.QA-class               Virtual class for representing quality
                        assessment results
.SRUtil-class           ".SRUtil" and related classes
AlignedDataFrame        AlignedDataFrame constructor
AlignedDataFrame-class
                        "AlignedDataFrame" representing alignment
                        annotations as a data frame
AlignedRead             Construct objects of class "AlignedRead"
AlignedRead-class       "AlignedRead" class for aligned short reads
ExperimentPath-class    "ExperimentPath" class representing a file
                        hierarchy of data files
NumericQuality          Construct objects indicating read or alignment
                        quality
QualityScore-class      Quality scores for short reads and their
                        alignments
RochePath-class         "RochePath" class representing a Roche (454)
                        experiment location
RocheSet-class          Roche (454) experiment-wide data container
SRFilter-class          "SRFilter" for representing functions operating
                        on ShortRead objects
SRSet-class             A base class for Roche experiment-wide data
ShortRead-class         "ShortRead" class for short reads
ShortReadBase-package   Base classes and methods for high-throughput
                        short-read sequencing data.
ShortReadQ-class        "ShortReadQ" class for short reads and their
                        quality scores
SolexaExportQA-class    Quality assessment summaries from Solexa export
                        files
SolexaPath-class        "SolexaPath" class representing a standard
                        output file hierarchy
SolexaSet-class         "SolexaSet" coordinating Solexa output
                        locations with sample annotations
accessors               Accessors for ShortRead classes
alphabetByCycle         Summarize short read nucleotide or quality
                        scores by cycle
alphabetScore           Efficiently calculate the sum of quality
                        scoares across bases
clean                   Remove sequences with ambiguous nucleotides
                        from short read classes
countLines              Count lines in all (text) files in a directory
                        whose file name matches a pattern
deprecated              Deprecated and defunct functions
detail                  Show (display) detailed object content
pileup                  Calculate a pile-up representation of
                        short-read mappings
polyn                   Utilities for common, simple operations
qa                      Perform quality assessment on short reads
readAligned             Read aligned reads and their quality scores
                        into R representations
readBaseQuality         Read short reads and their quality scores into
                        R representations
readBfaToc              Get a list of the sequences in a Maq .bfa file
readFastq               Read FASTQ-formatted files into compact R
                        representations
readPrb                 Read Solexa prb files as fastq-style quality
                        scores
readXStringColumns      Read one or more columns into XStringSet (e.g.,
                        DNAStringSet) objects
report                  Summarize quality assessment results into a
                        report
srFilter                Functions for user-created and built-in
                        ShortRead filters
srapply                 Apply-like function for distribution across
                        MPI-based clusters.
srdistance              Edit distances between reads and a small number
                        of short references
srduplicated            Order, sort, and find duplicates in XStringSet
                        objects
tables                  Summarize XStringSet read frequencies
