VS-1007 - Use default names for VQSR-Lite generated code. #8412
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Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8412 +/- ##
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Coverage ? 86.162%
Complexity ? 35523
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Files ? 2194
Lines ? 166533
Branches ? 17925
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Hits ? 143488
Misses ? 16663
Partials ? 6382 |
…ITY' (as it is named by VQSR Lite) to reduce confusion.
Add branches to .dockstore.yml
…dateVQSRLiteNaming
gbggrant
commented
Jul 14, 2023
| @@ -53,92 +48,6 @@ public static String getGTString(final VariantContext variant) { | |||
| return StringUtils.join(gsStrings, separator); | |||
| } | |||
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| public static VCFHeader generateVcfHeader(Set<String> sampleNames, | |||
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Migrated to ExtractFeaturesEngine
gbggrant
commented
Jul 14, 2023
| } | ||
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| // TODO is this specific for cohort extract? if so name it such | ||
| public static Set<VCFHeaderLine> getEvoquerVcfHeaderLines() { |
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Migrated to ExtractFeaturesEngine
gbggrant
commented
Jul 14, 2023
| @@ -123,12 +123,6 @@ public static VCFHeaderLine getVqsLodHeader(Double vqsLodThreshold, String model | |||
| "Site failed " + model + " model VQSLOD cutoff of " + vqsLodThreshold.toString()); | |||
| } | |||
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| public static VCFHeaderLine getExcessAllelesHeader(int excessAllelesThreshold, String model) { | |||
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Unreferenced header field
rsasch
approved these changes
Jul 14, 2023
mcovarr
approved these changes
Jul 14, 2023
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Passing integration test here - uses updated truth.
Example outputs can be found in this Extract run.