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

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

Keiran Raine

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.

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SamToGBrowse.pm.patch (126 bytes) Download Attachment