Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
Clusterer< T >::clusterRepresents a cluster
Clusterer< T >Generic class to cluster objects that are 'close by'
ReferenceGenome::LociStats::DifferenceA difference in this locus
DuplicateCounterVery simple duplicate count estimator using a simple hash. Also provides statistics
FASTQMappingPosition of a FastQRead that is mapped here, and how (reverse complemented or with an indel, and where)
FastQReadRepresents a FastQRead. Can be reversed or not
FASTQReaderReads 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
GeneAnnotationA Gene annotation
GeneAnnotationReaderProvides GeneAnnotation objects as read from a GFF3 file
GenomeLocusMappingList of all FASTQMapping s that map to a locus, plus coverage statistic
ReferenceGenome::LociStatsStatistics for a locus
ReferenceGenome::MatchDescriptorDescribes how a FastQRead (not mentioned) matches to the reference (straight or in reverse), and what the matching score is
qtallyKeeps a tally of correct and incorrect mappings
ReferenceGenomeRepresents a reference genome to be aligned against
SAMWriterWrite SAM files, with support for paired-end read mappings
Search16SA class to match reads to a 16S database
StereoFASTQReaderReads FASTQs from two (synchronised) files at a time. Does magic with 64 bits offsets to encode which of the two FASTQReader to read from
UnmatchedA region with little coverage
VarMeanEstimatorRapid estimator of variance and mean of a series of doubles
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