Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

Clusterer< T >::cluster	Represents a cluster
Clusterer< T >	Generic class to cluster objects that are 'close by'
ReferenceGenome::LociStats::Difference	A difference in this locus
DuplicateCounter	Very simple duplicate count estimator using a simple hash. Also provides statistics
Entry16S
FASTQMapping	Position of a FastQRead that is mapped here, and how (reverse complemented or with an indel, and where)
FastQRead	Represents a FastQRead. Can be reversed or not
FASTQReader	Reads a single FASTQ file, and can seek in it. Does adapation of quality scores (Sanger by default) and and can also snip off first n or last n bases
GeneAnnotation	A Gene annotation
GeneAnnotationReader	Provides GeneAnnotation objects as read from a GFF3 file
GenomeLocusMapping	List of all FASTQMapping s that map to a locus, plus coverage statistic
ReferenceGenome::LociStats	Statistics for a locus
ReferenceGenome::MatchDescriptor	Describes how a FastQRead (not mentioned) matches to the reference (straight or in reverse), and what the matching score is
qtally	Keeps a tally of correct and incorrect mappings
ReferenceGenome	Represents a reference genome to be aligned against
SAMWriter	Write SAM files, with support for paired-end read mappings
Search16S	A class to match reads to a 16S database
StereoFASTQReader	Reads FASTQs from two (synchronised) files at a time. Does magic with 64 bits offsets to encode which of the two FASTQReader to read from
Unmatched	A region with little coverage
VarMeanEstimator	Rapid estimator of variance and mean of a series of doubles