Here is a list of all documented functions with links to the class documentation for each member:

- a -

• addRemaps() : isaSpace::BAMfile
• addSecondaryAlignment() : isaSpace::BAMrecord
• at() : isaSpace::ExonGroup

- b -

• BAMfile() : isaSpace::BAMfile
• BAMrecord() : isaSpace::BAMrecord
• BAMsafeReader() : isaSpace::BAMsafeReader
• BAMtoGenome() : isaSpace::BAMtoGenome

- e -

• empty() : isaSpace::ExonGroup
• ExonGroup() : isaSpace::ExonGroup

- f -

• firstExonAfter() : isaSpace::ExonGroup
• firstExonLength() : isaSpace::ExonGroup
• firstExonSpan() : isaSpace::ExonGroup
• firstOverlappingExon() : isaSpace::ExonGroup

- g -

• geneName() : isaSpace::ExonGroup
• geneSpan() : isaSpace::ExonGroup
• getBestExonCoverageQuality() : isaSpace::ExonGroup
• getBestReferenceMatchStatus() : isaSpace::BAMrecord
• getBICdifference() : isaSpace::ReadMatchWindowBIC
• getCIGARstring() : isaSpace::BAMrecord
• getCIGARvector() : isaSpace::BAMrecord
• getExonCoverageQuality() : isaSpace::ExonGroup
• getFirstCIGAR() : isaSpace::BAMrecord
• getFirstIntronSpan() : isaSpace::ExonGroup
• getHeaderCopy() : isaSpace::BAMsafeReader
• getMapEnd() : isaSpace::BAMrecord
• getMapStart() : isaSpace::BAMrecord
• getmRNAstart() : isaSpace::BAMrecord
• getNextRecord() : isaSpace::BAMsafeReader
• getPoorlyMappedRegions() : isaSpace::BAMrecord
• getPrimaryAlignmentCount() : isaSpace::BAMfile
• getReadCentricMatchStatus() : isaSpace::BAMrecord
• getReadLength() : isaSpace::BAMrecord
• getReadName() : isaSpace::BAMrecord
• getReferenceName() : isaSpace::BAMrecord
• getSequenceAndQuality() : isaSpace::BAMrecord

- h -

• hasLocalSecondaryAlignments() : isaSpace::BAMrecord
• hasSecondaryAlignments() : isaSpace::BAMrecord

- i -

• isMapped() : isaSpace::BAMrecord
• isRevComp() : isaSpace::BAMrecord

- l -

• lastExonBefore() : isaSpace::ExonGroup
• lastOverlappingExon() : isaSpace::ExonGroup
• localReversedSecondaryAlignmentCount() : isaSpace::BAMrecord
• localSecondaryAlignmentCount() : isaSpace::BAMrecord

- n -

• nChromosomes() : isaSpace::BAMtoGenome
• nExons() : isaSpace::ExonGroup
• nExonSets() : isaSpace::BAMtoGenome

- o -

• operator()() : isaSpace::BAMheaderDeleter, isaSpace::BAMrecordDeleter, isaSpace::BGZFhandleDeleter
• operator=() : isaSpace::BAMfile, isaSpace::BAMrecord, isaSpace::BAMsafeReader, isaSpace::BAMtoGenome, isaSpace::ExonGroup, isaSpace::ReadMatchWindowBIC

- r -

• ReadMatchWindowBIC() : isaSpace::ReadMatchWindowBIC

- s -

• saveReadCoverageStats() : isaSpace::BAMtoGenome
• saveRemappedBAM() : isaSpace::BAMfile
• saveSortedRemappedBAM() : isaSpace::BAMfile
• saveUnmappedRegions() : isaSpace::BAMtoGenome
• secondaryAlignmentCount() : isaSpace::BAMrecord
• strand() : isaSpace::ExonGroup

- ~ -

• ~BAMfile() : isaSpace::BAMfile
• ~BAMrecord() : isaSpace::BAMrecord
• ~BAMsafeReader() : isaSpace::BAMsafeReader
• ~BAMtoGenome() : isaSpace::BAMtoGenome
• ~ExonGroup() : isaSpace::ExonGroup
• ~ReadMatchWindowBIC() : isaSpace::ReadMatchWindowBIC