Renamed OutputMode.EMIT_ALL_SITES to EMIT_ALL_ACTIVE_SITES #6181
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michaelgatzen
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Sep 24, 2019
michaelgatzen
commented
- Modified GenotypeGVCFsEngine.OutputMode enum documentation to reflect this change
| /** produces calls at any callable site regardless of confidence; this argument is intended only for point | ||
| * mutations (SNPs); it will not produce a comprehensive set of indels. */ | ||
| EMIT_ALL_SITES | ||
| /** produces calls at any callable site regardless of confidence. This does not necessarily output calls for all |
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produces calls at any callable site regardless of confidence -> Produces calls at any region over the activity threshold regardless of confidence
| @@ -376,7 +376,7 @@ protected final boolean hasTooManyAlternativeAlleles(final VariantContext vc) { | |||
| } | |||
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| protected boolean emitAllSites() { | |||
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Put a comment here explaining this in somewhat better detail I think.
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I put a similar comment there and referred to the OutputMode documentation. Do you want more detail?
I also renamed this function to emitAllActiveSites(), just to be consistent.
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Can you try running haplotype caller with this argument @droazen asked what exactly is happening when you run with this argument in VCF mode. Can you just run this on or test bam for example and let me know if it is making reference calls? Maybe the answer is to rename the argument to EMIT_ALL_LOW_QUALITY_SITES. That might be a little more clear as to what is going on and seeing if there are ref only calls would be helpful.
- Modified GenotypeGVCFsEngine.OutputMode enum documentation to reflect this change
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