamToBed/bamToBed.cpp: In function ‘int bamtobed_main(int, char**)’: src/bamToBed/bamToBed.cpp:88:10: warning: variable ‘useAlignmentScore’ set but not used [-Wunused-but-set-variable] 88 | bool useAlignmentScore = false; | ^~~~~~~~~~~~~~~~~ In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/bamToBed/bamToBed.cpp:12: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/bamToFastq/bamToFastqMain.cpp src/bamToFastq/bamToFastqMain.cpp: In function ‘int bamtofastq_main(int, char**)’: src/bamToFastq/bamToFastqMain.cpp:38:10: warning: variable ‘haveFastq2’ set but not used [-Wunused-but-set-variable] 38 | bool haveFastq2 = false; | ^~~~~~~~~~ * compiling src/bamToFastq/bamToFastq.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/bamToFastq/bamToFastq.h:15, from src/bamToFastq/bamToFastq.cpp:15: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/bedToBam/bedToBam.cpp src/bedToBam/bedToBam.cpp: In function ‘int bedtobam_main(int, char**)’: src/bedToBam/bedToBam.cpp:60:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable] 60 | bool haveMapQual = false; | ^~~~~~~~~~~ * compiling src/bedpeToBam/bedpeToBam.cpp src/bedpeToBam/bedpeToBam.cpp: In function ‘int bedpetobam_main(int, char**)’: src/bedpeToBam/bedpeToBam.cpp:61:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable] 61 | bool haveMapQual = false; | ^~~~~~~~~~~ * compiling src/bedToIgv/bedToIgv.cpp * compiling src/bed12ToBed6/bed12ToBed6.cpp * compiling src/closestFile/closestHelp.cpp * compiling src/closestFile/closestFile.cpp * compiling src/clusterBed/clusterMain.cpp src/clusterBed/clusterMain.cpp: In function ‘int cluster_main(int, char**)’: src/clusterBed/clusterMain.cpp:38:10: warning: variable ‘haveMaxDistance’ set but not used [-Wunused-but-set-variable] 38 | bool haveMaxDistance = false; | ^~~~~~~~~~~~~~~ * compiling src/clusterBed/clusterBed.cpp * compiling src/complementFile/complementHelp.cpp * compiling src/complementFile/complementFile.cpp * compiling src/coverageFile/coverageHelp.cpp * compiling src/coverageFile/coverageFile.cpp * compiling src/expand/expand.cpp * compiling src/fastaFromBed/fastaFromBedMain.cpp * compiling src/fastaFromBed/fastaFromBed.cpp * compiling src/flankBed/flankBedMain.cpp * compiling src/flankBed/flankBed.cpp * compiling src/genomeCoverageBed/genomeCoverageMain.cpp * compiling src/genomeCoverageBed/genomeCoverageBed.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/utils/GenomeFile/NewGenomeFile.h:20, from src/genomeCoverageBed/genomeCoverageBed.h:13, from src/genomeCoverageBed/genomeCoverageBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/getOverlap/getOverlap.cpp src/getOverlap/getOverlap.cpp: In function ‘int getoverlap_main(int, char**)’: src/getOverlap/getOverlap.cpp:44:10: warning: variable ‘haveColumns’ set but not used [-Wunused-but-set-variable] 44 | bool haveColumns = false; | ^~~~~~~~~~~ * compiling src/groupBy/groupByHelp.cpp * compiling src/groupBy/groupBy.cpp * compiling src/intersectFile/intersectHelp.cpp * compiling src/intersectFile/intersectFile.cpp * compiling src/fisher/fisherHelp.cpp * compiling src/fisher/fisher.cpp * compiling src/fisher/kfunc.cpp * compiling src/jaccard/jaccardHelp.cpp * compiling src/jaccard/jaccard.cpp * compiling src/linksBed/linksMain.cpp * compiling src/linksBed/linksBed.cpp * compiling src/maskFastaFromBed/maskFastaFromBedMain.cpp * compiling src/maskFastaFromBed/maskFastaFromBed.cpp * compiling src/mapFile/mapHelp.cpp * compiling src/mapFile/mapFile.cpp * compiling src/mergeFile/mergeHelp.cpp * compiling src/mergeFile/mergeFile.cpp * compiling src/multiBamCov/multiBamCovMain.cpp src/multiBamCov/multiBamCovMain.cpp: In function ‘int multibamcov_main(int, char**)’: src/multiBamCov/multiBamCovMain.cpp:38:10: warning: variable ‘haveBed’ set but not used [-Wunused-but-set-variable] 38 | bool haveBed = false; | ^~~~~~~ src/multiBamCov/multiBamCovMain.cpp:39:10: warning: variable ‘haveBams’ set but not used [-Wunused-but-set-variable] 39 | bool haveBams = false; | ^~~~~~~~ src/multiBamCov/multiBamCovMain.cpp:47:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] 47 | bool haveFraction = false; | ^~~~~~~~~~~~ * compiling src/multiBamCov/multiBamCov.cpp In file included from src/utils/BamTools/include/BamReader.hpp:4, from src/utils/BamTools/include/api/BamMultiReader.h:4, from src/multiBamCov/multiBamCov.h:16, from src/multiBamCov/multiBamCov.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/multiIntersectBed/multiIntersectBedMain.cpp src/multiIntersectBed/multiIntersectBedMain.cpp: In function ‘int multiintersect_main(int, char**)’: src/multiIntersectBed/multiIntersectBedMain.cpp:45:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable] 45 | bool haveFiles = false; | ^~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp:47:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable] 47 | bool haveGenome = false; | ^~~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable] 48 | bool haveFiller = true; | ^~~~~~~~~~ * compiling src/multiIntersectBed/multiIntersectBed.cpp * compiling src/nucBed/nucBedMain.cpp * compiling src/nucBed/nucBed.cpp * compiling src/pairToBed/pairToBedMain.cpp src/pairToBed/pairToBedMain.cpp: In function ‘int pairtobed_main(int, char**)’: src/pairToBed/pairToBedMain.cpp:43:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] 43 | bool haveFraction = false; | ^~~~~~~~~~~~ * compiling src/pairToBed/pairToBed.cpp src/pairToBed/pairToBed.cpp: In member function ‘void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const string&)’: src/pairToBed/pairToBed.cpp:257:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable] 257 | CHRPOS spanLength = 0; | ^~~~~~~~~~ src/pairToBed/pairToBed.cpp: In member function ‘bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)’: src/pairToBed/pairToBed.cpp:310:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable] 310 | CHRPOS spanLength = 0; | ^~~~~~~~~~ In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/pairToBed/pairToBed.h:15, from src/pairToBed/pairToBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/pairToPair/pairToPairMain.cpp src/pairToPair/pairToPairMain.cpp: In function ‘int pairtopair_main(int, char**)’: src/pairToPair/pairToPairMain.cpp:44:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] 44 | bool haveFraction = false; | ^~~~~~~~~~~~ * compiling src/pairToPair/pairToPair.cpp src/pairToPair/pairToPair.cpp: In member function ‘void PairToPair::FindOverlaps(const BEDPE&)’: src/pairToPair/pairToPair.cpp:112:14: warning: variable ‘found1’ set but not used [-Wunused-but-set-variable] 112 | bool found1 = false; | ^~~~~~ src/pairToPair/pairToPair.cpp:113:14: warning: variable ‘found2’ set but not used [-Wunused-but-set-variable] 113 | bool found2 = false; | ^~~~~~ * compiling src/randomBed/randomBedMain.cpp * compiling src/randomBed/randomBed.cpp * compiling src/regressTest/regressTestMain.cpp * compiling src/regressTest/RegressTest.cpp * compiling src/reldist/reldistMain.cpp * compiling src/reldist/reldist.cpp src/reldist/reldist.cpp: In member function ‘void RelativeDistance::ReportDistanceSummary()’: src/reldist/reldist.cpp:69:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘unsigned int’ [-Wformat=] 69 | printf("%.2f\t%lu\t%lu\t%.3lf\n", | ~~^ | | | long unsigned int | %u 70 | freqItr->first, 71 | freqItr->second, | ~~~~~~~~~~~~~~~ | | | unsigned int src/reldist/reldist.cpp:69:30: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 69 | printf("%.2f\t%lu\t%lu\t%.3lf\n", | ~~^ | | | long unsigned int | %u ...... 72 | _tot_queries, | ~~~~~~~~~~~~ | | | size_t {aka unsigned int} * compiling src/sampleFile/sampleHelp.cpp * compiling src/sampleFile/sampleFile.cpp * compiling src/shiftBed/shiftBedMain.cpp * compiling src/shiftBed/shiftBed.cpp * compiling src/shuffleBed/shuffleBedMain.cpp * compiling src/shuffleBed/shuffleBed.cpp * compiling src/slopBed/slopBedMain.cpp * compiling src/slopBed/slopBed.cpp * compiling src/sortBed/sortMain.cpp * compiling src/sortBed/sortBed.cpp * compiling src/spacingFile/spacingHelp.cpp * compiling src/spacingFile/spacingFile.cpp * compiling src/split/splitBedMain.cpp * compiling src/split/splitBed.cpp * compiling src/subtractFile/subtractHelp.cpp * compiling src/subtractFile/subtractFile.cpp * compiling src/summaryFile/summaryHelp.cpp * compiling src/summaryFile/summaryFile.cpp * compiling src/tagBam/tagBamMain.cpp * compiling src/tagBam/tagBam.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/tagBam/tagBam.h:17, from src/tagBam/tagBam.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/unionBedGraphs/unionBedGraphsMain.cpp src/unionBedGraphs/unionBedGraphsMain.cpp: In function ‘int unionbedgraphs_main(int, char**)’: src/unionBedGraphs/unionBedGraphsMain.cpp:46:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable] 46 | bool haveFiles = false; | ^~~~~~~~~ src/unionBedGraphs/unionBedGraphsMain.cpp:48:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable] 48 | bool haveGenome = false; | ^~~~~~~~~~ src/unionBedGraphs/unionBedGraphsMain.cpp:49:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable] 49 | bool haveFiller = true; | ^~~~~~~~~~ * compiling src/unionBedGraphs/unionBedGraphs.cpp * compiling src/windowBed/windowMain.cpp * compiling src/windowBed/windowBed.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/windowBed/windowBed.h:15, from src/windowBed/windowBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/windowMaker/windowMakerMain.cpp * compiling src/windowMaker/windowMaker.cpp * compiling src/utils/FileRecordTools/FileRecordMgr.cpp * compiling src/utils/FileRecordTools/FileRecordMergeMgr.cpp * compiling src/utils/FileRecordTools/FileReaders/FileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/BamFileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function ‘bool BufferedStreamMgr::readFileChunk()’: src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:148:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 148 | if (_mainBufCurrLen < _useBufSize) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:14, from src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:8: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/utils/FileRecordTools/Records/Record.cpp * compiling src/utils/FileRecordTools/Records/EmptyRecord.cpp * compiling src/utils/FileRecordTools/Records/Bed3Interval.cpp * compiling src/utils/FileRecordTools/Records/Bed4Interval.cpp * compiling src/utils/FileRecordTools/Records/BedGraphInterval.cpp * compiling src/utils/FileRecordTools/Records/Bed5Interval.cpp * compiling src/utils/FileRecordTools/Records/Bed6Interval.cpp * compiling src/utils/FileRecordTools/Records/PlusFields.cpp * compiling src/utils/FileRecordTools/Records/GffRecord.cpp * compiling src/utils/FileRecordTools/Records/GffPlusRecord.cpp * compiling src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp * compiling src/utils/FileRecordTools/Records/BedPlusInterval.cpp * compiling src/utils/FileRecordTools/Records/Bed12Interval.cpp * compiling src/utils/FileRecordTools/Records/BamRecord.cpp * compiling src/utils/FileRecordTools/Records/VcfRecord.cpp * compiling src/utils/FileRecordTools/Records/BlockMgr.cpp src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function ‘int BlockMgr::getNonRedundantOverlap()’: src/utils/FileRecordTools/Records/BlockMgr.cpp:194:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 194 | for (int i = 1; i < _overlapStarts.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/StrandQueue.cpp * compiling src/utils/FileRecordTools/Records/RecordMgr.cpp * compiling src/utils/FileRecordTools/Records/RecordList.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyList.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyVector.cpp * compiling src/utils/bedFile/bedFile.cpp * compiling src/utils/BinTree/BinTree.cpp * compiling src/utils/version/version.cpp * compiling src/utils/bedGraphFile/bedGraphFile.cpp * compiling src/utils/chromsweep/chromsweep.cpp * compiling src/utils/Contexts/ContextBase.cpp * compiling src/utils/Contexts/ContextIntersect.cpp * compiling src/utils/Contexts/ContextFisher.cpp * compiling src/utils/Contexts/ContextMap.cpp * compiling src/utils/Contexts/ContextSample.cpp * compiling src/utils/Contexts/ContextSpacing.cpp * compiling src/utils/Contexts/ContextMerge.cpp * compiling src/utils/Contexts/ContextJaccard.cpp * compiling src/utils/Contexts/ContextClosest.cpp * compiling src/utils/Contexts/ContextSubtract.cpp * compiling src/utils/Contexts/ContextCoverage.cpp * compiling src/utils/Contexts/ContextComplement.cpp * compiling src/utils/Contexts/ContextGroupBy.cpp * compiling src/utils/Contexts/ContextSummary.cpp * compiling src/utils/general/ParseTools.cpp * compiling src/utils/general/PushBackStreamBuf.cpp * compiling src/utils/general/CompressionTools.cpp * compiling src/utils/general/Tokenizer.cpp * compiling src/utils/general/CommonHelp.cpp * compiling src/utils/general/ErrorMsg.cpp * compiling src/utils/general/Random.cpp g++ -g -Wall -O2 -std=c++11 -O2 -march=i586 -mtune=i686 -Isrc/utils/gzstream -c -o obj/gzstream.o src/utils/gzstream/gzstream.C * compiling src/utils/fileType/fileType.cpp * compiling src/utils/fileType/FileRecordTypeChecker.cpp src/utils/fileType/FileRecordTypeChecker.cpp: In member function ‘bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)’: src/utils/fileType/FileRecordTypeChecker.cpp:366:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 366 | for (int j=0; j < len; j++) { | ~~^~~~~ * compiling src/utils/bedFilePE/bedFilePE.cpp * compiling src/utils/KeyListOps/KeyListOps.cpp * compiling src/utils/KeyListOps/KeyListOpsMethods.cpp * compiling src/utils/NewChromsweep/NewChromsweep.cpp * compiling src/utils/NewChromsweep/CloseSweep.cpp * compiling src/utils/sequenceUtilities/sequenceUtils.cpp * compiling src/utils/tabFile/tabFile.cpp * compiling src/utils/BamTools-Ancillary/BamAncillary.cpp * compiling src/utils/BlockedIntervals/BlockedIntervals.cpp * compiling src/utils/Fasta/Fasta.cpp * compiling src/utils/Fasta/split.cpp * compiling src/utils/VectorOps/VectorOps.cpp * compiling src/utils/GenomeFile/NewGenomeFile.cpp * compiling src/utils/GenomeFile/GenomeFile.cpp src/utils/GenomeFile/GenomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’: src/utils/GenomeFile/GenomeFile.cpp:60:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 60 | long c2; | ^~ * compiling src/utils/RecordOutputMgr/RecordOutputMgr.cpp src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function ‘void RecordOutputMgr::printClosest(RecordKeyVector&, const std::vector*)’: src/utils/RecordOutputMgr/RecordOutputMgr.cpp:170:56: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 170 | if (context->getNumClosestHitsWanted() > keyList.size()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function ‘void RecordOutputMgr::reportOverlapSummary(RecordKeyVector&)’: src/utils/RecordOutputMgr/RecordOutputMgr.cpp:455:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 455 | for (size_t i = 1; i < _context->getNumInputFiles(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling src/utils/ToolBase/ToolBase.cpp * compiling src/utils/driver/BedtoolsDriver.cpp cd src/utils/htslib && make config.h make[1]: Entering directory '/usr/src/slapt-src/academic/bedtools/bedtools2/src/utils/htslib' echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#ifndef __APPLE__' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#endif' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h echo '#define HAVE_DRAND48 1' >> config.h make[1]: Leaving directory '/usr/src/slapt-src/academic/bedtools/bedtools2/src/utils/htslib' cd src/utils/htslib && make lib-static make[1]: Entering directory '/usr/src/slapt-src/academic/bedtools/bedtools2/src/utils/htslib' gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -I. -c -o errmod.o errmod.c gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9"' > version.h gcc -g -Wall -O2 -I. -c -o hts.o hts.c hts.c: In function ‘hts_idx_init’: hts.c:1397:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 1397 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; | ^~~ gcc -g -Wall -O2 -I. -c -o hts_os.o hts_os.c gcc -g -Wall -O2 -I. -c -o md5.o md5.c gcc -g -Wall -O2 -I. -c -o multipart.o multipart.c gcc -g -Wall -O2 -I. -c -o probaln.o probaln.c gcc -g -Wall -O2 -I. -c -o realn.o realn.c gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c gcc -g -Wall -O2 -I. -c -o sam.o sam.c gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c gcc -g -Wall -O2 -I. -c -o textutils.o textutils.c gcc -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c: In function ‘cram_populate_ref’: cram/cram_io.c:2095:9: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2095 | strncpy(path, path2, PATH_MAX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘full_path’, inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3823:17: cram/cram_io.c:3748:13: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 3748 | strncpy(out, in, PATH_MAX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c: In function ‘cram_dopen’: cram/cram_io.c:4126:9: warning: ‘strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 4126 | strncpy(def->file_id, filename, 20); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c In function ‘string_ndup’, inlined from ‘string_dup’ at cram/string_alloc.c:143:12: cram/string_alloc.c:151:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 151 | strncpy(str, instr, len); | ^~~~~~~~~~~~~~~~~~~~~~~~ cram/string_alloc.c: In function ‘string_dup’: cram/string_alloc.c:143:12: note: length computed here 143 | return string_ndup(a_str, instr, strlen(instr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a make[1]: Leaving directory '/usr/src/slapt-src/academic/bedtools/bedtools2/src/utils/htslib' - Building main bedtools binary. done. - Creating executables for old CLI. done. * compiling src/htsutil.cpp 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/bedtools/bedtools-2.30.0-i586-1salix15.0.txz ./ install/ install/slack-desc usr/ usr/bin/ usr/bin/annotateBed usr/bin/bamToBed usr/bin/bamToFastq usr/bin/bed12ToBed6 usr/bin/bedToBam usr/bin/bedToIgv usr/bin/bedpeToBam usr/bin/bedtools usr/bin/closestBed usr/bin/clusterBed usr/bin/complementBed usr/bin/coverageBed usr/bin/expandCols usr/bin/fastaFromBed usr/bin/flankBed usr/bin/genomeCoverageBed usr/bin/getOverlap usr/bin/groupBy usr/bin/intersectBed usr/bin/linksBed usr/bin/mapBed usr/bin/maskFastaFromBed usr/bin/mergeBed usr/bin/multiBamCov usr/bin/multiIntersectBed usr/bin/nucBed usr/bin/pairToBed usr/bin/pairToPair usr/bin/randomBed usr/bin/shiftBed usr/bin/shuffleBed usr/bin/slopBed usr/bin/sortBed usr/bin/subtractBed usr/bin/tagBam usr/bin/unionBedGraphs usr/bin/windowBed usr/bin/windowMaker usr/doc/ usr/doc/bedtools-2.30.0/ usr/doc/bedtools-2.30.0/LICENSE usr/doc/bedtools-2.30.0/README.md usr/doc/bedtools-2.30.0/bedtools.SlackBuild usr/share/ usr/share/bedtools/ usr/share/bedtools/data/ usr/share/bedtools/data/aluY.chr1.bed.gz usr/share/bedtools/data/gerp.chr1.bed.gz usr/share/bedtools/data/knownGene.hg18.chr21.bed usr/share/bedtools/data/knownGene.hg18.chr21.short.bed usr/share/bedtools/data/refseq.chr1.exons.bed.gz usr/share/bedtools/data/simpleRepeats.chr1.bed.gz usr/share/bedtools/genomes/ usr/share/bedtools/genomes/human.hg18.genome usr/share/bedtools/genomes/human.hg19.genome usr/share/bedtools/genomes/human.hg38.genome usr/share/bedtools/genomes/mouse.mm10.genome usr/share/bedtools/genomes/mouse.mm8.genome usr/share/bedtools/genomes/mouse.mm9.genome usr/share/bedtools/scripts/ usr/share/bedtools/scripts/makeBashScripts.py usr/share/bedtools/scripts/vcfsort.sh Slackware package /usr/src/slapt-src/academic/bedtools/bedtools-2.30.0-i586-1salix15.0.txz created. Installing package bedtools-2.30.0-i586-1salix15.0... | bedtools (A powerful toolset for genome arithmetic) | | The bedtools utilities are a swiss-army knife of tools for a | wide-range of genomics analysis tasks. The most widely-used | tools enable genome arithmetic: that is, set theory on the | genome. | | Home: http://bedtools.readthedocs.org/ | | | | |