Hi Jillian,
is this question intended for this or vcftools-help mailing list?
Petr
On Wed, 2014-08-13 at 09:36 +0300, Jillian Rowe wrote:
> Hello,
>
> I was wondering if there were any plans for IO file handle support for
> bgzipped VCF files.
>
> When using VCF.pm I would like to do something like this:
>
>
> $fh = new IO::Uncompress::Gunzip $filename or warn "## File handle
> didn't work for gzipped file ".$filename."\n\n";
>
> $vcf = Vcf->new(fh => $fh);
> $vcf->parse_header();
>
> At some point this breaks and I end up getting lines that are truncated.
> So I will get an error that says a line is only "chr1 123 A G" when the
> line is really "chr1 123 A G all_the_other_fields"
>
> Instead I have to do this:
>
> $vcf = Vcf->new(file => $filename);
> $vcf->parse_header();
>
> Which looks like it carries out the command in Vcf.pm
>
> sub _open{
> #stuff
>
> $cmd = "gunzip -c '$$self{file}' |";
>
> #morestuff
>
> Which I think means its reading in from STDIN, and that seems to be very
> IO intensive. The upside to using an IO::Whatever in perl is that it
> should read in only one line at a time.
>
> Are there any plans to implement this?
>
> Best,
> Jillian
>
>
>
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