Lance:

Here is github URL:

https://github.com/nekrut/freebayes


On Wed, Jun 25, 2014 at 2:40 PM, Lance Parsons <lpars...@princeton.edu>
wrote:

> 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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-- 
Anton Nekrutenko
Associate Professor
Dept. of Biochemistry and Molecular Biology
*http://nekrut.bx.psu.edu <http://nekrut.bx.psu.edu>*
(814) 826-3051
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