## ----, message=FALSE-----------------------------------------------------
library(hiReadsProcessor)


## ------------------------------------------------------------------------
runData <- system.file("extdata/FLX_sample_run/", package = "hiReadsProcessor")
list.files(runData, recursive  = TRUE)


## ------------------------------------------------------------------------
seqProps <- read.SeqFolder(runData, seqfilePattern=".+fna.gz$")
seqProps


## ------------------------------------------------------------------------
seqProps$sectors$"1"$samples


## ------------------------------------------------------------------------
seqProps <- findBarcodes(seqProps, sector="all", showStats=TRUE)
seqProps
seqProps$sectors


## ------------------------------------------------------------------------
load(file.path(system.file("data", package = "hiReadsProcessor"),
               "FLX_seqProps.RData"))


## ----, eval=FALSE--------------------------------------------------------
## seqProps <- findPrimers(seqProps, showStats=TRUE)


## ----, eval=FALSE--------------------------------------------------------
## seqProps <- findLTRs(seqProps, showStats=TRUE)


## ----, eval=FALSE--------------------------------------------------------
## seqProps <- findVector(seqProps, showStats=TRUE)


## ----, eval=FALSE--------------------------------------------------------
## seqProps <- findLinkers(seqProps, showStats=TRUE, doRC=TRUE)


## ----, eval=FALSE--------------------------------------------------------
## seqProps <- findIntegrations(seqProps,
##                              genomeIndices=c("hg18"="/usr/local/genomeIndexes/hg18.noRandom.2bit"), numServers=2)


## ------------------------------------------------------------------------
sampleSummary(seqProps)


## ------------------------------------------------------------------------
sessionInfo()