[Bioperl-l] indexed fastq files

[Albert Vilella]

Hi Chris,

I am finding that Bio::Index::Fastq seek is chopping off the first
character of the fastq entry. I'm on Linux using bioperl-1.6.1 and
debugged the problem to this point in AbstractSeq.pm:143, where there
is this funny commented line:

		# $begin-- if( $^O =~ /mswin/i); # workaround for Win DB_File bug
		seek($fh, $begin, 0);

If I apply this $begin--, everything works fine, but I am not using
windows, I am on a Linux cluster.

Any ideas why this was tagged as a "Win DB_File bug"?

Cheers,

Albert.

On Mon, Jan 4, 2010 at 9:59 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Bio::Index::Fastq, maybe?  To tell the truth, I haven't tried it since we refactored FASTQ parsing, so let us know if it doesn't work.
>
> chris
>
> On Jan 4, 2010, at 2:00 PM, Albert Vilella wrote:
>
>> Hi all,
>>
>> What is the best way to index fastq files, so that once clustered, I
>> can provide a list of seq_ids and get
>> them back in fastq format from the indexed db?
>>
>> Cheers,
>>
>> Albert.
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>
>