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.
Rsamtools-package       'samtools' aligned sequence utilities interface
RsamtoolsFile-class     A base class for managing file references in
                        Rsamtools
ScanBamParam            Parameters for scanning BAM files
ScanBcfParam-class      Parameters for scanning VCF / BCF files
indexFa                 Operations on indexed 'fasta' files.
readBamGappedAlignments
                        GappedAlignments objects
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.
