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Cloud-enable IndexFeatureFile and change input arg name from -F to -I. #6246

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merged 3 commits into from
Nov 8, 2019

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cmnbroad
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@cmnbroad cmnbroad commented Nov 5, 2019

Fixes #6161. Requires an htsjdk update.

@lbergelson
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2.21.0 is out now

@cmnbroad cmnbroad force-pushed the cn_index_feature_file_cloud branch from 05cb8fd to 95a15d3 Compare November 6, 2019 21:21
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Looks good to me.

"IndexFeatureFile", "-I", vcfOnGCS
};

new Main().instanceMain(args);
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This is a bit unconventional, most tests just use runCommandLine there's nothing wrong with this though.

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@cmnbroad Looks good but I noticed failing tests in VariantsSparkSinkUnitTest where you missed an F -> I

@lbergelson lbergelson merged commit a632a05 into master Nov 8, 2019
@lbergelson lbergelson deleted the cn_index_feature_file_cloud branch November 8, 2019 21:22
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IndexFeatureFile should support GCS inputs/outputs
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