JaneliaSciComp/msg — Issue #21: msg.pl - updating genomes step - samtools view command references missing var
Author: gregpinero
Created: 2012-01-25 15:35:49+00:00
State: open

It appears that when this line is called:
&system_call("samtools", "view", "-bt", "$genomes{$sp}.msg.fai", "-o $out.bam", "$out.filtered.sam") ;

That %genomes has not been defined yet. This creates a command where the fai file doesn't exist.

The bam file is still created so I'm not sure what adverse effect this is having but it's worth investigating.

Maybe it is a typo and was intended to say genomes_fa?

We should probably always use strict mode in Perl to avoid issues like this.