[galaxy-dev] Updated Freebayes Wrapper (0.9.14) - Bug Report

Thanks for the major update of the Freebayes wrapper, excellent!

I've run into two issues, however.

1) When using "set allelic scope" I get the following error:

Fatal error: Exit code 1 () freebayes: unrecognized option `--min-repeat-length' did you mean --min-repeat-size ?

2) When using a vcf file as input I get the following error:

Fatal error: Exit code 1 () open: No such file or directory [bgzf_check_bgzf] failed to open the file: input_variant_vcf.vcf.gz [tabix++] was bgzip used to compress this file? input_variant_vcf.vcf.gz

I'd be happy to help resolve these. Is there a bitbucket repo somewhere to submit pull requests? Also, I'm not sure if this is best sent to this list or put into Trello, etc.