rbamtools (version 2.16.17)

rangeToFastq: rangeToFastq: Extract read information from alignments for given genomic range as fastq.

Description

The function rangeToFastq writes all (or selected) aligns from a bamRange into a compressed fastq file.

Usage

rangeToFastq(object, filename, which, append=FALSE)

Arguments

object

bamReader. Must be opened.

filename

Name of output 'fastq' file.

which

(Optional) Logical vector. When given, the routine checks for each of the given values the value of which. When TRUE the corresponding align will be written to the output file, otherwise will be skipped.

append

(Optional) When TRUE, the routine will append to an existing file. Otherwise existing files will be overwritten.

Examples

# NOT RUN {
bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader <- bamReader(bam, idx=TRUE)
coords <- as.integer(c(0, 0, 249250621))
range <- bamRange(reader, coords)
# }
# NOT RUN {
rangeToFastq(range, "range.fq.gz")
# }
# NOT RUN {
index <- sample(1:size(range), 100)
# }
# NOT RUN {
rangeToFastq(range, "range_subset.fq.gz", which=index)
# }