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test.isAboveQualityThresh <- function() {
## test simple read
## Sanger quality (see QualityScore-class): ASCII code - 33 ("A"=32, "<"=27)
read <- ShortReadQ(DNAStringSet("ATGAATAGTC"), quality=FastqQuality("AAAAAAAAAA")) ## 100% of 32
z <- HTSeqGenie::isAboveQualityThresh(read, minquality=30, minfrac=0.7)
checkEquals(z, TRUE)
## test simple read
read <- ShortReadQ(DNAStringSet("ATGAATAGTC"), quality=FastqQuality("<AA<AA<A<A")) ## 60% of 32
z <- HTSeqGenie::isAboveQualityThresh(read, minquality=30, minfrac=0.7)
checkEquals(z, FALSE)
## test simple read
read <- ShortReadQ(DNAStringSet("ATGCCTAGTC"), quality=FastqQuality("<ABADACA<A")) ## 80% of >=32
z <- HTSeqGenie::isAboveQualityThresh(read, minquality=30, minfrac=0.7)
checkEquals(z, TRUE)
}
test.filterByLength <- function() {
reads <- ShortReadQ(DNAStringSet(c("ATGAATAGTC", "ATGAATAGTCACGACG")),
quality=FastqQuality(c("AAAAAAAAAA", "AAAAAAAAAAAAAAAA")))
z <- filterByLength(c(reads), minlength=12)
checkEquals(z, c(FALSE, TRUE))
reads2 <- append(reads[2], reads[1])
z <- filterByLength(c(reads, reads2), minlength=12, TRUE)
checkEquals(z, c(FALSE, FALSE))
}
test.trimTailsByQuality <- function() {
reads <- c(ShortReadQ(DNAStringSet(c("GATCTGATAAATGCACGCATCCCCCCCCGGGGAAGGGGGTCAGCGCCCCGCGGCACTTATTAGACCCAGCATTAC")),
quality=FastqQuality(c("??@D;BBDFDDFDBEHF@FEGEEFHIGH:F#############################################"))))
checkEquals( width(trimTailsByQuality(reads, minqual='!')[[1]]), width(reads[[1]]))
checkEquals(width(trimTailsByQuality(reads, minqual='F')[[1]]), 28)
checkEquals(width(trimTailsByQuality(reads, minqual='H')[[1]]), 26)
checkEquals(width(trimTailsByQuality(reads, minqual='I')[[1]]), 0)
}
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