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harmonize genomic location coordinates
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@leexgh
leexgh committed Aug 25, 2023
1 parent cacc856 commit 93ecaa7
Showing 1 changed file with 15 additions and 35 deletions.
50 changes: 15 additions & 35 deletions ...ent/src/main/java/org/cbioportal/genome_nexus/component/annotation/NotationConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -135,46 +135,31 @@ public GenomicLocation normalizeGenomicLocation(GenomicLocation genomicLocation)
start = nStart;
LOG.info("Start position is changed from " + genomicLocation.getStart() + " to " + start + " for genomic location: " + genomicLocation.getChromosome() + "," + genomicLocation.getStart() + "," + genomicLocation.getEnd() + "," + genomicLocation.getReferenceAllele().trim() + "," + genomicLocation.getVariantAllele().trim() + ". Reason: remove common prefix alleles.");
}
end = harmonizeGenomicLocationCoordinate(genomicLocation, chr, start, end, ref, var);
normalizedGenomicLocation.setStart(start);
normalizedGenomicLocation.setEnd(end);
normalizedGenomicLocation.setReferenceAllele(ref);
normalizedGenomicLocation.setVariantAllele(var);
return normalizedGenomicLocation;
}

public Integer harmonizeGenomicLocationCoordinate(GenomicLocation genomicLocation, String chr, Integer start, Integer end, String ref, String var) {
if (ref.equals("-") || ref.length() == 0 || ref.equals("NA") || ref.contains("--")) {
// insertion variants: end = start + 1
if (end != start + 1) {
end = start + 1;
LOG.info("End position is changed from " + genomicLocation.getEnd() + " to " + end + " for genomic location: " + genomicLocation.getChromosome() + "," + genomicLocation.getStart() + "," + genomicLocation.getEnd() + "," + genomicLocation.getReferenceAllele().trim() + "," + genomicLocation.getVariantAllele().trim() + ". Reason: wrong coordinates, insersion variants' end position should be start + 1.");
}
}
else if (var.equals("-") || var.length() == 0 || var.equals("NA") || var.contains("--")) {
// deletion variants: ref.length() = end - start + 1
if (ref.length() != end - start + 1) {
end = start + ref.length() - 1;
LOG.info("End position is changed from " + genomicLocation.getEnd() + " to " + end + " for genomic location: " + genomicLocation.getChromosome() + "," + genomicLocation.getStart() + "," + genomicLocation.getEnd() + "," + genomicLocation.getReferenceAllele().trim() + "," + genomicLocation.getVariantAllele().trim() + ". Reason: wrong coordinates, deletion length should be end - start + 1.");
}
}
else if (ref.length() > 1 && var.length() >= 1) {
// delins variants with multiple ref alleles: ref.length() = end - start + 1
if (ref.length() != end - start + 1) {
end = start + 1;
LOG.info("End position is changed from " + genomicLocation.getEnd() + " to " + end + " for genomic location: " + genomicLocation.getChromosome() + "," + genomicLocation.getStart() + "," + genomicLocation.getEnd() + "," + genomicLocation.getReferenceAllele().trim() + "," + genomicLocation.getVariantAllele().trim() + ". Reason: wrong coordinates, delins variants with multiple deleted reference alleles should have end position equals to start + ref.length - 1.");
}
}
else if (ref.length() == 1 && var.length() > 1) {
// delins variants with single ref allele: ref.length() = end - start + 1
if (!end.equals(start)) {
end = start;
LOG.info("End position is changed from " + genomicLocation.getEnd() + " to " + end + " for genomic location: " + genomicLocation.getChromosome() + "," + genomicLocation.getStart() + "," + genomicLocation.getEnd() + "," + genomicLocation.getReferenceAllele().trim() + "," + genomicLocation.getVariantAllele().trim() + ". Reason: wrong coordinates, delins variants with single deleted reference allele should have end position equals to start.");
}
}
else {
// SNV
if (!end.equals(start)) {
end = start;
LOG.info("End position is changed from " + genomicLocation.getEnd() + " to " + end + " for genomic location: " + genomicLocation.getChromosome() + "," + genomicLocation.getStart() + "," + genomicLocation.getEnd() + "," + genomicLocation.getReferenceAllele().trim() + "," + genomicLocation.getVariantAllele().trim() + ". Reason: wrong coordinates, SNV end position should equal to start.");
// all deletion, delins, and SNV
// for single allele delins and SNV, ref.length() = 1, so end = start
if (end != start + ref.length() - 1) {
end = start + ref.length() - 1;
LOG.info("End position is changed from " + genomicLocation.getEnd() + " to " + end + " for genomic location: " + genomicLocation.getChromosome() + "," + genomicLocation.getStart() + "," + genomicLocation.getEnd() + "," + genomicLocation.getReferenceAllele().trim() + "," + genomicLocation.getVariantAllele().trim() + ". Reason: wrong coordinates, end position should be the range of nucleotides deleted/affected.");
}
}
normalizedGenomicLocation.setStart(start);
normalizedGenomicLocation.setEnd(end);
normalizedGenomicLocation.setReferenceAllele(ref);
normalizedGenomicLocation.setVariantAllele(var);
return normalizedGenomicLocation;
return end;
}

@Nullable
Expand Down Expand Up @@ -205,11 +190,6 @@ public String genomicToHgvs(GenomicLocation genomicLocation) {
return null;
}
} else if (var.equals("-") || var.length() == 0 || var.equals("NA") || var.contains("--")) {
if (end < start) {
// Special case for GENIE
// If end position is less than start position, change it to correct number
end = start + ref.length() - 1;
}
if (ref.length() == 1) {
/*
Process Deletion (single positon)
Expand Down

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