[ensembl-dev] Bugs in gtf2vep.pl script

Duarte Molha Duarte.Molha at ogt.co.uk
Thu Nov 8 15:24:39 GMT 2012

Dear Developers

I had a play around with the new gtf2vep script and came across a few bugs and incomplete help.

I have made some improvements on the help usage information and corrected the bugs on line 29 , 30 and 34

Briefly, the first issue I encountered is that I believe the "cache_region_size" and the "dir" arguments are suppose to be optional since they are assigned default values on lines 46 and 49
They are set to be required so the script does not pass the GetOptions step if you do not provide them.
Also the  "cache_region_size" wasn't even mentioned in the usage information so I added it.

In line 34 the if statement:
if(defined($config->{help}) || !@ARGV)
would always fail because on a correctly input command line, after the GetOptions step the @ARGV variable should be empty. So the expression for a valid syntax would always return true and the script would not continue.
I corrected it to:
if(defined($config->{help}) || @ARGV)

I also took the liberty to indicate in the help session what arguments a really required and what arguments are optional.

I hope you agree with the changes.

Best regards

Duarte Molha

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