[Bioc-devel] Append/combine option for filterFastq and similar?

[Ryan C. Thompson]

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 
> <rct at thompsonclan.org <mailto:rct at 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-request at r-project.org
>             <mailto:bioc-devel-request at r-project.org> wrote:
>
>             Re: Append/combine option for filterFastq and similar?
>
>         _______________________________________________
>         Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>         mailing list
>         https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>     _______________________________________________
>     Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing
>     list
>     https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>


	[[alternative HTML version deleted]]