Hi,
I would like to export certain reads filtered using Rsamtools, for example
aligning against contaminant references
to exclude a set of sequences filtering on the bitwise flag=0x4 (similar to
SamToFastq.jar in the picard http://picard.sourceforge.net/ tools),
but couldn't find much on exporting/writing to file in the
Rsamtools-Overview.pdf vignette or on google.

Is there a function/utility which converts an Rsamtools bam list region to
ShortReadQ object(s) for export using writeFastq()
with single end *and* paired end alignments which have been read in via the
Rsamtools interface?

## Load a bam
bam <- scanBam(...)

## Filter using R's subsetting,
bamRegion <- bam[[1]][ ... ] ## list of list

## Should work for single end alignments, but not paired end alignments
## Read pairs may have to index on mpos = PNEXT field
rfq <- ShortReadQ(bamRegion[["seq"]], bamRegion[["qual"]],
BStringSet(bamRegion[["qname"]]))

If not is the area of exporting from Rsamtools worth developing futher?

cheers,

Marcus

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