[Bioperl-l] hammer Results.pm trouble

[Michal Kurowski]

Hi,
I'm an eager user of various bioperl modules and I find most of them
of top quality but there seems a tricky bug is hidden in rather important
module: HMMER/Results.pm.

Method "filter_on_cutoff" is supposed to return a new object with a
narrowed set of score values but it doesn't do that. There's a
recurrent invoking of a class constructor that cannot be (easily)
provided with required parameters. In the end we've got an error:

MSG: No parse type provided. should be hmmsearch or hmmpfam
STACK Bio::Tools::HMMER::Results::new
/usr/lib/perl5/site_perl/5.6.0/Bio/Tools/HMMER/Results.pm:107
STACK Bio::Tools::HMMER::Results::filter_on_cutoff /usr/lib/perl5
/site_perl/5.6.0/Bio/Tools/HMMER/Results.pm:348
STACK toplevel /home/michal/bin/hammer2.pl:12

It can be circumvented in the client code with appropriate number of
ifs but...

The problem was reported : nr 1034.

With regards, 


-- 
Michal Kurowski
<michal@orfeus.bioinfo.pl>