Updated Freebayes Wrapper - Bugs

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Updated Freebayes Wrapper - Bugs

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?

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

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Re: Updated Freebayes Wrapper - Bugs

Anton Nekrutenko-2
Lance:

Here is github URL:

https://github.com/nekrut/freebayes


On Wed, Jun 25, 2014 at 2:40 PM, Lance Parsons <[hidden email]> 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
(814) 826-3051

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Re: Updated Freebayes Wrapper - Bugs

Nicola Soranzo
Il 2014-06-30 18:40 Anton Nekrutenko ha scritto:

> Lance:
>
> Here is github URL:
>
> https://github.com/nekrut/freebayes [3]
>
>  On Wed, Jun 25, 2014 at 2:40 PM, Lance Parsons
> <[hidden email] [4]> 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 ?

This bug (and other 2) would be fixed by this pull request:

https://github.com/nekrut/freebayes/pull/1

Best,
Nicola

>> 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
>>
>> ___________________________________________________________
>> 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:
>>  http://lists.bx.psu.edu/ [1]
>>
>> To search Galaxy mailing lists use the unified search at:
>>  http://galaxyproject.org/search/mailinglists/ [2]
>
> --
>
> Anton Nekrutenko
> Associate Professor
> Dept. of Biochemistry and Molecular Biology
> http://nekrut.bx.psu.edu [5]
>  (814) 826-3051
>
> Links:
> ------
> [1] http://lists.bx.psu.edu/
> [2] http://galaxyproject.org/search/mailinglists/
> [3] https://github.com/nekrut/freebayes
> [4] mailto:[hidden email]
> [5] http://nekrut.bx.psu.edu

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