Antonie
|
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 |