R-Rsamtools-2.8.0-2.fc35 - Fedora Packages

Date	Author	Change
2021-07-21	Fedora Release Engineering <releng at fedoraproject dot org> - 2.8.0-2	- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
2021-06-16	Tom Callaway <spot at fedoraproject dot org> - 2.8.0-1	- update to 2.8.0 - Rebuilt for R 4.1.0
2021-02-04	Tom Callaway <spot at fedoraproject dot org> - 2.6.0-1	- update to 2.6.0
2021-01-25	Fedora Release Engineering <releng at fedoraproject dot org> - 2.4.0-3	- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
2020-07-27	Fedora Release Engineering <releng at fedoraproject dot org> - 2.4.0-2	- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
2020-06-08	Tom Callaway <spot at fedoraproject dot org> - 2.4.0-1	- update to 2.4.0 - rebuild for R 4
2020-02-05	Tom Callaway <spot at fedoraproject dot org> - 2.2.1-1	- update to 2.2.1
2020-01-28	Fedora Release Engineering <releng at fedoraproject dot org> - 2.0.3-3	- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
2019-11-21	Elliott Sales de Andrade <quantum dot analyst at gmail dot com> - 2.0.3-2	- Exclude Suggests for unavailable packages
2019-10-30	Tom Callaway <spot at fedoraproject dot org> - 2.0.3-1	- update to 2.03 (devel package dies off)

usr/
- lib/
  - .build-id/
    - eb/
      - 827eb062429d087398bf2c35fe230578dfe5b6
- lib64/
  - R/
    - library/
      - Rsamtools/
        
        DESCRIPTION
        
        INDEX
        
        LICENSE
        
        Meta/
        
        Rd.rds
        
        features.rds
        
        hsearch.rds
        
        links.rds
        
        nsInfo.rds
        
        package.rds
        
        vignette.rds
        
        NAMESPACE
        
        NEWS
        
        R/
        
        Rsamtools
        
        Rsamtools.rdb
        
        Rsamtools.rdx
        
        doc/
        
        Rsamtools-Overview.R
        
        Rsamtools-Overview.Rnw
        
        Rsamtools-Overview.pdf
        
        index.html
        
        extdata/
        
        ce2dict1.fa
        
        ce2dict1.fa.fai
        
        ex1.bam
        
        ex1.bam.bai
        
        ex1.bcf.gz
        
        ex1.bcf.gz.csi
        
        ex1.sam
        
        ex1.vcf.gz
        
        ex1.vcf.gz.csi
        
        example.gtf.gz
        
        example.gtf.gz.tbi
        
        example_from_SAM_Spec.bam
        
        example_from_SAM_Spec.bam.bai
        
        example_from_SAM_Spec.sam
        
        no_which_buffered_pileup.bam
        
        no_which_buffered_pileup.bam.bai
        
        no_which_buffered_pileup.sam
        
        no_which_whole_file.bam
        
        no_which_whole_file.bam.bai
        
        no_which_whole_file.sam
        
        olaps.Rda
        
        pileup.txt
        
        querybins.bam
        
        querybins.bam.bai
        
        querybins.sam
        
        revbins.bam
        
        revbins.bam.bai
        
        revbins.sam
        
        samtools-github.txt
        
        slxMaq09_urls.txt
        
        tagfilter.bam
        
        tagfilter.bam.bai
        
        tagfilter.sam
        
        tiny.bam
        
        tiny.bam.bai
        
        tiny.sam
        
        tophat/
        
        README
        
        accepted_hits.sam
        
        coverage.wig
        
        junctions.bed
        
        help/
        
        AnIndex
        
        ApplyPileupsParam-class.html
        
        ApplyPileupsParam.html
        
        BamFile-class.html
        
        BamFile.html
        
        BamFileList-class.html
        
        BamFileList.html
        
        BamSampler-class.html
        
        BamSampler.html
        
        BamViews,GRanges-method.html
        
        BamViews,missing-method.html
        
        BamViews-class.html
        
        BamViews.html
        
        BcfFile-class.html
        
        BcfFile.html
        
        BcfFileList-class.html
        
        BcfFileList.html
        
        FLAG_BITNAMES.html
        
        FaFile-class.html
        
        FaFile.html
        
        FaFileList-class.html
        
        FaFileList.html
        
        PileupFiles,character-method.html
        
        PileupFiles,list-method.html
        
        PileupFiles-class.html
        
        PileupFiles.html
        
        PileupParam-class.html
        
        PileupParam.html
        
        Rsamtools-package.html
        
        Rsamtools.html
        
        Rsamtools.rdb
        
        Rsamtools.rdx
        
        RsamtoolsFile-class.html
        
        RsamtoolsFile.html
        
        RsamtoolsFileList-class.html
        
        RsamtoolsFileList.html
        
        ScanBVcfParam-class.html
        
        ScanBamParam,ANY-method.html
        
        ScanBamParam,GRanges-method.html
        
        ScanBamParam,IntegerRangesList-method.html
        
        ScanBamParam,missing-method.html
        
        ScanBamParam-class.html
        
        ScanBamParam.html
        
        ScanBcfParam,GRanges-method.html
        
        ScanBcfParam,GRangesList-method.html
        
        ScanBcfParam,IntegerRangesList-method.html
        
        ScanBcfParam,missing-method.html
        
        ScanBcfParam-class.html
        
        ScanBcfParam.html
        
        TabixFile-class.html
        
        TabixFile.html
        
        TabixFileList-class.html
        
        TabixFileList.html
        
        [,BamViews,ANY,ANY-method.html
        
        [,BamViews,ANY,missing-method.html
        
        [,BamViews,missing,ANY-method.html
        
        aliases.rds
        
        applyPileups,PileupFiles,ApplyPileupsParam-method.html
        
        applyPileups,PileupFiles,missing-method.html
        
        applyPileups.html
        
        asBam,character-method.html
        
        asBam.html
        
        asBcf,character-method.html
        
        asBcf.html
        
        asMates,BamFile-method.html
        
        asMates,BamFileList-method.html
        
        asMates.html
        
        asMates<-,BamFile-method.html
        
        asMates<-,BamFileList-method.html
        
        asMates<-.html
        
        asSam,character-method.html
        
        asSam.html
        
        bamDirname<-.html
        
        bamExperiment.html
        
        bamFlag.html
        
        bamFlag<-.html
        
        bamFlagAND.html
        
        bamFlagAsBitMatrix.html
        
        bamFlagTest.html
        
        bamIndicies.html
        
        bamMapqFilter.html
        
        bamMapqFilter<-.html
        
        bamPaths.html
        
        bamRanges.html
        
        bamRanges<-.html
        
        bamReverseComplement.html
        
        bamReverseComplement<-.html
        
        bamSamples.html
        
        bamSamples<-.html
        
        bamSimpleCigar.html
        
        bamSimpleCigar<-.html
        
        bamTag.html
        
        bamTag<-.html
        
        bamTagFilter.html
        
        bamTagFilter<-.html
        
        bamWhat.html
        
        bamWhat<-.html
        
        bamWhich.html
        
        bamWhich<-,ScanBamParam,ANY-method.html
        
        bamWhich<-,ScanBamParam,GRanges-method.html
        
        bamWhich<-,ScanBamParam,IntegerRangesList-method.html
        
        bamWhich<-.html
        
        bcfFixed.html
        
        bcfGeno.html
        
        bcfInfo.html
        
        bcfMode.html
        
        bcfSamples.html
        
        bcfTrimEmpty.html
        
        bcfWhich.html
        
        bgzip.html
        
        bgzipTabix.html
        
        bzfile-class.html
        
        close.BamFile.html
        
        close.BcfFile .html
        
        close.FaFile .html
        
        close.RsamtoolsFileList.html
        
        close.TabixFile .html
        
        countBam,BamFile-method.html
        
        countBam,BamFileList-method.html
        
        countBam,BamViews-method.html
        
        countBam,character-method.html
        
        countBam.html
        
        countFa,FaFile-method.html
        
        countFa,character-method.html
        
        countFa.html
        
        countTabix.html
        
        cycle_bins.html
        
        defunct.html
        
        deprecated.html
        
        dim,BamViews-method.html
        
        dimnames,BamViews-method.html
        
        dimnames<-,BamViews,ANY-method.html
        
        dimnames<-,BamViews-method.html
        
        distinguish_nucleotides.html
        
        distinguish_strands.html
        
        fifo-class.html
        
        filterBam,BamFile-method.html
        
        filterBam,character-method.html
        
        filterBam.html
        
        getSeq,FaFile-method.html
        
        getSeq,FaFileList-method.html
        
        gzfile-class.html
        
        gzindex,FaFile-method.html
        
        gzindex,FaFileList-method.html
        
        gzindex.html
        
        gzindex<-,FaFile-method.html
        
        gzindex<-,FaFileList-method.html
        
        gzindex<-.html
        
        hasUnmappedMate.html
        
        headerTabix,TabixFile-method.html
        
        headerTabix,character-method.html
        
        headerTabix.html
        
        idxstatsBam,BamFile-method.html
        
        idxstatsBam,character-method.html
        
        idxstatsBam.html
        
        ignore_query_Ns.html
        
        include_deletions.html
        
        include_insertions.html
        
        index,RsamtoolsFile-method.html
        
        index,RsamtoolsFileList-method.html
        
        index.html
        
        index<-,RsamtoolsFile-method.html
        
        index<-,RsamtoolsFileList-method.html
        
        index<-.html
        
        indexBam,BamFile-method.html
        
        indexBam,character-method.html
        
        indexBam.html
        
        indexBcf,BcfFile-method.html
        
        indexBcf,character-method.html
        
        indexBcf.html
        
        indexFa,FaFile-method.html
        
        indexFa,character-method.html
        
        indexFa.html
        
        indexTabix.html
        
        isDuplicate.html
        
        isFirstMateRead.html
        
        isIncomplete,BamFile-method.html
        
        isMateMinusStrand.html
        
        isMinusStrand.html
        
        isNotPassingQualityControls.html
        
        isNotPrimaryRead.html
        
        isOpen,BamFile-method.html
        
        isOpen,BcfFile-method.html
        
        isOpen,FaFile-method.html
        
        isOpen,PileupFiles-method.html
        
        isOpen,RsamtoolsFile-method.html
        
        isOpen,RsamtoolsFileList-method.html
        
        isOpen,TabixFile-method.html
        
        isPaired.html
        
        isProperPair.html
        
        isSecondMateRead.html
        
        isSecondaryAlignment.html
        
        isUnmappedQuery.html
        
        left_bins.html
        
        max_depth.html
        
        mergeBam,BamFileList-method.html
        
        mergeBam,character-method.html
        
        mergeBam.html
        
        min_base_quality.html
        
        min_mapq.html
        
        min_minor_allele_depth.html
        
        min_nucleotide_depth.html
        
        names,BamViews-method.html
        
        names,RsamtoolsFileList-method.html
        
        names<-,BamViews-method.html
        
        obeyQname,BamFile-method.html
        
        obeyQname,BamFileList-method.html
        
        obeyQname.html
        
        obeyQname<-,BamFile-method.html
        
        obeyQname<-,BamFileList-method.html
        
        obeyQname<-.html
        
        open.BamFile.html
        
        open.BcfFile.html
        
        open.FaFile.html
        
        open.RsamtoolsFileList.html
        
        open.TabixFile.html
        
        path,RsamtoolsFile-method.html
        
        path,RsamtoolsFileList-method.html
        
        path.html
        
        paths.rds
        
        phred2ASCIIOffset.html
        
        pileup,BamFile-method.html
        
        pileup,character-method.html
        
        pileup.html
        
        pipe-class.html
        
        plpFiles.html
        
        plpFlag.html
        
        plpFlag<-.html
        
        plpMaxDepth.html
        
        plpMaxDepth<-.html
        
        plpMinBaseQuality.html
        
        plpMinBaseQuality<-.html
        
        plpMinDepth.html
        
        plpMinDepth<-.html
        
        plpMinMapQuality.html
        
        plpMinMapQuality<-.html
        
        plpParam.html
        
        plpWhat.html
        
        plpWhat<-.html
        
        plpWhich.html
        
        plpWhich<-.html
        
        plpYieldAll.html
        
        plpYieldAll<-.html
        
        plpYieldBy.html
        
        plpYieldBy<-.html
        
        plpYieldSize.html
        
        plpYieldSize<-.html
        
        qnamePrefixEnd,BamFile-method.html
        
        qnamePrefixEnd,BamFileList-method.html
        
        qnamePrefixEnd.html
        
        qnamePrefixEnd<-,BamFile-method.html
        
        qnamePrefixEnd<-,BamFileList-method.html
        
        qnamePrefixEnd<-.html
        
        qnameSuffixStart,BamFile-method.html
        
        qnameSuffixStart,BamFileList-method.html
        
        qnameSuffixStart.html
        
        qnameSuffixStart<-,BamFile-method.html
        
        qnameSuffixStart<-,BamFileList-method.html
        
        qnameSuffixStart<-.html
        
        query_bins.html
        
        quickBamCounts.html
        
        quickBamFlagSummary,BamFile-method.html
        
        quickBamFlagSummary,character-method.html
        
        quickBamFlagSummary,list-method.html
        
        quickBamFlagSummary.html
        
        quickCountBam.html
        
        razip.html
        
        readPileup,character-method.html
        
        readPileup,connection-method.html
        
        readPileup.html
        
        scanBam,BamFile-method.html
        
        scanBam,BamSampler-method.html
        
        scanBam,BamViews-method.html
        
        scanBam,character-method.html
        
        scanBam.html
        
        scanBamFlag.html
        
        scanBamHeader,BamFile-method.html
        
        scanBamHeader,character-method.html
        
        scanBamHeader.html
        
        scanBamWhat.html
        
        scanBcf,BcfFile-method.html
        
        scanBcf,character-method.html
        
        scanBcf.html
        
        scanBcfHeader,BcfFile-method.html
        
        scanBcfHeader,character-method.html
        
        scanBcfHeader.html
        
        scanFa,FaFile,GRanges-method.html
        
        scanFa,FaFile,IntegerRangesList-method.html
        
        scanFa,FaFile,missing-method.html
        
        scanFa,character,GRanges-method.html
        
        scanFa,character,IntegerRangesList-method.html
        
        scanFa,character,missing-method.html
        
        scanFa.html
        
        scanFaIndex,FaFile-method.html
        
        scanFaIndex,FaFileList-method.html
        
        scanFaIndex,character-method.html
        
        scanFaIndex.html
        
        scanTabix,TabixFile,GRanges-method.html
        
        scanTabix,TabixFile,IntegerRangesList-method.html
        
        scanTabix,TabixFile,missing-method.html
        
        scanTabix,character,ANY-method.html
        
        scanTabix,character,GRanges-method.html
        
        scanTabix,character,IntegerRangesList-method.html
        
        scanTabix,character,missing-method.html
        
        scanTabix.html
        
        seqinfo,BamFile-method.html
        
        seqinfo,BamFileList-method.html
        
        seqinfo,FaFile-method.html
        
        seqnamesTabix,TabixFile-method.html
        
        seqnamesTabix,character-method.html
        
        seqnamesTabix.html
        
        show,ApplyPileupsParam-method.html
        
        show,BamFile-method.html
        
        show,BamFileList-method.html
        
        show,BamSampler-method.html
        
        show,BamViews-method.html
        
        show,FaFile-method.html
        
        show,PileupFiles-method.html
        
        show,PileupParam-method.html
        
        show,RsamtoolsFile-method.html
        
        show,ScanBVcfParam-method.html
        
        show,ScanBamParam-method.html
        
        sortBam,BamFile-method.html
        
        sortBam,character-method.html
        
        sortBam.html
        
        testPairedEndBam,BamFile-method.html
        
        testPairedEndBam,character-method.html
        
        testPairedEndBam.html
        
        unz-class.html
        
        url-class.html
        
        yieldSize,RsamtoolsFile-method.html
        
        yieldSize,RsamtoolsFileList-method.html
        
        yieldSize.html
        
        yieldSize<-,RsamtoolsFile-method.html
        
        yieldSize<-,RsamtoolsFileList-method.html
        
        yieldSize<-.html
        
        yieldTabix,TabixFile-method.html
        
        yieldTabix.html
        
        zip.html
        
        html/
        
        00Index.html
        
        ApplyPileupsParam-class.html
        
        BamFile-class.html
        
        BamViews-class.html
        
        BcfFile-class.html
        
        FaFile-class.html
        
        PileupFiles-class.html
        
        R.css
        
        Rsamtools-package.html
        
        RsamtoolsFile-class.html
        
        RsamtoolsFileList-class.html
        
        ScanBamParam-class.html
        
        ScanBcfParam-class.html
        
        TabixFile-class.html
        
        applyPileups.html
        
        defunct.html
        
        deprecated.html
        
        headerTabix.html
        
        indexTabix.html
        
        pileup.html
        
        quickBamFlagSummary.html
        
        readPileup.html
        
        scanBam.html
        
        scanBcf.html
        
        scanFa.html
        
        scanTabix.html
        
        seqnamesTabix.html
        
        testPairedEndBam.html
        
        zip.html
        
        libs/
        
        Rsamtools.so
        
        scripts/
        
        BamViews-1000g.R
        
        features.R
        
        remote_test.R
        
        update-samtools.sh
        
        unitTests/
        
        cases/
        
        RNEXT.bam
        
        ex1.sam.gz
        
        ex1_noindex.bam
        
        ex1_shuf1000.bam
        
        ex1_shuf1000.bam.bai
        
        ex1_unsort.bam
        
        ex1_zero_index.bam.bai
        
        no_SAMPLE_header.vcf.gz
        
        no_header_line.vcf.gz
        
        pileup-no-stars.txt
        
        plp_refskip.bam
        
        plp_refskip.bam.bai
        
        test_BamFile.R
        
        test_BamViews.R
        
        test_BcfFile.R
        
        test_FaFile.R
        
        test_RsamtoolsFile.R
        
        test_TabixFile.R
        
        test_applyPileups.R
        
        test_asBam.R
        
        test_bam.R
        
        test_bam_count.R
        
        test_bam_header.R
        
        test_compression.R
        
        test_mapqfilter.R
        
        test_phred2ASCIIOffset.R
        
        test_pileup_nowhich.R
        
        test_pileup_querybins.R
        
        test_pileup_revbins.R
        
        test_pileup_single_range.R
        
        test_readPileup.R
        
        test_scanBamFlag.R
        
        test_sortBam_test.R
        
        test_tagfilter.R
        
        test_testPairedEndBam.R
        
        test_utilities.R

R-Rsamtools-2.8.0-2.fc35 in Fedora 35

Changelog

Dependencies

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Files