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Add AbstractVariant.alleleKey field and alleleKey() accessor method
Update AllelePropertiesDaoMvStore, ClinVarDaoMvStore, RemmDao and LocalFrequencyDao use memoised Variant.alleleKey()
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -37,6 +37,8 @@ | |
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| import java.io.IOException; | ||
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| import static org.monarchinitiative.svart.VariantType.INS; | ||
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| /** | ||
| * | ||
| * @author Jules Jacobsen <[email protected]> | ||
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@@ -52,8 +54,8 @@ public RemmDao(TabixDataSource remmTabixDataSource) { | |
| } | ||
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| @Caching(cacheable = { | ||
| @Cacheable(cacheNames = "hg19.remm", keyGenerator = "variantKeyGenerator", condition = "#variant.genomeAssembly == T(org.monarchinitiative.exomiser.core.genome.GenomeAssembly).HG19"), | ||
| @Cacheable(cacheNames = "hg38.remm", keyGenerator = "variantKeyGenerator", condition = "#variant.genomeAssembly == T(org.monarchinitiative.exomiser.core.genome.GenomeAssembly).HG38"), | ||
| @Cacheable(cacheNames = "hg19.remm", key = "#variant.alleleKey()", condition = "#variant.genomeAssembly == T(org.monarchinitiative.exomiser.core.genome.GenomeAssembly).HG19"), | ||
| @Cacheable(cacheNames = "hg38.remm", key = "#variant.alleleKey()", condition = "#variant.genomeAssembly == T(org.monarchinitiative.exomiser.core.genome.GenomeAssembly).HG38"), | ||
| }) | ||
| @Override | ||
| public PathogenicityData getPathogenicityData(Variant variant) { | ||
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@@ -62,46 +64,13 @@ public PathogenicityData getPathogenicityData(Variant variant) { | |
| if (variant.getVariantEffect() == VariantEffect.MISSENSE_VARIANT) { | ||
| return PathogenicityData.empty(); | ||
| } | ||
| return processResults(variant); | ||
| } | ||
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| private PathogenicityData processResults(Variant variant) { | ||
| String chromosome = variant.contigName(); | ||
| int start = variant.start(); | ||
| int end = calculateEndPosition(variant); | ||
| // test bases either side of insertion or all bases of a SNV/MNV/DEL | ||
| int end = variant.variantType() == INS ? variant.end() + 1 : variant.end(); | ||
| return getRemmData(chromosome, start, end); | ||
| } | ||
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| private int calculateEndPosition(Variant variant) { | ||
| int pos = variant.start(); | ||
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| //we're doing this here in order not to have to count all this each time we need the value | ||
| int refLength = variant.ref().length(); | ||
| int altLength = variant.alt().length(); | ||
| //What about MNV? | ||
| if (refLength == altLength) { | ||
| return pos; | ||
| } | ||
| //these end positions are calculated according to recommendation by Max and Peter who produced the REMM score | ||
| //don't change this unless they say. | ||
| if (isDeletion(refLength, altLength)) { | ||
| // test all deleted bases (being 1-based we need to correct the length) | ||
| return pos + refLength - 1; | ||
| } else if (isInsertion(refLength, altLength)) { | ||
| // test bases either side of insertion | ||
| return pos + 1; | ||
| } | ||
| return pos; | ||
| } | ||
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| private static boolean isDeletion(int refLength, int altLength) { | ||
| return refLength > altLength; | ||
| } | ||
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| private static boolean isInsertion(int refLength, int altLength) { | ||
| return refLength < altLength; | ||
| } | ||
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| private synchronized PathogenicityData getRemmData(String chromosome, int start, int end) { | ||
| try { | ||
| float score = Float.NaN; | ||
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