| readerToFastq {rbamtools} | R Documentation |
The function readerToFastq writes (remaining) aligns or
some part of the stored aligns in a BAM file as reads into a
compressed fastq file.
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. |
The function 'reader2fastq' is deprecated and will be replaced by 'readerToFastq' soon.
numeric
Wolfgang Kaisers
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)