[Bioperl-l] Bio::Index::Fastq support for gzipped files

[Chris Fields]

On Feb 23, 2010, at 11:01 AM, Peter wrote:

> On Tue, Feb 23, 2010 at 4:51 PM, Albert Vilella <avilella at gmail.com> wrote:
>> Hi,
>> 
>> Maybe already answered somewhere but, do we have support for
>> gzipped fasta/fastq files?
>> 
>> Google tells me biopython does, but I couldn't guess for bioperl...
>> 
> 
> To clarify, we've discussed this on the Biopython mailing list, and
> Renato Alves and I have been exploring possible implementation
> on git branches, but we don't yet have indexing of gzipped files on
> the trunk. But it would be nice :)
> 
> Peter

I don't think the various PerlIO gzip modules implement tell() to index the positions.  Mark Jensen released the PerlIO::via::gzip module on CPAN, so he would be the one who could say more about it and the possible problems one would face.

chris