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# R expressions for the track.bam$crawl() method, to get full read data in the genomic window
# Author : Sylvain Mareschal <maressyl@gmail.com>
# License : GPL3 http://www.gnu.org/licenses/gpl.html
extract.init <- function(env) {
env$output <- vector("list", 5000L)
return(TRUE)
}
extract.loop <- function(read, env) {
# Extend output list if necessary
if(env$totalReads > length(env$output)) {
eval(expression(output <- c(output, vector("list", 5000L))), envir=env)
}
# Store whole read
env$read <- read
eval(expression(output[[ totalReads ]] <- read), envir=env)
return(TRUE)
}
extract.final <- function(env) {
# Remove unused read slots
eval(
expression({
# Remove unused read slots
output <- output[ 1:totalReads ]
# Apply S3 class
attr(output, "bam") <- self$bamPath
attr(output, "chrom") <- chrom
attr(output, "start") <- start
attr(output, "end") <- end
class(output) <- "bamSlice"
}),
envir = env
)
return(TRUE)
}
# S3 method for BAI printing
print.bamSlice <- function(x, ...) {
cat("Read list\n")
cat("- BAM : ", attr(x, "bam"), "\n", sep="")
cat("- Region : ", attr(x, "chrom"), ":", attr(x, "start"), "-", attr(x, "end"), "\n", sep="")
if(length(x) > 0) {
reads <- x[[1]]$QNAME
if(length(x) > 1) reads <- sprintf("%s ...", reads)
reads <- sprintf(" (%s)", reads)
} else {
reads <- ""
}
cat("- Reads : ", length(x), reads, "\n", sep="")
invisible(x)
}
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