- c -

• coverage : GenomeLocusMapping

- d -

• d_aCount : ReferenceGenome
• d_cCount : ReferenceGenome
• d_clusters : Clusterer< T >
• d_correctMappings : ReferenceGenome
• d_fastqs : GenomeLocusMapping
• d_gcMappings : ReferenceGenome
• d_gCount : ReferenceGenome
• d_header : FastQRead
• d_insertCounts : ReferenceGenome
• d_kmerMappings : ReferenceGenome
• d_locimap : ReferenceGenome
• d_mapping : ReferenceGenome
• d_members : Clusterer< T >::cluster
• d_name : ReferenceGenome
• d_nucleotides : FastQRead
• d_quality : FastQRead
• d_taMappings : ReferenceGenome
• d_tCount : ReferenceGenome
• d_unmRegions : ReferenceGenome
• d_wrongMappings : ReferenceGenome

- h -

• headOrTail : ReferenceGenome::LociStats::Difference
• hits : Entry16S

- i -

• id : Entry16S
• incorrect : qtally
• indel : FASTQMapping

- l -

• left : Unmatched

- n -

• name : GeneAnnotation
• nucleotide : ReferenceGenome::LociStats::Difference

- p -

• pos : FASTQMapping , Unmatched , ReferenceGenome::MatchDescriptor
• position : FastQRead

- q -

• quality : ReferenceGenome::LociStats::Difference

- r -

• reverse : FASTQMapping , ReferenceGenome::MatchDescriptor
• reversed : FastQRead
• right : Unmatched

- s -

• samples : ReferenceGenome::LociStats
• score : ReferenceGenome::MatchDescriptor
• startPos : GeneAnnotation
• stopPos : GeneAnnotation
• strand : GeneAnnotation

- t -

• tag : GeneAnnotation
• type : GeneAnnotation

- u -

• unmatched : Unmatched