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test.truncateReads <- function() {
## make some random ShortReads
reads <- HTSeqGenie:::makeRandomSreads(10, 100)
## check there are 10 reads of 50 nucleotides
treads <- truncateReads(reads, 50)
checkEquals(length(treads), 10)
checkTrue(all(width(treads)==50))
## check we can trim with a number of nucleotides higher than the size of the reads
treads <- truncateReads(reads, 110)
checkTrue(all(width(treads)<=110))
## check quality encoding remains the same after truncateReads
cqreads <- class(quality(reads))
cqtreads <- class(quality(treads))
checkEquals(cqreads, cqtreads)
## check we can trim variable size reads
reads <- append(reads, HTSeqGenie:::makeRandomSreads(10, 80))
treads <- truncateReads(reads, 50)
checkEquals(length(treads), 20)
checkTrue(all(width(treads)==50))
## check that the trimmed reads are the same ones produced by substr(...)
a <- sread(reads)
b <- sread(treads)
checkTrue(all(substr(a, 1, nchar(b))==b))
}
test.truncateReads.trim5 <- function() {
## make some random ShortReads
reads <- HTSeqGenie:::makeRandomSreads(10, 100)
reads <- append(reads, HTSeqGenie:::makeRandomSreads(10, 80))
treads <- truncateReads(reads, 50, 10)
## check there are 20 reads of 50 nucleotides
checkEquals(length(treads), 20)
checkTrue(all(width(treads)==50))
## check that the 10 first nucleotides were trimmed
a <- sread(reads)
b <- sread(treads)
c <- paste0(substr(a, 1, 10), b)
checkTrue(all(c==substr(a, 1, nchar(c))))
## make some random ShortReads, some shorter than the desired length
reads <- HTSeqGenie:::makeRandomSreads(10, 100)
reads <- append(reads, HTSeqGenie:::makeRandomSreads(10, 50))
treads <- truncateReads(reads, 75, 10)
## basic checks
checkEquals(length(treads), 20)
checkTrue(all(width(treads)<=width(reads)))
checkTrue(all(width(treads)<=75))
## check that the 10 first nucleotides were trimmed
a <- sread(reads)
b <- sread(treads)
c <- paste0(substr(a, 1, 10), b)
checkTrue(all(c==substr(a, 1, nchar(c))))
## make some random ShortReads, some shorter than the desired trim5
reads <- HTSeqGenie:::makeRandomSreads(10, 100)
reads <- append(reads, HTSeqGenie:::makeRandomSreads(10, 20))
reads <- append(reads, HTSeqGenie:::makeRandomSreads(2, 0))
reads <- append(reads, HTSeqGenie:::makeRandomSreads(2, 1))
treads <- truncateReads(reads, 60, 30)
checkTrue(sum(width(treads)==60)==10 && sum(width(treads)==0)==14)
treads <- truncateReads(reads, 75, 30)
checkTrue(sum(width(treads)==70)==10 && sum(width(treads)==0)==14)
treads <- truncateReads(reads, 75, 19)
checkTrue(sum(width(treads)==75)==10 && sum(width(treads)==1)==10 && sum(width(treads)==0)==4)
treads <- truncateReads(reads, 1, 0)
checkTrue(sum(width(treads)==0)==2 && sum(width(treads)==1)==22)
## test with trim5 only
treads <- truncateReads(reads, trim5=20)
checkTrue(sum(width(treads)==0)==14 && sum(width(treads)==80)==10)
treads <- truncateReads(reads, trim5=1)
checkTrue(all(substring(as.character(sread(reads)), 2)==as.character(sread(treads))))
checkTrue(sum(width(treads)==0)==4 && sum(width(treads)==19)==10 && sum(width(treads)==99)==10)
treads <- truncateReads(reads)
checkTrue(all(sread(treads)==sread(reads)))
}
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