Add a --numeric-gt option to VariantsToTable #8219
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Github actions tests reported job failures from actions build 4246430995
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Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## master #8219 +/- ##
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+ Coverage 86.654% 86.655% +0.001%
- Complexity 39165 39167 +2
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Files 2346 2346
Lines 183659 183673 +14
Branches 20151 20152 +1
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+ Hits 159147 159161 +14
Misses 17451 17451
Partials 7061 7061
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* add an new option to VariantsToTable to allow output VCF style numeric GT fields previously it always output the actual bases of the Allele in the GT spot * resolves #8160 * updates htsjdk to 3.0.5
lbergelson
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jonn-smith
requested changes
Aug 16, 2024
| for ( final String gf : genotypeFieldsToTake ) { | ||
| if ( vc.hasGenotype(sample) && vc.getGenotype(sample).hasAnyAttribute(gf) ) { | ||
| if ( vc.hasGenotype(sample) && genotype.hasAnyAttribute(gf) ) { |
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Pulling the genotype into a variable above before doing the hasGenotype check seems strange to me.
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that's.... a good point...
jamesemery
approved these changes
Aug 16, 2024
| @@ -122,6 +123,7 @@ | |||
| public final class VariantsToTable extends VariantWalker { | |||
| public final static String SPLIT_MULTI_ALLELIC_LONG_NAME = "split-multi-allelic"; | |||
| public final static String SPLIT_MULTI_ALLELIC_SHORT_NAME = "SMA"; | |||
| public static final String NUMERIC_GT_FULLNAME = "numeric-gt"; | |||
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perhaps "use-numeric-gt" to make it verbed appropriately?
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@jonn-smith I changed the check to be equivalent but less weird looking. |
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previously it always output the actual bases of the Allele in the GT spot