Align the Funcotator checkIfAlreadyAnnotated test with the Funcotator engine code. #7555
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droazen
previously requested changes
Nov 9, 2021
| public static final String VCF_HEADER_ALREADY_ANNOTATED_1 = "Funcotator"; | ||
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| /** Name of the second header line key which indicates that a file has already been annotated. */ | ||
| public static final String VCF_HEADER_ALREADY_ANNOTATED_2 = "Funcotator Version"; |
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I believe there may have been a good reason for checking both of these -- see the original PR for context (#7349). @jonn-smith can confirm one way or another when he returns.
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Ok, but I can find neither a file that contains the other line, nor code that sets it. Maybe its a legacy thing, but if not I just need to know where the code is that creates the first header line (plain "Funcotator").
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I don't think that there is necessarily a good reason for this check. I think the updates are good.
jonn-smith
approved these changes
Nov 22, 2021
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@jonn-smith Quick one when you get a chance - this fixes some things I noticed on my GATK branch when testing my new htsjdk
VCFHeadercode. TheFuncotator.checkIfAlreadyAnnotatedcode was checking for a header line that was never generated byFuncotatorAFAICT, and this also ties together theFuncotatorengine and test code to use the same constants. More could probably be done here but it would require a bigger refactoring.