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Funcotator - Cannot set splice site window size from CLI #8276

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jonn-smith opened this issue Apr 3, 2023 · 4 comments · Fixed by #8463
Closed

Funcotator - Cannot set splice site window size from CLI #8276

jonn-smith opened this issue Apr 3, 2023 · 4 comments · Fixed by #8463
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@jonn-smith
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The splice site window size (in bases) was never hooked into the CLI. This should be added as a CLI option.
@zhanyinx
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Hi there,

is there any update on this?
Thanks

Best
Zhan

jonn-smith added a commit that referenced this issue Aug 10, 2023
@jonn-smith
Connected the splice site window size to CLI parameters.
c74d4c8 
Fixes #8276
@jonn-smith jonn-smith mentioned this issue Aug 10, 2023
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@jonn-smith
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@zhanyinx I just put in a fix for it - #8463

When it gets merged it will be in the nightly builds.

@zhanyinx
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@jonn-smith thanks a lot

jonn-smith added a commit that referenced this issue Aug 11, 2023
@jonn-smith
Funcotator: Connected the splice site window size to CLI parameters. (#…
4212fdf 
…8463)

* Funcotator: Connected the splice site window size to CLI parameters.

Fixes #8276
@jonn-smith
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@zhanyinx Just merged a fix to this, which exposes a new CLI parameter. Tonight's nightly build will have the new option for you to try.

rickymagner pushed a commit that referenced this issue Nov 28, 2023
@jonn-smith @rickymagner
Funcotator: Connected the splice site window size to CLI parameters. (#…
ed33e87 
…8463)

* Funcotator: Connected the splice site window size to CLI parameters.

Fixes #8276
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Connected the splice site window size to CLI parameters. broadinstitute/gatk
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@jonn-smith @zhanyinx