[Bioperl-l] Next-Gen and the next point release - updates

[Chris Fields]

All,

I just pushed one very key bit for nextgen sequence analysis to svn,  
mainly parsing of all three FASTQ variants.  These can be called by  
using:

   # grabs the FASTQ parser, specifies the Illumina variant
   my $in = Bio::SeqIO->new(-format    => 'fastq-illumina',
                            -file      => 'mydata.fq');

   # same, explicitly specifies the Illumina variant
   my $in = Bio::SeqIO->new(-format    => 'fastq',
                            -variant   => 'illumina',
                            -file      => 'mydata.fq');

   # simple 'fastq' format defaults to 'sanger' variant
   my $out = Bio::SeqIO->new(-format    => 'fastq',
                            -file      => '>mydata.fq');

FASTQ works for both input and output.  As mentioned before, the  
next_dataset() method also exists for getting simple hashrefs, see the  
module documentation for more.

This was one of the few remaining blockers for the 1.6.1 point  
release.  I'll run a clean checkout of main trunk to test, then work  
on merging everything over from trunk starting Friday and push out  
1.6.0_1 (first alpha) beginning of next week to get some CPAN Tester  
information.  If everything looks fine the final point release will  
follow soon after.

Cheers!

chris