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?

--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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