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

Chris Fields cjfields at illinois.edu
Tue Feb 23 12:47:44 EST 2010

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.


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