ShortReadBase-package	ShortRead-package
!,SRFilterResult-method	SRFilterResult-class
%in%,AlignedRead,IntegerRangesList-method	AlignedRead-class
.QA-class	dotQA-class
.QA2-class	QA-class
.Roche-class	ShortRead-package
.ShortReadBase-class	ShortRead-package
.Solexa-class	ShortRead-package
.SRUtil-class	SRUtil-class
accessors	accessors
alignData	accessors
alignDataFilter	srFilter
AlignedDataFrame	AlignedDataFrame
AlignedDataFrame-class	AlignedDataFrame-class
AlignedRead	AlignedRead
AlignedRead-class	AlignedRead-class
alignQuality	accessors
alignQualityFilter	srFilter
alphabet,FastqQuality-method	QualityScore-class
alphabetByCycle	alphabetByCycle
alphabetByCycle,BStringSet-method	alphabetByCycle
alphabetByCycle,FastqQuality-method	QualityScore-class
alphabetByCycle,ShortRead-method	ShortRead-class
alphabetByCycle,ShortReadQ-method	ShortReadQ-class
alphabetFrequency,FastqQuality-method	QualityScore-class
alphabetScore	alphabetScore
alphabetScore,FastqQuality-method	QualityScore-class
alphabetScore,PhredQuality-method	QualityScore-class
alphabetScore,SFastqQuality-method	QualityScore-class
alphabetScore,ShortReadQ-method	ShortReadQ-class
analysisPath	accessors
annTrack	Snapshot-class
annTrack,Snapshot-method	Snapshot-class
append,.ShortReadBase,.ShortReadBase-method	ShortRead-package
append,AlignedDataFrame,AlignedDataFrame-method	AlignedDataFrame-class
append,AlignedRead,AlignedRead-method	AlignedRead-class
append,MatrixQuality,MatrixQuality-method	QualityScore-class
append,QualityScore,QualityScore-method	QualityScore-class
append,ShortRead,ShortRead-method	ShortRead-class
append,ShortReadQ,ShortReadQ-method	ShortReadQ-class
ArrayIntensity	Intensity-class
ArrayIntensity-class	Intensity-class
baseCallPath	accessors
basePath	deprecated
BowtieQA-class	BowtieQA-class
c,SRFilter-method	SRFilter-class
chromosome	accessors
chromosome,AlignedRead-method	AlignedRead-class
chromosomeFilter	srFilter
clean	clean
clean,DNAStringSet-method	clean
clean,ShortRead-method	ShortRead-class
close.ShortReadFile	Sampler-class
coerce,AlignedRead,GAlignments-method	AlignedRead-class
coerce,AlignedRead,GappedReads-method	AlignedRead-class
coerce,AlignedRead,GRanges-method	AlignedRead-class
coerce,AlignedRead,IntegerRangesList-method	AlignedRead-class
coerce,FastqQuality,matrix-method	QualityScore-class
coerce,FastqQuality,numeric-method	QualityScore-class
coerce,FastqQuality,PhredQuality-method	QualityScore-class
coerce,PairwiseAlignments,AlignedRead-method	AlignedRead-class
coerce,SFastqQuality,matrix-method	QualityScore-class
coerce,SFastqQuality,SolexaQuality-method	QualityScore-class
coerce,ShortRead,DNAStringSet-method	ShortRead-class
coerce,ShortReadQ,QualityScaledDNAStringSet-method	ShortReadQ-class
coerce,SRFilter,FilterRules-method	SRFilter-class
compose	srFilter
countFastq	readFastq
countFastq,character-method	readFastq
countFastq,FastqFile-method	Sampler-class
countLines	countLines
coverage,AlignedRead-method	AlignedRead-class
dataPath	accessors
defunct	deprecated
deprecated	deprecated
detail,.ShortReadBase-method	SRUtil-class
detail,AlignedRead-method	AlignedRead-class
detail,ExperimentPath-method	ExperimentPath-class
detail,QualityScore-method	QualityScore-class
detail,RochePath-method	RochePath-class
detail,ShortRead-method	ShortRead-class
detail,ShortReadQ-method	ShortReadQ-class
detail,SolexaPath-method	SolexaPath-class
detail,SolexaSet-method	SolexaSet-class
detail,SRList-method	SRUtil-class
detail,SRSet-method	SRSet-class
detail,SRVector-method	SRUtil-class
dim,Intensity-method	Intensity-class
dim,MatrixQuality-method	QualityScore-class
dustyFilter	srFilter
dustyScore	dustyScore
dustyScore,DNAStringSet-method	dustyScore
dustyScore,ShortRead-method	dustyScore
encoding,FastqQuality-method	QualityScore-class
encoding,SFastqQuality-method	QualityScore-class
ExperimentPath	ExperimentPath-class
experimentPath	accessors
experimentPath,SRSet-method	SRSet-class
ExperimentPath-class	ExperimentPath-class
fac	Snapshot-class
fac,Snapshot-method	Snapshot-class
FastqFile	Sampler-class
FastqFile-class	Sampler-class
FastqFileList	Sampler-class
FastqFileList,ANY-method	Sampler-class
FastqFileList,character-method	Sampler-class
FastqFileList-class	Sampler-class
FastqFileReader-class	Sampler-class
FastqQA	FastqQA-class
FastqQA-class	FastqQA-class
FastqQuality	QualityScore
FastqQuality,BStringSet-method	QualityScore
FastqQuality,character-method	QualityScore
FastqQuality,missing-method	QualityScore
FastqQuality-class	QualityScore-class
FastqSampler	Sampler-class
FastqSampler-class	Sampler-class
FastqSamplerList	Sampler-class
FastqSamplerList,ANY-method	Sampler-class
FastqSamplerList,character-method	Sampler-class
FastqSamplerList-class	Sampler-class
FastqStreamer	Sampler-class
FastqStreamer,ANY,IRanges-method	Sampler-class
FastqStreamer,ANY,missing-method	Sampler-class
FastqStreamer,ANY,numeric-method	Sampler-class
FastqStreamer-class	Sampler-class
FastqStreamerList	Sampler-class
FastqStreamerList,ANY-method	Sampler-class
FastqStreamerList,character-method	Sampler-class
FastqStreamerList-class	Sampler-class
files	Snapshot-class
files,Snapshot-method	Snapshot-class
filterFastq	filterFastq
flag	qa2
flag,.QA2-method	qa2
flag,QAFrequentSequence-method	qa2
flag,QAReadQuality-method	qa2
flag,QASource-method	qa2
functions	Snapshot-class
functions,Snapshot-method	Snapshot-class
getTrellis	Snapshot-class
getTrellis,Snapshot-method	Snapshot-class
id	ShortRead-class
id,ShortRead-method	ShortRead-class
idFilter	srFilter
ignore.strand	Snapshot-class
ignore.strand,Snapshot-method	Snapshot-class
imageAnalysisPath	accessors
IntegerQuality	QualityScore
IntegerQuality-class	QualityScore-class
intensity	Intensity-class
Intensity-class	Intensity-class
IntensityInfo-class	Intensity-class
IntensityMeasure-class	Intensity-class
laneDescription	accessors
laneNames	accessors
laneNames,AnnotatedDataFrame-method	SolexaSet-class
laneNames,SolexaSet-method	SolexaSet-class
lapply,SRList,ANY-method	SRUtil-class
lapply,SRList-method	SRUtil-class
left	SpTrellis-class
left,SpTrellis-method	SpTrellis-class
length,MatrixQuality-method	QualityScore-class
length,QualityScore-method	QualityScore-class
length,ShortRead-method	ShortRead-class
length,SRList-method	SRUtil-class
limits	SnapshotFunction-class
Logic,SRFilterResult,SRFilterResult-method	SRFilterResult-class
MAQMapQA	MAQMapQA-class
MAQMapQA-class	MAQMapQA-class
MatrixQuality	QualityScore
MatrixQuality-class	QualityScore-class
measurementError	Intensity-class
name	SRFilter-class
name,SRFilter-method	SRFilter-class
name,SRFilterResult-method	SRFilterResult-class
names,SRList-method	SRUtil-class
names<-,SRList,character-method	SRUtil-class
narrow,FastqQuality-method	QualityScore-class
narrow,MatrixQuality-method	QualityScore-class
narrow,ShortRead-method	ShortRead-class
narrow,ShortReadQ-method	ShortReadQ-class
nFilter	srFilter
NumericQuality	QualityScore
NumericQuality-class	QualityScore-class
occurrenceFilter	srFilter
open.ShortReadFile	Sampler-class
pan	Snapshot-class
pan,Snapshot-method	Snapshot-class
phenoData,SRSet-method	SRSet-class
polyn	polyn
polynFilter	srFilter
position	accessors
position,AlignedRead-method	AlignedRead-class
positionFilter	srFilter
QA	qa2
qa	qa
qa,character-method	qa
qa,list-method	qa
qa,ShortReadQ-method	ShortReadQ-class
qa,SolexaPath-method	SolexaPath-class
QA-class	QA-class
qa2	qa2
qa2,FastqSampler-method	qa2
qa2,QAAdapterContamination-method	qa2
qa2,QACollate-method	qa2
qa2,QAFastqSource-method	qa2
qa2,QAFrequentSequence-method	qa2
qa2,QANucleotideByCycle-method	qa2
qa2,QANucleotideUse-method	qa2
qa2,QAQualityByCycle-method	qa2
qa2,QAQualityUse-method	qa2
qa2,QAReadQuality-method	qa2
qa2,QASequenceUse-method	qa2
QAAdapterContamination	qa2
QAAdapterContamination-class	QA-class
QACollate	qa2
QACollate,missing-method	qa2
QACollate,QAFastqSource-method	qa2
QACollate-class	QA-class
QAData	qa2
QAData-class	QA-class
QAFastqSource	qa2
QAFastqSource-class	QA-class
QAFiltered	qa2
QAFiltered-class	QA-class
QAFlagged	qa2
QAFlagged-class	QA-class
QAFrequentSequence	qa2
QAFrequentSequence-class	QA-class
QANucleotideByCycle	qa2
QANucleotideByCycle-class	QA-class
QANucleotideUse	qa2
QANucleotideUse-class	QA-class
QAQualityByCycle	qa2
QAQualityByCycle-class	QA-class
QAQualityUse	qa2
QAQualityUse-class	QA-class
QAReadQuality	qa2
QAReadQuality-class	QA-class
QASequenceUse	qa2
QASequenceUse-class	QA-class
QASource-class	QA-class
QASummary-class	QA-class
QualityScore-class	QualityScore-class
qualPath	RochePath-class
rbind,.QA-method	dotQA-class
rbind,QASummary-method	qa2
read454	RochePath-class
read454,RochePath-method	RochePath-class
readAligned	readAligned
readAligned,BamFile-method	deprecated
readAligned,character-method	readAligned
readAligned,SolexaPath-method	SolexaPath-class
readAligned,SolexaSet-method	SolexaSet-class
readBaseQuality	readBaseQuality
readBaseQuality,character-method	readBaseQuality
readBaseQuality,RochePath-method	RochePath-class
readBaseQuality,SolexaPath-method	SolexaPath-class
readBfaToc	readBfaToc
readCount	SRSet-class
readData	SRSet-class
reader	SnapshotFunction-class
readFasta	readFasta
readFasta,character-method	readFasta
readFasta,RochePath-method	RochePath-class
readFasta,SolexaPath-method	SolexaPath-class
readFastaQual	RochePath-class
readFastaQual,character-method	RochePath-class
readFastaQual,RochePath-method	RochePath-class
readFastq	readFastq
readFastq,character-method	readFastq
readFastq,FastqFile-method	Sampler-class
readFastq,SolexaPath-method	SolexaPath-class
readIndex	SRSet-class
readIntensities	readIntensities
readIntensities,character-method	readIntensities
readIntensities,SolexaPath-method	SolexaPath-class
readIntensityInfo	Intensity-class
readPath	RochePath-class
readPrb	readPrb
readPrb,character-method	readPrb
readPrb,SolexaPath-method	SolexaPath-class
readQseq	readQseq
readQseq,character-method	readQseq
readQseq,SolexaPath-method	SolexaPath-class
readQual	RochePath-class
readQual,character-method	RochePath-class
readQual,RochePath-method	RochePath-class
readXStringColumns	readXStringColumns
renew	renew
renew,.ShortReadBase-method	renew
renewable	renew
renewable,.ShortReadBase-method	renew
renewable,character-method	renew
renewable,missing-method	renew
report	report
report,ANY-method	report
report,BowtieQA-method	BowtieQA-class
report,FastqQA-method	FastqQA-class
report,MAQMapQA-method	MAQMapQA-class
report,QA-method	qa2
report,QAAdapterContamination-method	qa2
report,QAFiltered-method	qa2
report,QAFlagged-method	qa2
report,QAFrequentSequence-method	qa2
report,QANucleotideByCycle-method	qa2
report,QANucleotideUse-method	qa2
report,QAQualityByCycle-method	qa2
report,QAQualityUse-method	qa2
report,QAReadQuality-method	qa2
report,QASequenceUse-method	qa2
report,QASource-method	qa2
report,SolexaExportQA-method	SolexaExportQA-class
report,SolexaPath-method	SolexaPath-class
report_html	report
report_html,BowtieQA-method	BowtieQA-class
report_html,FastqQA-method	FastqQA-class
report_html,MAQMapQA-method	MAQMapQA-class
report_html,ShortReadQQA-method	FastqQA-class
report_html,SolexaExportQA-method	SolexaExportQA-class
report_html,SolexaRealignQA-method	SolexaExportQA-class
restore	SpTrellis-class
restore,SpTrellis-method	SpTrellis-class
reverse,FastqQuality-method	QualityScore-class
reverse,ShortReadQ-method	ShortReadQ-class
reverseComplement,ShortReadQ-method	ShortReadQ-class
right	SpTrellis-class
right,SpTrellis-method	SpTrellis-class
RochePath	RochePath-class
RochePath-class	RochePath-class
RocheSet	RocheSet-class
RocheSet,character-method	RochePath-class
RocheSet,RochePath-method	RochePath-class
RocheSet-class	RocheSet-class
RtaIntensity	RtaIntensity
RtaIntensity-class	RtaIntensity-class
runNames	RochePath-class
runNames,RochePath-method	RochePath-class
sapply,SRList-method	SRUtil-class
scanPath	accessors
SFastqQuality	QualityScore
SFastqQuality,BStringSet-method	QualityScore
SFastqQuality,character-method	QualityScore
SFastqQuality,missing-method	QualityScore
SFastqQuality-class	QualityScore-class
ShortRead	ShortRead-class
ShortRead,DNAStringSet,BStringSet-method	ShortRead-class
ShortRead,DNAStringSet,missing-method	ShortRead-class
ShortRead,missing,missing-method	ShortRead-class
ShortRead-class	ShortRead-class
ShortReadFile-class	Sampler-class
ShortReadQ	ShortReadQ-class
ShortReadQ,DNAStringSet,BStringSet,BStringSet-method	ShortReadQ-class
ShortReadQ,DNAStringSet,BStringSet,missing-method	ShortReadQ-class
ShortReadQ,DNAStringSet,QualityScore,BStringSet-method	ShortReadQ-class
ShortReadQ,DNAStringSet,QualityScore,missing-method	ShortReadQ-class
ShortReadQ,missing,missing,missing-method	ShortReadQ-class
ShortReadQ-class	ShortReadQ-class
ShortReadQQA-class	FastqQA-class
show,.QA-method	dotQA-class
show,.ShortReadBase-method	ShortRead-package
show,AlignedRead-method	AlignedRead-class
show,ExperimentPath-method	ExperimentPath-class
show,FastqQuality-method	QualityScore-class
show,Intensity-method	Intensity-class
show,IntensityMeasure-method	Intensity-class
show,NumericQuality-method	QualityScore-class
show,QAAdapterContamination-method	qa2
show,QACollate-method	qa2
show,QAFastqSource-method	qa2
show,QAFrequentSequence-method	qa2
show,QAReadQuality-method	qa2
show,QASummary-method	qa2
show,RochePath-method	RochePath-class
show,ShortRead-method	ShortRead-class
show,Snapshot-method	Snapshot-class
show,SnapshotFunction-method	SnapshotFunction-class
show,SolexaExportQA-method	SolexaExportQA-class
show,SolexaPath-method	SolexaPath-class
show,SolexaSet-method	SolexaSet-class
show,SpTrellis-method	SpTrellis-class
show,SRFilter-method	SRFilter-class
show,SRFilterResult-method	SRFilterResult-class
show,SRList-method	SRUtil-class
show,SRSet-method	SRSet-class
show,SRVector-method	SRUtil-class
Snapshot	Snapshot-class
Snapshot,BamFileList,GRanges-method	Snapshot-class
Snapshot,character,GRanges-method	Snapshot-class
Snapshot,character,missing-method	Snapshot-class
Snapshot-class	Snapshot-class
SnapshotFunction	SnapshotFunction-class
SnapshotFunction-class	SnapshotFunction-class
SnapshotFunctionList	SnapshotFunction-class
SnapshotFunctionList,ANY-method	SnapshotFunction-class
SnapshotFunctionList,SnapshotFunction-method	SnapshotFunction-class
SnapshotFunctionList-class	SnapshotFunction-class
SolexaExportQA	SolexaExportQA-class
SolexaExportQA-class	SolexaExportQA-class
SolexaIntensity	SolexaIntensity
SolexaIntensity-class	SolexaIntensity-class
SolexaIntensityInfo	SolexaIntensity
SolexaIntensityInfo-class	SolexaIntensity-class
SolexaPath	SolexaPath-class
solexaPath	accessors
SolexaPath-class	SolexaPath-class
SolexaRealignQA-class	SolexaExportQA-class
SolexaSet	SolexaSet-class
SolexaSet,character-method	SolexaSet-class
SolexaSet,SolexaPath-method	SolexaPath-class
SolexaSet-class	SolexaSet-class
sourcePath	SRSet-class
SpTrellis	SpTrellis-class
SpTrellis-class	SpTrellis-class
spViewPerFeature	spViewPerFeature
srapply	deprecated
srdistance	srdistance
srdistance,DNAStringSet,character-method	srdistance
srdistance,DNAStringSet,DNAString-method	srdistance
srdistance,DNAStringSet,DNAStringSet-method	srdistance
srdistance,ShortRead,ANY-method	ShortRead-class
srdistanceFilter	srFilter
srduplicated	srduplicated
srduplicated,AlignedRead-method	AlignedRead-class
srduplicated,FastqQuality-method	QualityScore-class
srduplicated,ShortRead-method	ShortRead-class
srduplicated,XStringSet-method	srduplicated
sread	ShortRead-class
sread,ShortRead-method	ShortRead-class
SRError	SRUtil-class
SRError-class	SRUtil-class
srFilter	srFilter
srFilter,function-method	srFilter
srFilter,missing-method	srFilter
srFilter,SRFilter-method	SRFilter-class
SRFilter-class	SRFilter-class
SRFilterResult	SRFilterResult-class
SRFilterResult-class	SRFilterResult-class
SRList	SRUtil-class
srlist	SRUtil-class
SRList-class	SRUtil-class
srorder	srduplicated
srorder,AlignedRead-method	AlignedRead-class
srorder,FastqQuality-method	QualityScore-class
srorder,ShortRead-method	ShortRead-class
srorder,XStringSet-method	srduplicated
srrank	srduplicated
srrank,AlignedRead-method	AlignedRead-class
srrank,FastqQuality-method	QualityScore-class
srrank,ShortRead-method	ShortRead-class
srrank,XStringSet-method	srduplicated
SRSet-class	SRSet-class
srsort	srduplicated
srsort,FastqQuality-method	QualityScore-class
srsort,ShortRead-method	ShortRead-class
srsort,XStringSet-method	srduplicated
SRVector	SRUtil-class
SRVector-class	SRUtil-class
SRWarn	SRUtil-class
SRWarn-class	SRUtil-class
stats	SRFilterResult-class
stats,SRFilterResult-method	SRFilterResult-class
strand,AlignedRead-method	AlignedRead-class
strandFilter	srFilter
tables	tables
tables,ShortRead-method	ShortRead-class
tables,XStringSet-method	tables
togglefun	Snapshot-class
togglefun,Snapshot-method	Snapshot-class
togglep	Snapshot-class
togglep,Snapshot-method	Snapshot-class
togglez	Snapshot-class
togglez,Snapshot-method	Snapshot-class
trellis-class	Snapshot-class
trimEnds	trimTails
trimEnds,character-method	trimTails
trimEnds,FastqQuality-method	trimTails
trimEnds,ShortRead-method	trimTails
trimEnds,ShortReadQ-method	trimTails
trimEnds,XStringQuality-method	trimTails
trimEnds,XStringSet-method	trimTails
trimLRPatterns,ShortRead-method	ShortRead-class
trimTails	trimTails
trimTails,BStringSet-method	trimTails
trimTails,character-method	trimTails
trimTails,FastqQuality-method	QualityScore-class
trimTails,ShortReadQ-method	ShortReadQ-class
trimTails,XStringQuality-method	trimTails
trimTailw	trimTails
trimTailw,BStringSet-method	trimTails
trimTailw,character-method	trimTails
trimTailw,FastqQuality-method	QualityScore-class
trimTailw,ShortReadQ-method	ShortReadQ-class
trimTailw,XStringQuality-method	trimTails
uniqueFilter	ShortRead-deprecated
vclass	accessors
view	Snapshot-class
view,Snapshot-method	Snapshot-class
viewer	SnapshotFunction-class
vrange	Snapshot-class
vrange,Snapshot-method	Snapshot-class
width,FastqQuality-method	QualityScore-class
width,MatrixQuality-method	QualityScore-class
width,NumericQuality-method	QualityScore-class
width,QualityScore-method	QualityScore-class
width,ShortRead-method	ShortRead-class
writeFasta	readFasta
writeFasta,DNAStringSet-method	readFasta
writeFasta,ShortRead-method	ShortRead-class
writeFastq	readFastq
writeFastq,ShortReadQ,character-method	ShortReadQ-class
writeFastq,ShortReadQ,FastqFile-method	ShortReadQ-class
yield	Sampler-class
yield,FastqFileReader-method	Sampler-class
yield,FastqSampler-method	Sampler-class
yield,FastqStreamer-method	Sampler-class
zi	SpTrellis-class
zi,SpTrellis-method	SpTrellis-class
zo	SpTrellis-class
zo,SpTrellis-method	SpTrellis-class
zoom	Snapshot-class
zoom,Snapshot-method	Snapshot-class
[,AlignedRead,ANY,ANY,ANY-method	AlignedRead-class
[,AlignedRead,ANY,ANY-method	AlignedRead-class
[,AlignedRead,ANY,missing,ANY-method	AlignedRead-class
[,AlignedRead,ANY,missing-method	AlignedRead-class
[,AlignedRead,missing,ANY,ANY-method	AlignedRead-class
[,AlignedRead,missing,ANY-method	AlignedRead-class
[,AlignedRead,missing,missing,ANY-method	AlignedRead-class
[,AlignedRead,missing,missing-method	AlignedRead-class
[,IntensityMeasure,ANY,ANY,ANY-method	Intensity-class
[,IntensityMeasure,ANY,ANY-method	Intensity-class
[,IntensityMeasure,ANY,missing,ANY-method	Intensity-class
[,IntensityMeasure,missing,ANY,ANY-method	Intensity-class
[,IntensityMeasure,missing,missing,ANY-method	Intensity-class
[,MatrixQuality,ANY,missing,ANY-method	QualityScore-class
[,MatrixQuality,ANY,missing-method	QualityScore-class
[,QualityScore,ANY,missing,ANY-method	QualityScore-class
[,QualityScore,ANY,missing-method	QualityScore-class
[,ShortRead,ANY,ANY,ANY-method	ShortRead-class
[,ShortRead,ANY,ANY-method	ShortRead-class
[,ShortRead,ANY,missing,ANY-method	ShortRead-class
[,ShortRead,ANY,missing-method	ShortRead-class
[,ShortRead,missing,ANY,ANY-method	ShortRead-class
[,ShortRead,missing,ANY-method	ShortRead-class
[,ShortRead,missing,missing,ANY-method	ShortRead-class
[,ShortRead,missing,missing-method	ShortRead-class
[,ShortReadQ,ANY,ANY,ANY-method	ShortReadQ-class
[,ShortReadQ,ANY,ANY-method	ShortReadQ-class
[,ShortReadQ,ANY,missing,ANY-method	ShortReadQ-class
[,ShortReadQ,ANY,missing-method	ShortReadQ-class
[,ShortReadQ,missing,ANY,ANY-method	ShortReadQ-class
[,ShortReadQ,missing,ANY-method	ShortReadQ-class
[,ShortReadQ,missing,missing,ANY-method	ShortReadQ-class
[,ShortReadQ,missing,missing-method	ShortReadQ-class
[,SolexaIntensity,ANY,ANY,ANY-method	SolexaIntensity-class
[,SolexaIntensity,ANY,ANY-method	SolexaIntensity-class
[,SolexaIntensity,ANY,missing,ANY-method	SolexaIntensity-class
[,SolexaIntensity,missing,ANY,ANY-method	SolexaIntensity-class
[,SolexaIntensity,missing,missing,ANY-method	SolexaIntensity-class
[,SRList,ANY,missing,ANY-method	SRUtil-class
[,SRList,ANY,missing-method	SRUtil-class
[<-,ShortReadQ,ANY,missing,ShortReadQ-method	ShortReadQ-class
[[,ArrayIntensity,ANY,ANY-method	Intensity-class
[[,MatrixQuality,ANY,missing-method	QualityScore-class
[[,QualityScore,ANY,missing-method	QualityScore-class
[[,SRList,ANY,missing-method	SRUtil-class
