R-GenomicAlignments-1.28.0-2.fc35

Date	Author	Change
2021-07-21	Fedora Release Engineering <releng at fedoraproject dot org> - 1.28.0-2	- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
2021-06-17	Tom Callaway <spot at fedoraproject dot org> - 1.28.0-1	- update to 1.28.0 - Rebuilt for R 4.1.0
2021-02-04	Tom Callaway <spot at fedoraproject dot org> - 1.26.0-1	- update to 1.26.0
2021-01-25	Fedora Release Engineering <releng at fedoraproject dot org> - 1.22.1-4	- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
2020-07-27	Fedora Release Engineering <releng at fedoraproject dot org> - 1.22.1-3	- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
2020-07-04	José Abílio Matos <jamatos at fc dot up dot pt> - 1.22.1-2	- rebuild for R 4
2020-02-01	Tom Callaway <spot at fedoraproject dot org> - 1.22.1-1	- update to 1.22.1
2020-01-28	Fedora Release Engineering <releng at fedoraproject dot org> - 1.22.0-3	- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
2019-11-21	Elliott Sales de Andrade <quantum dot analyst at gmail dot com> - 1.22.0-2	- Exclude Suggests for unavailable packages
2019-11-06	Tom Callaway <spot at fedoraproject dot org> - 1.22.0-1	- update to 1.22.0

usr/
- lib/
  - .build-id/
    - 20/
      - 1adff1f141348e1c80c896f3323d2579c24116
- lib64/
  - R/
    - library/
      - GenomicAlignments/
        
        CITATION
        
        DESCRIPTION
        
        INDEX
        
        Meta/
        
        Rd.rds
        
        features.rds
        
        hsearch.rds
        
        links.rds
        
        nsInfo.rds
        
        package.rds
        
        vignette.rds
        
        NAMESPACE
        
        NEWS
        
        R/
        
        GenomicAlignments
        
        GenomicAlignments.rdb
        
        GenomicAlignments.rdx
        
        doc/
        
        GenomicAlignmentsIntroduction.R
        
        GenomicAlignmentsIntroduction.Rnw
        
        GenomicAlignmentsIntroduction.pdf
        
        OverlapEncodings.R
        
        OverlapEncodings.Rnw
        
        OverlapEncodings.pdf
        
        WorkingWithAlignedNucleotides.R
        
        WorkingWithAlignedNucleotides.Rnw
        
        WorkingWithAlignedNucleotides.pdf
        
        index.html
        
        summarizeOverlaps.R
        
        summarizeOverlaps.Rnw
        
        summarizeOverlaps.pdf
        
        extdata/
        
        sm_treated1.bam
        
        sm_untreated1.bam
        
        help/
        
        AnIndex
        
        CIGAR_OPS.html
        
        GAlignmentPairs-class.html
        
        GAlignmentPairs.html
        
        GAlignments-class.html
        
        GAlignments.html
        
        GAlignmentsList-class.html
        
        GAlignmentsList.html
        
        GappedReads-class.html
        
        GappedReads.html
        
        GenomicAlignments.rdb
        
        GenomicAlignments.rdx
        
        IntersectionNotEmpty.html
        
        IntersectionStrict.html
        
        Lencoding.html
        
        Lnjunc.html
        
        Loffset,OverlapEncodings-method.html
        
        Loffset.html
        
        NATURAL_INTRON_MOTIFS.html
        
        OverlapEncodings-class.html
        
        OverlapEncodings.html
        
        Rencoding.html
        
        Rnjunc.html
        
        Roffset,OverlapEncodings-method.html
        
        Roffset.html
        
        Union.html
        
        [[,GAlignmentPairs,ANY,ANY-method.html
        
        aliases.rds
        
        alphabetFrequencyFromBam.html
        
        as.data.frame,GAlignmentPairs-method.html
        
        as.data.frame,GAlignments-method.html
        
        as.data.frame,OverlapEncodings-method.html
        
        as.data.frame.OverlapEncodings.html
        
        bindROWS,GAlignmentPairs-method.html
        
        bindROWS,GAlignments-method.html
        
        c,GappedReads-method.html
        
        cigar,GAlignments-method.html
        
        cigar,GAlignmentsList-method.html
        
        cigar-utils.html
        
        cigar.html
        
        cigarNarrow.html
        
        cigarOpTable.html
        
        cigarQNarrow.html
        
        cigarRangesAlongPairwiseSpace.html
        
        cigarRangesAlongQuerySpace.html
        
        cigarRangesAlongReferenceSpace.html
        
        cigarToRleList.html
        
        cigarWidthAlongPairwiseSpace.html
        
        cigarWidthAlongQuerySpace.html
        
        cigarWidthAlongReferenceSpace.html
        
        class:GAlignmentPairs.html
        
        class:GAlignments.html
        
        class:GAlignmentsList.html
        
        class:GappedReads.html
        
        class:OverlapEncodings.html
        
        coerce,GAlignmentPairs,DataFrame-method.html
        
        coerce,GAlignmentPairs,GAlignments-method.html
        
        coerce,GAlignmentPairs,GAlignmentsList-method.html
        
        coerce,GAlignmentPairs,GRanges-method.html
        
        coerce,GAlignmentPairs,GRangesList-method.html
        
        coerce,GAlignmentPairs,IntegerRanges-method.html
        
        coerce,GAlignments,DataFrame-method.html
        
        coerce,GAlignments,GRanges-method.html
        
        coerce,GAlignments,GRangesList-method.html
        
        coerce,GAlignments,IntegerRanges-method.html
        
        coerce,GAlignments,IntegerRangesList-method.html
        
        coerce,GAlignmentsList,GAlignmentPairs-method.html
        
        coerce,GAlignmentsList,GRanges-method.html
        
        coerce,GAlignmentsList,GRangesList-method.html
        
        coerce,GAlignmentsList,IntegerRanges-method.html
        
        coerce,GAlignmentsList,IntegerRangesList-method.html
        
        coerce,GenomicRanges,GAlignments-method.html
        
        coerce,list,GAlignmentsList-method.html
        
        coordinate-mapping-methods.html
        
        countCompatibleOverlaps.html
        
        countDumpedAlignments.html
        
        coverage,BamFile-method.html
        
        coverage,GAlignmentPairs-method.html
        
        coverage,GAlignments-method.html
        
        coverage,GAlignmentsList-method.html
        
        coverage,character-method.html
        
        coverage-methods.html
        
        coverage.html
        
        elementMetadata,GAlignmentsList-method.html
        
        elementMetadata<-,GAlignmentsList-method.html
        
        encodeOverlaps,GRangesList,GRangesList-method.html
        
        encodeOverlaps,IntegerRanges,IntegerRangesList-method.html
        
        encodeOverlaps,IntegerRangesList,IntegerRanges-method.html
        
        encodeOverlaps,IntegerRangesList,IntegerRangesList-method.html
        
        encodeOverlaps-methods.html
        
        encodeOverlaps.html
        
        encodeOverlaps1.html
        
        encoding,OverlapEncodings-method.html
        
        encodingHalves,OverlapEncodings-method.html
        
        encodingHalves,character-method.html
        
        encodingHalves,factor-method.html
        
        encodingHalves.html
        
        explodeCigarOpLengths.html
        
        explodeCigarOps.html
        
        extractAlignmentRangesOnReference.html
        
        extractQueryStartInTranscript.html
        
        extractSkippedExonRanks,OverlapEncodings-method.html
        
        extractSkippedExonRanks,character-method.html
        
        extractSkippedExonRanks,factor-method.html
        
        extractSkippedExonRanks.html
        
        extractSpannedExonRanks,OverlapEncodings-method.html
        
        extractSpannedExonRanks,character-method.html
        
        extractSpannedExonRanks,factor-method.html
        
        extractSpannedExonRanks.html
        
        extractSteppedExonRanks,OverlapEncodings-method.html
        
        extractSteppedExonRanks,character-method.html
        
        extractSteppedExonRanks,factor-method.html
        
        extractSteppedExonRanks.html
        
        findCompatibleOverlaps,GAlignmentPairs,GRangesList-method.html
        
        findCompatibleOverlaps,GAlignments,GRangesList-method.html
        
        findCompatibleOverlaps-methods.html
        
        findCompatibleOverlaps.html
        
        findMateAlignment.html
        
        findOverlaps,GAlignmentPairs,GAlignmentPairs-method.html
        
        findOverlaps,GAlignmentPairs,Vector-method.html
        
        findOverlaps,GAlignments,GAlignments-method.html
        
        findOverlaps,GAlignments,Vector-method.html
        
        findOverlaps,GAlignmentsList,GAlignmentsList-method.html
        
        findOverlaps,GAlignmentsList,Vector-method.html
        
        findOverlaps,Vector,GAlignmentPairs-method.html
        
        findOverlaps,Vector,GAlignments-method.html
        
        findOverlaps,Vector,GAlignmentsList-method.html
        
        findOverlaps-methods.html
        
        findOverlaps.html
        
        findSpliceOverlaps,BamFile,ANY-method.html
        
        findSpliceOverlaps,GAlignmentPairs,GRangesList-method.html
        
        findSpliceOverlaps,GAlignments,GRangesList-method.html
        
        findSpliceOverlaps,GRangesList,GRangesList-method.html
        
        findSpliceOverlaps,character,ANY-method.html
        
        findSpliceOverlaps-methods.html
        
        findSpliceOverlaps.html
        
        first,GAlignmentPairs-method.html
        
        first.html
        
        flipQuery.html
        
        flippedQuery,OverlapEncodings-method.html
        
        flippedQuery.html
        
        flushDumpedAlignments.html
        
        getDumpedAlignments.html
        
        getListElement,GAlignments-method.html
        
        granges,GAlignmentPairs-method.html
        
        granges,GAlignments-method.html
        
        granges,GAlignmentsList-method.html
        
        grglist,GAlignmentPairs-method.html
        
        grglist,GAlignments-method.html
        
        grglist,GAlignmentsList-method.html
        
        intra-range-methods.html
        
        invertStrand,GAlignmentPairs-method.html
        
        is.unsorted,GAlignments-method.html
        
        isCompatibleWithSkippedExons,OverlapEncodings-method.html
        
        isCompatibleWithSkippedExons,character-method.html
        
        isCompatibleWithSkippedExons,factor-method.html
        
        isCompatibleWithSkippedExons.html
        
        isCompatibleWithSplicing,OverlapEncodings-method.html
        
        isCompatibleWithSplicing,character-method.html
        
        isCompatibleWithSplicing,factor-method.html
        
        isCompatibleWithSplicing.html
        
        isProperPair,GAlignmentPairs-method.html
        
        isProperPair.html
        
        junctions,GAlignmentPairs-method.html
        
        junctions,GAlignments-method.html
        
        junctions,GAlignmentsList-method.html
        
        junctions-methods.html
        
        junctions.html
        
        last,GAlignmentPairs-method.html
        
        last.html
        
        levels,OverlapEncodings-method.html
        
        levels.OverlapEncodings.html
        
        makeGAlignmentPairs.html
        
        mapFromAlignments,GenomicRanges,GAlignments-method.html
        
        mapFromAlignments,IntegerRanges,GAlignments-method.html
        
        mapFromAlignments.html
        
        mapToAlignments,GenomicRanges,GAlignments-method.html
        
        mapToAlignments,IntegerRanges,GAlignments-method.html
        
        mapToAlignments.html
        
        names,GAlignmentPairs-method.html
        
        names,GAlignments-method.html
        
        names,GAlignmentsList-method.html
        
        names<-,GAlignmentPairs-method.html
        
        names<-,GAlignments-method.html
        
        names<-,GAlignmentsList-method.html
        
        narrow,GappedReads-method.html
        
        njunc,ANY-method.html
        
        njunc,GAlignmentPairs-method.html
        
        njunc,GAlignments-method.html
        
        njunc,GAlignmentsList-method.html
        
        njunc.html
        
        order,GAlignments-method.html
        
        parallel_slot_names,GAlignmentPairs-method.html
        
        parallel_slot_names,GAlignments-method.html
        
        parallel_slot_names,OverlapEncodings-method.html
        
        paths.rds
        
        pcompare,GAlignments,GAlignments-method.html
        
        pileLettersAt.html
        
        pintersect,GAlignments,GRanges-method.html
        
        pintersect,GRanges,GAlignments-method.html
        
        pintersect.html
        
        pmapFromAlignments,GenomicRanges,GAlignments-method.html
        
        pmapFromAlignments,IntegerRanges,GAlignments-method.html
        
        pmapFromAlignments.html
        
        pmapToAlignments,GenomicRanges,GAlignments-method.html
        
        pmapToAlignments,IntegerRanges,GAlignments-method.html
        
        pmapToAlignments.html
        
        qnarrow,GAlignments-method.html
        
        qnarrow,GAlignmentsList-method.html
        
        qnarrow,GappedReads-method.html
        
        qnarrow.html
        
        qseq,GappedReads-method.html
        
        qseq.html
        
        queryLoc2refLoc.html
        
        queryLocs2refLocs.html
        
        qwidth,GAlignments-method.html
        
        qwidth,GAlignmentsList-method.html
        
        qwidth,GappedReads-method.html
        
        qwidth.html
        
        ranges,GAlignmentPairs-method.html
        
        ranges,GAlignments-method.html
        
        ranges,GAlignmentsList-method.html
        
        rank,GAlignments-method.html
        
        readGAlignmentPairs,BamFile-method.html
        
        readGAlignmentPairs,character-method.html
        
        readGAlignmentPairs.html
        
        readGAlignments,BamFile-method.html
        
        readGAlignments,BamViews-method.html
        
        readGAlignments,character-method.html
        
        readGAlignments.html
        
        readGAlignmentsList,BamFile-method.html
        
        readGAlignmentsList,character-method.html
        
        readGAlignmentsList.html
        
        readGappedReads,BamFile-method.html
        
        readGappedReads,character-method.html
        
        readGappedReads.html
        
        readSTARJunctions.html
        
        readTopHatJunctions.html
        
        relistToClass,GAlignments-method.html
        
        rglist,GAlignments-method.html
        
        rglist,GAlignmentsList-method.html
        
        rname,GAlignments-method.html
        
        rname,GAlignmentsList-method.html
        
        rname.html
        
        rname<-,GAlignments-method.html
        
        rname<-,GAlignmentsList-method.html
        
        rname<-.html
        
        second,GAlignmentPairs-method.html
        
        second.html
        
        selectEncodingWithCompatibleStrand.html
        
        seqinfo,GAlignmentPairs-method.html
        
        seqinfo,GAlignments-method.html
        
        seqinfo,GAlignmentsList-method.html
        
        seqinfo<-,GAlignmentPairs-method.html
        
        seqinfo<-,GAlignments-method.html
        
        seqinfo<-,GAlignmentsList-method.html
        
        seqlevelsInUse,GAlignmentPairs-method.html
        
        seqnames,GAlignmentPairs-method.html
        
        seqnames,GAlignments-method.html
        
        seqnames,GAlignmentsList-method.html
        
        seqnames<-,GAlignments-method.html
        
        seqnames<-,GAlignmentsList-method.html
        
        sequenceLayer.html
        
        setops-methods.html
        
        show,GAlignmentPairs-method.html
        
        show,GAlignments-method.html
        
        show,GAlignmentsList-method.html
        
        show,OverlapEncodings-method.html
        
        sort,GAlignments-method.html
        
        stackStringsFromBam.html
        
        stackStringsFromGAlignments.html
        
        start,GAlignments-method.html
        
        strand,GAlignmentPairs-method.html
        
        strand,GAlignments-method.html
        
        strand,GAlignmentsList-method.html
        
        strand<-,GAlignments,ANY-method.html
        
        strand<-,GAlignmentsList,character-method.html
        
        strand<-,GAlignmentsList-method.html
        
        strandMode,GAlignmentPairs-method.html
        
        strandMode.html
        
        strandMode<-,GAlignmentPairs-method.html
        
        strandMode<-.html
        
        summarizeJunctions.html
        
        summarizeOverlaps,BamViews,missing-method.html
        
        summarizeOverlaps,GRanges,BamFile-method.html
        
        summarizeOverlaps,GRanges,BamFileList-method.html
        
        summarizeOverlaps,GRanges,GAlignmentPairs-method.html
        
        summarizeOverlaps,GRanges,GAlignments-method.html
        
        summarizeOverlaps,GRanges,GAlignmentsList-method.html
        
        summarizeOverlaps,GRanges,GRanges-method.html
        
        summarizeOverlaps,GRanges,GRangesList-method.html
        
        summarizeOverlaps,GRanges,character-method.html
        
        summarizeOverlaps,GRangesList,BamFile-method.html
        
        summarizeOverlaps,GRangesList,BamFileList-method.html
        
        summarizeOverlaps,GRangesList,GAlignmentPairs-method.html
        
        summarizeOverlaps,GRangesList,GAlignments-method.html
        
        summarizeOverlaps,GRangesList,GAlignmentsList-method.html
        
        summarizeOverlaps,GRangesList,GRanges-method.html
        
        summarizeOverlaps,GRangesList,GRangesList-method.html
        
        summarizeOverlaps,GRangesList,character-method.html
        
        summarizeOverlaps-methods.html
        
        summarizeOverlaps.html
        
        unlist,GAlignmentPairs-method.html
        
        update,GAlignments-method.html
        
        updateObject,GAlignments-method.html
        
        validCigar.html
        
        width,GAlignments-method.html
        
        windows,GAlignments-method.html
        
        html/
        
        00Index.html
        
        GAlignmentPairs-class.html
        
        GAlignments-class.html
        
        GAlignmentsList-class.html
        
        GappedReads-class.html
        
        OverlapEncodings-class.html
        
        R.css
        
        cigar-utils.html
        
        coordinate-mapping-methods.html
        
        coverage-methods.html
        
        encodeOverlaps-methods.html
        
        findCompatibleOverlaps-methods.html
        
        findMateAlignment.html
        
        findOverlaps-methods.html
        
        findSpliceOverlaps-methods.html
        
        intra-range-methods.html
        
        junctions-methods.html
        
        pileLettersAt.html
        
        readGAlignments.html
        
        sequenceLayer.html
        
        setops-methods.html
        
        stackStringsFromGAlignments.html
        
        summarizeOverlaps-methods.html
        
        libs/
        
        GenomicAlignments.so
        
        unitTests/
        
        test_GAlignments-class.R
        
        test_GAlignmentsList-class.R
        
        test_cigar-utils.R
        
        test_coordinate-mapping-methods.R
        
        test_findSpliceOverlaps-methods.R
        
        test_intra-range-methods.R
        
        test_readGAlignmentPairs.R
        
        test_readGAlignments.R
        
        test_readGAlignmentsList.R
        
        test_summarizeOverlaps-methods.R

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