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lib: use the same normalization parameters as OpenCGA, #TASK-6427, #T…
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…ASK-5318

On branch TASK-5318
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalIndexer.java
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jtarraga committed Jun 28, 2024
1 parent fff65d1 commit 78662d6
Showing 1 changed file with 3 additions and 4 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -74,13 +74,12 @@ public abstract class ClinicalIndexer {
protected VariantNormalizer normalizer;

public ClinicalIndexer(Path genomeSequenceFilePath) throws IOException {
// Forcing decomposition here in all cases - assuming the way CellBase stores clinical variants from here
// onwards will be decomposed and Adaptors will deal with phased/no-phased queries
// Use the same OpenCGA normalization parameters
VariantNormalizer.VariantNormalizerConfig variantNormalizerConfig
= (new VariantNormalizer.VariantNormalizerConfig())
.setReuseVariants(true)
.setNormalizeAlleles(false)
.setDecomposeMNVs(true);
.setNormalizeAlleles(true)
.setDecomposeMNVs(false);

if (genomeSequenceFilePath != null) {
logger.info("Enabling left aligning by using sequence at {}", genomeSequenceFilePath.toString());
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