R-GenomicAlignments-1.32.1-6.fc40

Date	Author	Change
2024-01-22	Fedora Release Engineering <releng at fedoraproject dot org> - 1.32.1-6	- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
2024-01-19	Fedora Release Engineering <releng at fedoraproject dot org> - 1.32.1-5	- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
2023-07-19	Fedora Release Engineering <releng at fedoraproject dot org> - 1.32.1-4	- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
2023-04-21	Iñaki Úcar <iucar at fedoraproject dot org> - 1.32.1-3	- R-maint-sig mass rebuild
2023-01-18	Fedora Release Engineering <releng at fedoraproject dot org> - 1.32.1-2	- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
2022-09-03	Tom Callaway <spot at fedoraproject dot org> - 1.32.1-1	- update to 1.32.1 - rebuild for R 4.2.1
2022-07-20	Fedora Release Engineering <releng at fedoraproject dot org> - 1.28.0-4	- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild

usr/
- lib/
  - .build-id/
    - 69/
      - f54ce53702f7a8a5d3ce5cb769fa0ef1d73b21
- 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/
        
        +5B+5B+2CGAlignmentPairs+2CANY+2CANY-method.html
        
        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+2COverlapEncodings-method.html
        
        Loffset.html
        
        NATURAL_INTRON_MOTIFS.html
        
        OverlapEncodings-class.html
        
        OverlapEncodings.html
        
        Rencoding.html
        
        Rnjunc.html
        
        Roffset+2COverlapEncodings-method.html
        
        Roffset.html
        
        Union.html
        
        aliases.rds
        
        alphabetFrequencyFromBam.html
        
        as.data.frame+2CGAlignmentPairs-method.html
        
        as.data.frame+2CGAlignments-method.html
        
        as.data.frame+2COverlapEncodings-method.html
        
        as.data.frame.OverlapEncodings.html
        
        bindROWS+2CGAlignmentPairs-method.html
        
        bindROWS+2CGAlignments-method.html
        
        c+2CGappedReads-method.html
        
        cigar+2CGAlignments-method.html
        
        cigar+2CGAlignmentsList-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+3AGAlignmentPairs.html
        
        class+3AGAlignments.html
        
        class+3AGAlignmentsList.html
        
        class+3AGappedReads.html
        
        class+3AOverlapEncodings.html
        
        coerce+2CGAlignmentPairs+2CDataFrame-method.html
        
        coerce+2CGAlignmentPairs+2CGAlignments-method.html
        
        coerce+2CGAlignmentPairs+2CGAlignmentsList-method.html
        
        coerce+2CGAlignmentPairs+2CGRanges-method.html
        
        coerce+2CGAlignmentPairs+2CGRangesList-method.html
        
        coerce+2CGAlignmentPairs+2CIntegerRanges-method.html
        
        coerce+2CGAlignments+2CDataFrame-method.html
        
        coerce+2CGAlignments+2CGRanges-method.html
        
        coerce+2CGAlignments+2CGRangesList-method.html
        
        coerce+2CGAlignments+2CIntegerRanges-method.html
        
        coerce+2CGAlignments+2CIntegerRangesList-method.html
        
        coerce+2CGAlignmentsList+2CGAlignmentPairs-method.html
        
        coerce+2CGAlignmentsList+2CGRanges-method.html
        
        coerce+2CGAlignmentsList+2CGRangesList-method.html
        
        coerce+2CGAlignmentsList+2CIntegerRanges-method.html
        
        coerce+2CGAlignmentsList+2CIntegerRangesList-method.html
        
        coerce+2CGenomicRanges+2CGAlignments-method.html
        
        coerce+2Clist+2CGAlignmentsList-method.html
        
        coordinate-mapping-methods.html
        
        countCompatibleOverlaps.html
        
        countDumpedAlignments.html
        
        coverage+2CBamFile-method.html
        
        coverage+2CGAlignmentPairs-method.html
        
        coverage+2CGAlignments-method.html
        
        coverage+2CGAlignmentsList-method.html
        
        coverage+2Ccharacter-method.html
        
        coverage-methods.html
        
        coverage.html
        
        elementMetadata+2CGAlignmentsList-method.html
        
        elementMetadata+3C-+2CGAlignmentsList-method.html
        
        encodeOverlaps+2CGRangesList+2CGRangesList-method.html
        
        encodeOverlaps+2CIntegerRanges+2CIntegerRangesList-method.html
        
        encodeOverlaps+2CIntegerRangesList+2CIntegerRanges-method.html
        
        encodeOverlaps+2CIntegerRangesList+2CIntegerRangesList-method.html
        
        encodeOverlaps-methods.html
        
        encodeOverlaps.html
        
        encodeOverlaps1.html
        
        encoding+2COverlapEncodings-method.html
        
        encodingHalves+2COverlapEncodings-method.html
        
        encodingHalves+2Ccharacter-method.html
        
        encodingHalves+2Cfactor-method.html
        
        encodingHalves.html
        
        explodeCigarOpLengths.html
        
        explodeCigarOps.html
        
        extractAlignmentRangesOnReference.html
        
        extractQueryStartInTranscript.html
        
        extractSkippedExonRanks+2COverlapEncodings-method.html
        
        extractSkippedExonRanks+2Ccharacter-method.html
        
        extractSkippedExonRanks+2Cfactor-method.html
        
        extractSkippedExonRanks.html
        
        extractSpannedExonRanks+2COverlapEncodings-method.html
        
        extractSpannedExonRanks+2Ccharacter-method.html
        
        extractSpannedExonRanks+2Cfactor-method.html
        
        extractSpannedExonRanks.html
        
        extractSteppedExonRanks+2COverlapEncodings-method.html
        
        extractSteppedExonRanks+2Ccharacter-method.html
        
        extractSteppedExonRanks+2Cfactor-method.html
        
        extractSteppedExonRanks.html
        
        findCompatibleOverlaps+2CGAlignmentPairs+2CGRangesList-method.html
        
        findCompatibleOverlaps+2CGAlignments+2CGRangesList-method.html
        
        findCompatibleOverlaps-methods.html
        
        findCompatibleOverlaps.html
        
        findMateAlignment.html
        
        findOverlaps+2CGAlignmentPairs+2CGAlignmentPairs-method.html
        
        findOverlaps+2CGAlignmentPairs+2CVector-method.html
        
        findOverlaps+2CGAlignments+2CGAlignments-method.html
        
        findOverlaps+2CGAlignments+2CVector-method.html
        
        findOverlaps+2CGAlignmentsList+2CGAlignmentsList-method.html
        
        findOverlaps+2CGAlignmentsList+2CVector-method.html
        
        findOverlaps+2CVector+2CGAlignmentPairs-method.html
        
        findOverlaps+2CVector+2CGAlignments-method.html
        
        findOverlaps+2CVector+2CGAlignmentsList-method.html
        
        findOverlaps-methods.html
        
        findOverlaps.html
        
        findSpliceOverlaps+2CBamFile+2CANY-method.html
        
        findSpliceOverlaps+2CGAlignmentPairs+2CGRangesList-method.html
        
        findSpliceOverlaps+2CGAlignments+2CGRangesList-method.html
        
        findSpliceOverlaps+2CGRangesList+2CGRangesList-method.html
        
        findSpliceOverlaps+2Ccharacter+2CANY-method.html
        
        findSpliceOverlaps-methods.html
        
        findSpliceOverlaps.html
        
        first+2CGAlignmentPairs-method.html
        
        first.html
        
        flipQuery.html
        
        flippedQuery+2COverlapEncodings-method.html
        
        flippedQuery.html
        
        flushDumpedAlignments.html
        
        getDumpedAlignments.html
        
        getListElement+2CGAlignments-method.html
        
        granges+2CGAlignmentPairs-method.html
        
        granges+2CGAlignments-method.html
        
        granges+2CGAlignmentsList-method.html
        
        grglist+2CGAlignmentPairs-method.html
        
        grglist+2CGAlignments-method.html
        
        grglist+2CGAlignmentsList-method.html
        
        intra-range-methods.html
        
        invertStrand+2CGAlignmentPairs-method.html
        
        is.unsorted+2CGAlignments-method.html
        
        isCompatibleWithSkippedExons+2COverlapEncodings-method.html
        
        isCompatibleWithSkippedExons+2Ccharacter-method.html
        
        isCompatibleWithSkippedExons+2Cfactor-method.html
        
        isCompatibleWithSkippedExons.html
        
        isCompatibleWithSplicing+2COverlapEncodings-method.html
        
        isCompatibleWithSplicing+2Ccharacter-method.html
        
        isCompatibleWithSplicing+2Cfactor-method.html
        
        isCompatibleWithSplicing.html
        
        isProperPair+2CGAlignmentPairs-method.html
        
        isProperPair.html
        
        junctions+2CGAlignmentPairs-method.html
        
        junctions+2CGAlignments-method.html
        
        junctions+2CGAlignmentsList-method.html
        
        junctions-methods.html
        
        junctions.html
        
        last+2CGAlignmentPairs-method.html
        
        last.html
        
        levels+2COverlapEncodings-method.html
        
        levels.OverlapEncodings.html
        
        makeGAlignmentPairs.html
        
        mapFromAlignments+2CGenomicRanges+2CGAlignments-method.html
        
        mapFromAlignments+2CIntegerRanges+2CGAlignments-method.html
        
        mapFromAlignments.html
        
        mapToAlignments+2CGenomicRanges+2CGAlignments-method.html
        
        mapToAlignments+2CIntegerRanges+2CGAlignments-method.html
        
        mapToAlignments.html
        
        names+2CGAlignmentPairs-method.html
        
        names+2CGAlignments-method.html
        
        names+2CGAlignmentsList-method.html
        
        names+3C-+2CGAlignmentPairs-method.html
        
        names+3C-+2CGAlignments-method.html
        
        names+3C-+2CGAlignmentsList-method.html
        
        narrow+2CGappedReads-method.html
        
        njunc+2CANY-method.html
        
        njunc+2CGAlignmentPairs-method.html
        
        njunc+2CGAlignments-method.html
        
        njunc+2CGAlignmentsList-method.html
        
        njunc.html
        
        order+2CGAlignments-method.html
        
        parallel_slot_names+2CGAlignmentPairs-method.html
        
        parallel_slot_names+2CGAlignments-method.html
        
        parallel_slot_names+2COverlapEncodings-method.html
        
        paths.rds
        
        pcompare+2CGAlignments+2CGAlignments-method.html
        
        pileLettersAt.html
        
        pintersect+2CGAlignments+2CGRanges-method.html
        
        pintersect+2CGRanges+2CGAlignments-method.html
        
        pintersect.html
        
        pmapFromAlignments+2CGenomicRanges+2CGAlignments-method.html
        
        pmapFromAlignments+2CIntegerRanges+2CGAlignments-method.html
        
        pmapFromAlignments.html
        
        pmapToAlignments+2CGenomicRanges+2CGAlignments-method.html
        
        pmapToAlignments+2CIntegerRanges+2CGAlignments-method.html
        
        pmapToAlignments.html
        
        qnarrow+2CGAlignments-method.html
        
        qnarrow+2CGAlignmentsList-method.html
        
        qnarrow+2CGappedReads-method.html
        
        qnarrow.html
        
        qseq+2CGappedReads-method.html
        
        qseq.html
        
        queryLoc2refLoc.html
        
        queryLocs2refLocs.html
        
        qwidth+2CGAlignments-method.html
        
        qwidth+2CGAlignmentsList-method.html
        
        qwidth+2CGappedReads-method.html
        
        qwidth.html
        
        ranges+2CGAlignmentPairs-method.html
        
        ranges+2CGAlignments-method.html
        
        ranges+2CGAlignmentsList-method.html
        
        rank+2CGAlignments-method.html
        
        readGAlignmentPairs+2CBamFile-method.html
        
        readGAlignmentPairs+2Ccharacter-method.html
        
        readGAlignmentPairs.html
        
        readGAlignments+2CBamFile-method.html
        
        readGAlignments+2CBamViews-method.html
        
        readGAlignments+2Ccharacter-method.html
        
        readGAlignments.html
        
        readGAlignmentsList+2CBamFile-method.html
        
        readGAlignmentsList+2Ccharacter-method.html
        
        readGAlignmentsList.html
        
        readGappedReads+2CBamFile-method.html
        
        readGappedReads+2Ccharacter-method.html
        
        readGappedReads.html
        
        readSTARJunctions.html
        
        readTopHatJunctions.html
        
        relistToClass+2CGAlignments-method.html
        
        rglist+2CGAlignments-method.html
        
        rglist+2CGAlignmentsList-method.html
        
        rname+2CGAlignments-method.html
        
        rname+2CGAlignmentsList-method.html
        
        rname+3C-+2CGAlignments-method.html
        
        rname+3C-+2CGAlignmentsList-method.html
        
        rname+3C-.html
        
        rname.html
        
        second+2CGAlignmentPairs-method.html
        
        second.html
        
        selectEncodingWithCompatibleStrand.html
        
        seqinfo+2CGAlignmentPairs-method.html
        
        seqinfo+2CGAlignments-method.html
        
        seqinfo+2CGAlignmentsList-method.html
        
        seqinfo+3C-+2CGAlignmentPairs-method.html
        
        seqinfo+3C-+2CGAlignments-method.html
        
        seqinfo+3C-+2CGAlignmentsList-method.html
        
        seqlevelsInUse+2CGAlignmentPairs-method.html
        
        seqnames+2CGAlignmentPairs-method.html
        
        seqnames+2CGAlignments-method.html
        
        seqnames+2CGAlignmentsList-method.html
        
        seqnames+3C-+2CGAlignments-method.html
        
        seqnames+3C-+2CGAlignmentsList-method.html
        
        sequenceLayer.html
        
        setops-methods.html
        
        show+2CGAlignmentPairs-method.html
        
        show+2CGAlignments-method.html
        
        show+2CGAlignmentsList-method.html
        
        show+2COverlapEncodings-method.html
        
        sort+2CGAlignments-method.html
        
        stackStringsFromBam.html
        
        stackStringsFromGAlignments.html
        
        start+2CGAlignments-method.html
        
        strand+2CGAlignmentPairs-method.html
        
        strand+2CGAlignments-method.html
        
        strand+2CGAlignmentsList-method.html
        
        strand+3C-+2CGAlignments+2CANY-method.html
        
        strand+3C-+2CGAlignmentsList+2Ccharacter-method.html
        
        strand+3C-+2CGAlignmentsList-method.html
        
        strandMode+2CGAlignmentPairs-method.html
        
        strandMode+3C-+2CGAlignmentPairs-method.html
        
        strandMode+3C-.html
        
        strandMode.html
        
        summarizeJunctions.html
        
        summarizeOverlaps+2CBamViews+2Cmissing-method.html
        
        summarizeOverlaps+2CGRanges+2CBamFile-method.html
        
        summarizeOverlaps+2CGRanges+2CBamFileList-method.html
        
        summarizeOverlaps+2CGRanges+2CGAlignmentPairs-method.html
        
        summarizeOverlaps+2CGRanges+2CGAlignments-method.html
        
        summarizeOverlaps+2CGRanges+2CGAlignmentsList-method.html
        
        summarizeOverlaps+2CGRanges+2CGRanges-method.html
        
        summarizeOverlaps+2CGRanges+2CGRangesList-method.html
        
        summarizeOverlaps+2CGRanges+2Ccharacter-method.html
        
        summarizeOverlaps+2CGRangesList+2CBamFile-method.html
        
        summarizeOverlaps+2CGRangesList+2CBamFileList-method.html
        
        summarizeOverlaps+2CGRangesList+2CGAlignmentPairs-method.html
        
        summarizeOverlaps+2CGRangesList+2CGAlignments-method.html
        
        summarizeOverlaps+2CGRangesList+2CGAlignmentsList-method.html
        
        summarizeOverlaps+2CGRangesList+2CGRanges-method.html
        
        summarizeOverlaps+2CGRangesList+2CGRangesList-method.html
        
        summarizeOverlaps+2CGRangesList+2Ccharacter-method.html
        
        summarizeOverlaps-methods.html
        
        summarizeOverlaps.html
        
        unlist+2CGAlignmentPairs-method.html
        
        update+2CGAlignments-method.html
        
        updateObject+2CGAlignmentPairs-method.html
        
        updateObject+2CGAlignments-method.html
        
        validCigar.html
        
        width+2CGAlignments-method.html
        
        windows+2CGAlignments-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

R-GenomicAlignments-1.32.1-6.fc40 in Fedora Rawhide

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