rSFFreader-package	rSFFreader-package
.sffValidity	rSFFreader-internals
.solveIRangeSEW	rSFFreader-internals
adapterClip	SffReads-class
adapterClip,SffReads-method	SffReads-class
adapterClip<-	SffReads-class
adapterClip<-,SffReads-method	SffReads-class
append,SffReads,SffReads,missing-method	SffReads-class
append,SffReadsQ,SffReadsQ,missing-method	SffReadsQ-class
availableClipModes	availableClipModes
class:SffHeader	SffHeader-class
class:SffReads	SffReads-class
class:SffReadsQ	SffReadsQ-class
clipMode	SffReads-class
clipMode,SffReads-method	SffReads-class
clipMode<-	SffReads-class
clipMode<-,SffReads-method	SffReads-class
customClip	SffReads-class
customClip,SffReads-method	SffReads-class
customClip<-	SffReads-class
customClip<-,SffReads-method	SffReads-class
detail,SffHeader-method	SffHeader-class
detail,SffReads-method	SffReads-class
detail,SffReadsQ-method	SffReadsQ-class
fullClip	SffReads-class
fullClip,SffReads-method	SffReads-class
header	SffHeader-class
header,SffHeader-method	SffHeader-class
id,SffReads-method	SffReads-class
length,SffReads-method	SffReads-class
load454SampleData	load454SampleData
loadIonSampleData	loadIonSampleData
name,SffReads-method	SffReads-class
names,SffReads-method	SffReads-class
names<-,SffReads,ANY-method	SffReads-class
quality	SffReadsQ-class
quality,ANY-method	SffReadsQ-class
qualityClip	SffReads-class
qualityClip,SffReads-method	SffReads-class
qualityClip<-	SffReads-class
qualityClip<-,SffReads-method	SffReads-class
rawClip	SffReads-class
rawClip,SffReads-method	SffReads-class
readSff	readsff
readSffGeometry	readsffgeometry
readSffHeader	readsffheader
rSFFreader	rSFFreader-package
SffHeader	SffHeader-class
SffHeader-class	SffHeader-class
SffReads	SffReads-class
SffReads-class	SffReads-class
SffReadsQ	SffReadsQ-class
SffReadsQ-class	SffReadsQ-class
show,SffHeader-method	SffHeader-class
show,SffReads-method	SffReads-class
solveSffSEW	SffReads-class
sread	SffReads-class
width,SffReads-method	SffReads-class
writeFasta,SffReads-method	SffReads-class
writeFastaQual	SffReadsQ-class
writeFastaQual,SffReadsQ-method	SffReadsQ-class
writeFastq,SffReadsQ,ANY-method	SffReadsQ-class
writePhredQual	SffReadsQ-class
writePhredQual,FastqQuality-method	SffReadsQ-class
writePhredQual,SffReadsQ-method	SffReadsQ-class
[,SffReads,ANY,ANY-method	SffReads-class
[,SffReads,ANY,missing-method	SffReads-class
[,SffReads,missing,ANY-method	SffReads-class
[,SffReads,missing,missing-method	SffReads-class
[,SffReadsQ,ANY,ANY-method	SffReadsQ-class
[,SffReadsQ,ANY,missing-method	SffReadsQ-class
[,SffReadsQ,missing,ANY-method	SffReadsQ-class
[,SffReadsQ,missing,missing-method	SffReadsQ-class
