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GatkSparkTool doesn't support fasta.gz #5258

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lbergelson opened this issue Oct 3, 2018 · 1 comment
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GatkSparkTool doesn't support fasta.gz #5258

lbergelson opened this issue Oct 3, 2018 · 1 comment
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@tomwhite @jamesemery
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@lbergelson
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GatkSparkTool doesn't propagate the '.gzi' file when passing fasta files around. This means it can't read fasta.gz files. We should fix this and add tests for fasta.gz.

Fasta support was recently introduced here: #5127
@droazen droazen added the bug label Oct 3, 2018
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droazen commented Oct 3, 2018

@tomwhite take note

@tomwhite tomwhite mentioned this issue Oct 8, 2018
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lbergelson pushed a commit that referenced this issue Oct 9, 2018
@tomwhite @lbergelson
Support fasta.gz in GATKSparkTool (#5290)
2880ddd 
* fasta.gz references can now be used in GATKSparkTools
* fixes #5258
EdwardDixon pushed a commit to EdwardDixon/gatk that referenced this issue Nov 9, 2018
@tomwhite @EdwardDixon
Support fasta.gz in GATKSparkTool (broadinstitute#5290)
da1bb69 
* fasta.gz references can now be used in GATKSparkTools
* fixes broadinstitute#5258
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@tomwhite @droazen @lbergelson @jamesemery