###################################################
### chunk number 1: 
###################################################
#line 51 "vignettes/Rsubread/inst/doc/Rsubread.Rnw"
library(Rsubread)
ref <- system.file("extdata","reference.fa",package="Rsubread")
path <- system.file("extdata",package="Rsubread")
buildindex(basename=file.path(path,"reference_index"),reference=ref)


###################################################
### chunk number 2: 
###################################################
#line 75 "vignettes/Rsubread/inst/doc/Rsubread.Rnw"
reads <- system.file("extdata","reads.txt",package="Rsubread")
align(index=file.path(path,"reference_index"),readfile1=reads,output_file=file.path(path,"alignResults.SAM"))


###################################################
### chunk number 3: 
###################################################
#line 105 "vignettes/Rsubread/inst/doc/Rsubread.Rnw"
library(Rsubread)
reads <- system.file("extdata","reads.txt",package="Rsubread")
x <- qualityScores(filename=reads,nreads=1000)
boxplot(x)


###################################################
### chunk number 4: 
###################################################
#line 116 "vignettes/Rsubread/inst/doc/Rsubread.Rnw"
library(Rsubread)
reads <- system.file("extdata","reads.txt",package="Rsubread")
## Fraction of A,T,G and C in the entire dataset
x <- atgcContent(filename=reads,basewise=FALSE)
## Fraction of A,T,G and C at each base location across all the reads
xb <- atgcContent(filename=reads,basewise=TRUE)


###################################################
### chunk number 5: 
###################################################
#line 130 "vignettes/Rsubread/inst/doc/Rsubread.Rnw"
library(Rsubread)
results <- system.file("extdata","alignResults.SAM",package="Rsubread")
propmapped(results)