samtools_slice_bam/2.0.1 no options available

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samtools_slice_bam/2.0.1 no options available

Eric Kuyt-2
Hey all,

I have a question about the samtools_slice_bam tool in the samtools suite.

It seems the references variable remains empty after re-detecting metadata.
I now tried sorting the bam in galaxy and manually in samtools, but no
references coming up.

I also ran a breakpoint in the binary.Bam.set_meta but it doesn't seem to
be catched.

Any ideas? Thx.

Eric
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Re: samtools_slice_bam/2.0.1 no options available

Eric Kuyt-2
Is this the right spot for this question? Or is it better to ask elsewhere?

On Mon, 13 May 2019 at 09:50, Eric Kuyt <[hidden email]> wrote:

> Hey all,
>
> I have a question about the samtools_slice_bam tool in the samtools suite.
>
> It seems the references variable remains empty after re-detecting
> metadata. I now tried sorting the bam in galaxy and manually in samtools,
> but no references coming up.
>
> I also ran a breakpoint in the binary.Bam.set_meta but it doesn't seem to
> be catched.
>
> Any ideas? Thx.
>
> Eric
>
>
>
>
>
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Re: samtools_slice_bam/2.0.1 no options available

Paula Berrutti
Please,

Remove my email fro the list

Thank you,

Paula

Obter o Outlook para Android<https://aka.ms/ghei36>

________________________________
From: Eric Kuyt <[hidden email]>
Sent: Wednesday, May 22, 2019 9:33:57 AM
To: [hidden email]
Subject: [galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available

Is this the right spot for this question? Or is it better to ask elsewhere?

On Mon, 13 May 2019 at 09:50, Eric Kuyt <[hidden email]> wrote:

> Hey all,
>
> I have a question about the samtools_slice_bam tool in the samtools suite.
>
> It seems the references variable remains empty after re-detecting
> metadata. I now tried sorting the bam in galaxy and manually in samtools,
> but no references coming up.
>
> I also ran a breakpoint in the binary.Bam.set_meta but it doesn't seem to
> be catched.
>
> Any ideas? Thx.
>
> Eric
>
>
>
>
>
___________________________________________________________
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:
  %(web_page_url)s

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  http://galaxyproject.org/search/
___________________________________________________________
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Re: samtools_slice_bam/2.0.1 no options available

Martin Čech
Eric: I recommend https://help.galaxyproject.org/ for your question, it
might reach a better audience there.

Paula: I believe you can unsubscribe here:
https://lists.galaxyproject.org/lists/galaxy-dev.lists.galaxyproject.org/

Regards,

Martin

On Wed, May 22, 2019 at 12:49 PM Paula Berrutti <[hidden email]>
wrote:

> Please,
>
> Remove my email fro the list
>
> Thank you,
>
> Paula
>
> Obter o Outlook para Android<https://aka.ms/ghei36>
>
> ________________________________
> From: Eric Kuyt <[hidden email]>
> Sent: Wednesday, May 22, 2019 9:33:57 AM
> To: [hidden email]
> Subject: [galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available
>
> Is this the right spot for this question? Or is it better to ask elsewhere?
>
> On Mon, 13 May 2019 at 09:50, Eric Kuyt <[hidden email]> wrote:
>
> > Hey all,
> >
> > I have a question about the samtools_slice_bam tool in the samtools
> suite.
> >
> > It seems the references variable remains empty after re-detecting
> > metadata. I now tried sorting the bam in galaxy and manually in samtools,
> > but no references coming up.
> >
> > I also ran a breakpoint in the binary.Bam.set_meta but it doesn't seem to
> > be catched.
> >
> > Any ideas? Thx.
> >
> > Eric
> >
> >
> >
> >
> >
> ___________________________________________________________
> 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:
>   %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
> ___________________________________________________________
> 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:
>   %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
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