BamFile                 Maintain SAM and BAM files
BamViews                Views into a set of BAM files
BcfFile                 Manipulate BCF or VCF 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 VCF / BCF files
TabixFile               Manipulate tabix indexed tab-delimited files.
applyPileups            Create summary pile-up statistics across
                        multiple BAM files.
bgzipTabix              File compression for tabix (bgzip) and fasta
                        (razip) files.
headerTabix             Retrieve sequence names defined in a tabix
                        file.
indexFa                 Operations on indexed 'fasta' files.
indexTabix              Compress and index tabix-compatible files.
readBamGappedAlignments
                        Reading GappedAlignments or GappedReads objects
                        from a BAM file
readPileup              Import samtools 'pileup' files.
scanBam                 Import, count, index, and other operations on
                        'BAM' (binary alignment) files.
scanBcfHeader           Operations on 'VCF' or 'BCF' (variant call)
                        files.
scanTabix               Operations on 'tabix' (indexed, tab-delimited)
                        files.
seqnamesTabix           Retrieve sequence names defined in a tabix
                        file.
yieldTabix              Yield records from a stream of records
                        contained in a tabix file.
