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IndexFeatureFile should support GCS inputs/outputs #6161

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droazen opened this issue Sep 13, 2019 · 3 comments · Fixed by #6246
Closed

IndexFeatureFile should support GCS inputs/outputs #6161

droazen opened this issue Sep 13, 2019 · 3 comments · Fixed by #6246
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@droazen
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droazen commented Sep 13, 2019

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@droazen
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droazen commented Sep 13, 2019

Requested by @yfarjoun

@droazen droazen self-assigned this Sep 13, 2019
@droazen droazen added this to the Engine-Q3-2019 milestone Sep 13, 2019
@droazen droazen assigned cmnbroad and unassigned droazen Sep 23, 2019
@droazen droazen modified the milestones: Engine-Q3-2019, GATK-Triaged-Issues Sep 23, 2019
This was referenced Oct 23, 2019
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While we're at it, we're going to change the name of the input argument from -F to -I.

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I've had to index VCFs in the cloud and it made me sad, but part of what made me sad was that I didn't have write permissions to save my index. Any chance of indexing on the fly in those cases?

@cmnbroad cmnbroad mentioned this issue Nov 5, 2019
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lbergelson pushed a commit that referenced this issue Nov 8, 2019
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Cloud-enable IndexFeatureFile and change input arg name from -F to -I. (
a632a05 
#6246)

* Cloud-enable IndexFeatureFile.
* Change IndexFeatureFile to use -I instead of -F.
* Fixes #6161
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Cloud-enable IndexFeatureFile and change input arg name from -F to -I. broadinstitute/gatk
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@droazen @ldgauthier @cmnbroad