GenomePartition-class   Class '"GenomePartition"': .
alignDepth-class        Class '"alignDepth"': Alignment depth
                        information from bamRange objects.
as.data.frame-methods   Conversion of bamRange or gapList into a
                        data.frame
bamAlign                bamAlign
bamAlign-class          Class '"bamAlign"': Representation of single
                        genomic alignments.
bamClose-methods        bamClose(bamReader), bamClose(bamWriter):
                        Closing of file connections.
bamCount                bamCount: Counting of CIGAR-OP items
bamCountAll             bamCountAll
bamGapList-class        Class '"bamGapList"'
bamHeader-class         Class '"bamHeader"': Representation of data
                        contained in the header section of BAM files.
bamHeaderText-class     Class '"bamHeader"': Textual representation of
                        header section of BAM files.
bamRange                bamRange(object, coordinates, complex=FALSE):
                        Function for reading of alignments in genomic
                        regions.
bamRange-class          Class '"bamRange"': Representation of genomic
                        alignments in defined regions.
bamReader               bamReader: Connection to BAM file for reading
                        access.
bamReader-class         Class '"bamReader"': Representation for file
                        connection to BAM file for reading access.
bamSave                 bamSave: Creation of a sorted copy of a BAM
                        file.
bamSort                 bamSort: Creation of a sorted copy of a BAM
                        file.
bamWriter               bamWriter: Opening a file connection to a BAM
                        file for writing access.
bamWriter-class         Class '"bamWriter"': Representation of a file
                        connection to a BAM file for writing access.
countNucs               Counting nucleotides in 'bamAlign' and
                        'bamRange'
countTextLines          countTextLines: Counting lines in text files.
createIdxBatch          createIdxBatch: Creation of index files for
                        multiple BAM files.
exonAlignDepth-class    Class '"exonAlignDepth"': Align-depth data for
                        single genes on multiple samples (BAM files).
                        Intronic regions are cut out of align depth
                        matrix.
exonLoessModel-class    Class '"exonLoessModel"': Align-depth data for
                        single genes on multiple samples (BAM files).
                        Intronic regions are cut out of align depth
                        matrix.
extractBamRegions       extractBamRegions: Extraction of alignments
                        from given (genetic) regions and BAM files into
                        a set of output BAM files..
extractGeneRegions      Extraction of alignments from given genetic
                        regions and BAM files into a set of output BAM
                        files.
extractRanges           extractRanges: Extraction of alignments
filename-methods        Reading 'filename' from bamReader or bamWriter
gapList-class           Class '"gapList"': Representation of genomic
                        alignment gaps.
gapSiteList-class       Class '"gapSiteList"': Representation of
                        genomic alignment gap positions.
geneAlignDepth-class    Class '"geneAlignDepth"': Align-depth data for
                        single genes on multiple samples (BAM files).
getHeaderText-methods   'getHeaderText' Assembling member data into
                        Header-Text
getNextAlign-methods    'getNextAlign': Retrieving next align from
                        bamReader or bamRange
getQualDf               Read and display Phred qualities from bamRange
getRefData              Retrieve reference sequence from a BAM file as
                        data.frame
getVal                  getVal(object,members): Retrieving values for
                        given types from an object
groupRatio              Calculates group-wise ratios of alignment depth
                        (AD)
headerLine-class        Class '"headerLine"': Representation of header
                        line segment of header section for BAM files.
headerProgram-class     Class '"headerProgram"': Represention of header
                        - program section of BAM header.
headerReadGroup-class   Class '"headerReadGroup"': Representation of
                        read - group data in header section of BAM
                        files
isOpen-methods          isOpen(bamReader), isOpen(bamWriter): Checking
                        for opened file connection to BAM file.
multSeq                 Create combined sequences of sequential
                        numbers.
nucStats                Table nucleotides in whole BAM file(s)
rangeSegCount-class     Class '"rangeSegCount"': Represents alignment
                        counts in segments of genetic regions.
rangeToFastq            rangeToFastq: Extract read information from
                        alignments for given genomic range as fastq.
rbamtools-package       Reading, writing and manipulating BAM-file
                        format.
readPooledBamGapDf      readPooledBamGapDf: Position data for
                        alignments gaps from multiple BAM files.
readPooledBamGaps       readPooledBamGaps: Position data for alignments
                        gaps from multiple BAM files.
readerToFastq           readerToFastq: Extraction of a subset of
                        alignments from a BAM files into fastq format.
refSeqDict-class        Class '"refSeqDict"': Repesentation of data
                        from reference sequence dictionary in BAM file
                        header.
sampleBamFiles-class    Class '"sampleBamFiles"': Data on multiple BAM
                        files from an experimental setting.
saveAldData             saveAldData: Save alignment depth plots for
                        single genes
segmentize              Segmentation of vector using segment
                        coordinates
setVal                  setVal(object,members,values): Setting values
                        for given data items
