readerToFastq: readerToFastq: Extraction of a subset of alignments from a...
In rbamtools: Read and Write BAM (Binary Alignment) Files

Description Usage Arguments Value Author(s) Examples

The function readerToFastq writes (remaining) aligns or some part of the stored aligns in a BAM file as reads into a compressed fastq file.

1	readerToFastq(object, filename, which, append=FALSE)

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 next retrieved 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.

numeric

Wolfgang Kaisers

bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader <- bamReader(bam)
readerToFastq(reader, "out.fq.gz")
bamClose(reader)
# Reopen in order to point to first align
reader <- bamReader(bam)
index <- sample(1:100, 20)
readerToFastq(reader, "out_subset.fq.gz", which=index)