readerToFastq: readerToFastq: Extraction of a subset of alignments from a...

Description Usage Arguments Details Value Author(s) Examples

Description

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

Usage

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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 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.

Details

The function 'reader2fastq' is deprecated and will be replaced by 'readerToFastq' soon.

Value

numeric

Author(s)

Wolfgang Kaisers

Examples

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bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader <- bamReader(bam)
## Not run: readerToFastq(reader, "out.fq.gz")
bamClose(reader)
# Reopen in order to point to first align
reader <- bamReader(bam)
index <- sample(1:100, 20)
## Not run: readerToFastq(reader, "out_subset.fq.gz", which=index)

wokai/rbamtools documentation built on May 28, 2017, 5:12 a.m.