Updated Freebayes Wrapper (0.9.14) - Bug Report

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

Updated Freebayes Wrapper (0.9.14) - Bug Report

Lance Parsons
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.

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

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at: