Re-added --only-output-calls-starting-in-intervals as a deprecated argument with warning.
#9000
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lbergelson
reviewed
Oct 15, 2024
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@jamesemery Thanks for doing this. I think it needs a few changes but it should be good to merge after that.
| * This option can only be activated if intervals are specified. | ||
| */ | ||
| @Deprecated | ||
| @Argument(fullName= ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME, |
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I think this was previously advanced as well, I'd tag it again.
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Also, I believe we should be using barclay's @DeprecatedFeature instead of java deprecated. You can include a "detail" message in it that explains what to use instead.
| @@ -1,21 +1,17 @@ | |||
| package org.broadinstitute.hellbender.tools.walkers.mutect; | |||
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This change seems accidental.
| @Deprecated | ||
| @Argument(fullName= GenotypeGVCFs.ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME, | ||
| doc="Restrict variant output to sites that start within provided intervals", | ||
| optional=true, |
lbergelson
approved these changes
Oct 17, 2024
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@lbergelson