BamFile                 Maintain and use BAM files
BamSampler              Sample from a BAM files
BamViews                Views into a set of BAM files
BcfFile                 Manipulate BCF files.
FaFile                  Manipulate indexed fasta files.
PileupFiles             Represent BAM files for pileup summaries.
PileupParam             Parameters for creating pileups from BAM files
Rsamtools-package       'samtools' aligned sequence utilities interface
RsamtoolsFile-class     A base class for managing file references in
                        Rsamtools
RsamtoolsFileList       A base class for managing lists of Rsamtools
                        file references
ScanBamParam            Parameters for scanning BAM files
ScanBcfParam-class      Parameters for scanning BCF files
TabixFile               Manipulate tabix indexed tab-delimited files.
applyPileups            Create summary pile-up statistics across
                        multiple BAM files.
bgzip                   File compression for tabix (bgzip) and fasta
                        (razip) files.
findMateAlignment       Pairing the elements of a GAlignments object
headerTabix             Retrieve sequence names defined in a tabix
                        file.
indexFa                 Operations on indexed 'fasta' files.
indexTabix              Compress and index tabix-compatible files.
quickCountBam           Group the records of a BAM file based on their
                        flag bits and count the number of records in
                        each group
readGAlignmentsFromBam
                        Reading a GAlignments, GappedReads,
                        GAlignmentPairs, or GAlignmentsList object from
                        a BAM file
readPileup              Import samtools 'pileup' files.
scanBam                 Import, count, index, filter, sort, and merge
                        'BAM' (binary alignment) files.
scanBcfHeader           Operations on 'BCF' files.
scanTabix               Operations on 'tabix' (indexed, tab-delimited)
                        files.
seqnamesTabix           Retrieve sequence names defined in a tabix
                        file.
sequenceLayer           Lay read sequences alongside the reference
                        space, using their CIGARs
stackStringsFromBam     Stack the read sequences stored in a BAM file
                        on a region of interest
yieldTabix              Deprecated functions
