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GenerateStatistics() :
SamFile
GenomeSequence() :
GenomeSequence
get0BasedAlignmentEnd() :
SamRecord
get0BasedMatePosition() :
SamRecord
get0BasedPosition() :
SamRecord
get0BasedUnclippedEnd() :
SamRecord
get0BasedUnclippedStart() :
SamRecord
get1BasedAlignmentEnd() :
SamRecord
get1BasedMatePosition() :
SamRecord
get1BasedPosition() :
SamRecord
get1BasedUnclippedEnd() :
SamRecord
get1BasedUnclippedStart() :
SamRecord
getAlignmentLength() :
SamRecord
GetBamIndex() :
SamFile
getBases() :
SequenceCoverageReader
getBin() :
SamRecord
getBlockSize() :
SamRecord
getChar() :
SamRecord
,
Cigar::CigarOperator
getCharTag() :
SamRecord
getChromosome() :
GenomeSequence
getChromosomeCount() :
GenomeSequence
getChromosomeSize() :
GenomeSequence
getChromosomeStart() :
GenomeSequence
getChunksForRegion() :
BamIndex
getCigar() :
SamRecord
getCigarInfo() :
SamRecord
getCigarLength() :
SamRecord
getCigarString() :
Cigar
GetCurrentPosition() :
SamFile
GetCurrentRecordCount() :
SamFile
getCurrentRecordCount() :
GlfFile
getDataPtr() :
GenomeSequence
getDouble() :
SamRecord
getDoubleTag() :
SamRecord
getExpandedString() :
Cigar
getExpectedQueryBaseCount() :
Cigar
getExpectedReferenceBaseCount() :
Cigar
GetFailure() :
SamFile
getFailure() :
GlfFile
getFields() :
SamRecord
getFileName() :
InputFile
getFlag() :
SamRecord
getGenomePosition() :
GenomeSequence
getHeaderTextString() :
GlfHeader
getIndel1() :
GlfRecord
getIndel2() :
GlfRecord
getInsertSize() :
SamRecord
getInteger() :
SamRecord
getIntegerTag() :
SamRecord
getLk() :
GlfRecord
getLkHet() :
GlfRecord
getLkHom1() :
GlfRecord
getLkHom2() :
GlfRecord
getMapQuality() :
SamRecord
getMatchPositionOffset() :
CigarRoller
getMateReferenceID() :
SamRecord
getMateReferenceName() :
SamRecord
getMateReferenceNameOrEqual() :
SamRecord
getMinDepth() :
GlfRecord
getMinLk() :
GlfRecord
getMismatchCount() :
GenomeSequence
getName() :
GlfRefSection
getNextMatchMismatch() :
SamQuerySeqWithRefIter
getNextRecord() :
GlfFile
getNextRefSection() :
GlfFile
getNextSamTag() :
SamRecord
getNumBeginClips() :
Cigar
getNumberBases() :
GenomeSequence
getNumEndClips() :
Cigar
getNumMappedReads() :
BamIndex
getNumMappedReadsFromIndex() :
SamFile
getNumOverlaps() :
SamRecord
,
Cigar
GetNumOverlaps() :
SamFile
getNumRefs() :
BamIndex
getNumUnMappedReads() :
BamIndex
getNumUnMappedReadsFromIndex() :
SamFile
getOffset() :
GlfRecord
getOperator() :
Cigar
getQualities() :
ReadInsertion
getQuality() :
SamRecord
getQueryIndex() :
SamSingleBaseMatchInfo
,
Cigar
getReadDepth() :
GlfRecord
getReadLength() :
SamRecord
getReadName() :
SamRecord
getReadNameLength() :
SamRecord
getRecordBuffer() :
SamRecord
getRecordType() :
GlfRecord
getRefBase() :
GlfRecord
getRefBaseChar() :
GlfRecord
getReference() :
SamRecord
getReferenceID() :
SamRecord
getReferenceMinMax() :
BamIndex
getReferenceName() :
SamRecord
getRefLen() :
GlfRefSection
getRefOffset() :
Cigar
getRefPosition() :
Cigar
getRmsMapQ() :
GlfRecord
getSequence() :
SamRecord
GetStatus() :
SamFile
getStatus() :
SamRecord
,
GlfFile
,
GlfStatus
getStatusMessage() :
GlfFile
GetStatusMessage() :
SamFile
getStatusMessage() :
GlfStatus
getStatusString() :
GlfStatus
getString() :
SamRecord
,
CigarRoller
getStringTag() :
SamRecord
getSumQ() :
GenomeSequence
getTagLength() :
SamRecord
getTagsString() :
SamRecord
getType() :
SamSingleBaseMatchInfo
GlfException() :
GlfException
GlfFile() :
GlfFile
GlfFileReader() :
GlfFileReader
GlfFileWriter() :
GlfFileWriter
GlfHeader() :
GlfHeader
GlfRecord() :
GlfRecord
GlfRefSection() :
GlfRefSection
GlfStatus() :
GlfStatus
Generated on Tue Aug 23 18:19:06 2011 for libStatGen Software by
1.6.3