As far as I know, filterFastq only accepts file names.
On 04/22/2015 10:28 AM, Jim Hester wrote:
> I typically use pipe() in these circumstances which avoids using any
> additional storage
>
> readLines(pipe("cat file1 file2"))
>
> It should work with filterFastq assuming it can read from connections
> rather than just files, but I have not tested it to be sure.
>
> On Wed, Apr 22, 2015 at 1:16 PM, Ryan C. Thompson
> <r...@thompsonclan.org <mailto:r...@thompsonclan.org>> wrote:
>
> That's not ideal because it's duplicating storage unnecessarily.
>
>
> On 04/22/2015 04:07 AM, Aedin wrote:
>
> This is one instance were a system or simple unix command is
> very easy
>
> system('cat *.fastq > all.fastq')
>
>
> ---
>
> On Apr 22, 2015, at 6:00, bioc-devel-requ...@r-project.org
> <mailto:bioc-devel-requ...@r-project.org> wrote:
>
> Re: Append/combine option for filterFastq and similar?
>
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