ChromatogramParam-class	ChromatogramParam-class
chromatogram_overwrite	chromatogram_overwrite
chromatogram_plotly	chromatogram_plotly
generateReport	generateReport
generateReportSA	generateReportSA-methods
generateReportSA,SangerAlignment-method	SangerAlignment-class-generateReportSA
generateReportSC	generateReportSC-methods
generateReportSC,SangerContig-method	SangerContig-class-generateReportSC
generateReportSR	generateReportSR-methods
generateReportSR,SangerRead-method	SangerRead-class-generateReportSR
globalTrimApp	globalTrimApp
launchApp	launchApp
launchAppSA	launchAppSA-methods
launchAppSA,SangerAlignment-method	SangerAlignment-class-launchAppSA
launchAppSC	launchAppSC-methods
launchAppSC,SangerContig-method	SangerContig-class-launchAppSC
MakeBaseCalls	MakeBaseCalls-methods
MakeBaseCalls,SangerRead-method	SangerRead-class-MakeBaseCalls
ObjectResults-class	ObjectResults-class
primaryAASeqS1	primaryAASeqS1-methods
primaryAASeqS1,SangerRead-method	primaryAASeqS1-methods
primaryAASeqS2	primaryAASeqS2-methods
primaryAASeqS2,SangerRead-method	primaryAASeqS2-methods
primaryAASeqS3	primaryAASeqS3-methods
primaryAASeqS3,SangerRead-method	primaryAASeqS3-methods
qualityBasePlot	qualityBasePlot-methods
qualityBasePlot,QualityReport-method	QualityReport-class-qualityBasePlot
qualityBasePlot,SangerRead-method	SangerRead-class-qualityBasePlot
QualityReport-class	QualityReport-class
QualityReport-class-qualityBasePlot	QualityReport-class-qualityBasePlot
QualityReport-class-updateQualityParam	QualityReport-class-updateQualityParam
qualityReportData	qualityReportData
readTable	readTable-methods
readTable,SangerContig-method	SangerContig-class-readTable
readTable,SangerRead-method	SangerRead-class-readTable
SangerAlignment	SangerAlignment
SangerAlignment-class	SangerAlignment-class
SangerAlignment-class-generateReportSA	SangerAlignment-class-generateReportSA
SangerAlignment-class-launchAppSA	SangerAlignment-class-launchAppSA
SangerAlignment-class-updateQualityParam	SangerAlignment-class-updateQualityParam
SangerAlignment-class-writeFastaSA	SangerAlignment-class-writeFastaSA
sangerAlignmentData	sangerAlignmentData
sangeranalyseR	sangeranalyseR
SangerContig	SangerContig
SangerContig-class	SangerContig-class
SangerContig-class-generateReportSC	SangerContig-class-generateReportSC
SangerContig-class-launchAppSC	SangerContig-class-launchAppSC
SangerContig-class-readTable	SangerContig-class-readTable
SangerContig-class-updateQualityParam	SangerContig-class-updateQualityParam
SangerContig-class-writeFastaSC	SangerContig-class-writeFastaSC
sangerContigData	sangerContigData
SangerRead	SangerRead
SangerRead-class	SangerRead-class
SangerRead-class-generateReportSR	SangerRead-class-generateReportSR
SangerRead-class-MakeBaseCalls	SangerRead-class-MakeBaseCalls
SangerRead-class-qualityBasePlot	SangerRead-class-qualityBasePlot
SangerRead-class-readTable	SangerRead-class-readTable
SangerRead-class-updateQualityParam	SangerRead-class-updateQualityParam
SangerRead-class-writeFastaSR	SangerRead-class-writeFastaSR
sangerReadFData	sangerReadFData
updateQualityParam	updateQualityParam-methods
updateQualityParam,QualityReport-method	QualityReport-class-updateQualityParam
updateQualityParam,SangerAlignment-method	SangerAlignment-class-updateQualityParam
updateQualityParam,SangerContig-method	SangerContig-class-updateQualityParam
updateQualityParam,SangerRead-method	SangerRead-class-updateQualityParam
writeFasta	writeFasta
writeFastaSA	writeFastaSA-methods
writeFastaSA,SangerAlignment-method	SangerAlignment-class-writeFastaSA
writeFastaSC	writeFastaSC-methods
writeFastaSC,SangerContig-method	SangerContig-class-writeFastaSC
writeFastaSR	writeFastaSR-methods
writeFastaSR,SangerRead-method	SangerRead-class-writeFastaSR
