ApplyPileupsParam       Parameters for creating pileups from BAM files
BamFile                 Maintain and use BAM files
BamSampler              Deprecated functions
BamViews                Views into a set of BAM files
BcfFile                 Manipulate BCF files.
FaFile                  Manipulate indexed fasta files.
PileupFiles             Represent BAM files for pileup summaries.
Rsamtools-package       'samtools' aligned sequence utilities interface
RsamtoolsFile           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            Apply a user-provided function to calculate
                        pile-up statistics across multiple BAM files.
bgzip                   File compression for tabix (bgzip) and fasta
                        (razip) files. IMPORTANT NOTE: Starting with
                        Rsamtools 1.99.0 (Bioconductor 3.9), 'razip()'
                        is defunct. Please use 'bgzip()' instead.
headerTabix             Retrieve sequence names defined in a tabix
                        file.
indexFa                 Operations on indexed 'fasta' files.
indexTabix              Compress and index tabix-compatible files.
pileup                  Use filters and output formats to calculate
                        pile-up statistics for a BAM file.
quickBamFlagSummary     Group the records of a BAM file based on their
                        flag bits and count the number of records in
                        each group
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.
testPairedEndBam        Quickly test if a BAM file has paired end reads
