hiReadsProcessor-package	hiReadsProcessor
addFeature	addFeature
addListNameToReads	addListNameToReads
annotateSites	annotateSites
blatListedSet	blatListedSet
blatSeqs	blatSeqs
chunkize	chunkize
clusterSites	clusterSites
crossOverCheck	crossOverCheck
decodeByBarcode	findBarcodes
dereplicateReads	dereplicateReads
doRCtest	doRCtest
extractFeature	extractFeature
extractSeqs	extractSeqs
findAndRemoveVector	findAndRemoveVector
findAndTrimSeq	findAndTrimSeq
findBarcodes	findBarcodes
findIntegrations	findIntegrations
findLinkers	findLinkers
findLTRs	findLTRs
findPrimers	findPrimers
findVector	findVector
getIntegrationSites	getIntegrationSites
getSectorsForSamples	getSectorsForSamples
getSonicAbund	getSonicAbund
hiReadsProcessor	hiReadsProcessor
isuSites	isuSites
otuSites	otuSites
pairUpAlignments	pairUpAlignments
pairwiseAlignSeqs	pairwiseAlignSeqs
primerIDAlignSeqs	primerIDAlignSeqs
psl	psl
pslCols	pslCols
pslToRangedObject	pslToRangedObject
read.BAMasPSL	read.BAMasPSL
read.blast8	read.blast8
read.psl	read.psl
read.sampleInfo	read.sampleInfo
read.SeqFolder	read.SeqFolder
read.seqsFromSector	read.seqsFromSector
removeReadsWithNs	removeReadsWithNs
replicateReads	replicateReads
sampleSummary	sampleSummary
seqProps	seqProps
splitByBarcode	splitByBarcode
splitSeqsToFiles	splitSeqsToFiles
startgfServer	startgfServer
stopgfServer	startgfServer
trimSeqs	trimSeqs
troubleshootLinkers	troubleshootLinkers
vpairwiseAlignSeqs	vpairwiseAlignSeqs
write.listedDNAStringSet	write.listedDNAStringSet
write.psl	write.psl
