Bug in Bio::DB::Sam::SamToGBrowse->wiggle_one_bam()

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Bug in Bio::DB::Sam::SamToGBrowse->wiggle_one_bam()

Keiran Raine
Hi,

There appears to be a bug when running the above module when running the bw generation script in the form:

bin/bamToGBrowse.pl /path_to_bams/ /path_to_ref/fasta.fa

The module is attempting to check for the $chrom_sizes file before evaluating if the path should be generated from the $self->fasta variable.

The attached patch will resolve this problem.

Kind regards,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.


------------------------------------------------------------------------------
Free Software Download: Index, Search & Analyze Logs and other IT data in
Real-Time with Splunk. Collect, index and harness all the fast moving IT data
generated by your applications, servers and devices whether physical, virtual
or in the cloud. Deliver compliance at lower cost and gain new business
insights. http://p.sf.net/sfu/splunk-dev2dev 
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

SamToGBrowse.pm.patch (126 bytes) Download Attachment