[Bioperl-l] scf writing issues

Marc Logghe Marc.Logghe at devgen.com
Sun Dec 26 19:30:51 EST 2004

Think I was able to solve this.
The issue was the version after all.

>It makes no difference when you pass the version 
> paramater or not.

diff -r1.30 scf.pm
<            if ($writer_fodder->{comments}->{version} != 2 && $comments{version} != 3) {
>            if ($writer_fodder->{comments}->{version} != 2 && $writer_fodder->{comments}->{version} != 3) {

I commited the fix to cvs.
> When you open the produced test.scf file in trev for 
> instance, the sequence is
> rubbish. 
This is only the case with version 3.00 scf format, because trev seems not to like this.
When you create real version 2 scf format (after the fix) trev shows the sequences allright ...
except for the last nucleotide. Meaning there is another (minor) bug around. I'll try to look into that and hope it won't need some poking around in binaries ;-)

Enjoy your holidays !!

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