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Bug fix in flow allele filtering #8775

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merged 5 commits into from
May 2, 2024
Merged

Bug fix in flow allele filtering #8775

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1d4cbfd
Fixed a bug that prevented filtering by SOR in many cases
ilyasoifer Apr 12, 2024
82e8b10
Updated .gitignore
ilyasoifer Apr 12, 2024
e60afd5
Test added
ilyasoifer Apr 14, 2024
96cb514
Test added
ilyasoifer Apr 14, 2024
cfc01ce
Added direct test for identifyBadAlleles
ilyasoifer Apr 28, 2024
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8 changes: 5 additions & 3 deletions ...ain/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleFiltering.java
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Original file line number Diff line number Diff line change
Expand Up @@ -303,9 +303,11 @@ private List<Event> identifyBadAlleles(final List<Integer> collectedRPLs, final
//we then add alleles with high SOR. Note that amongh all allleles with the SOR higher than the SOR_THRESHOLD
//we will first filter the one with the lowest QUAL.
logger.debug(() -> String.format("SHA:: Have %d candidates with low QUAL", rplCount));
for (int i = sorIndices.length-1 ; (i >= 0) && (collectedSORs.get(sorIndices[i])>SOR_THRESHOLD) ; i--) {
if (!result.contains(alleles.get(sorIndices[i]))) {
result.add(alleles.get(sorIndices[i]));
for (int i = sorIndices.length-1 ; (i >= 0) ; i--) {
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ahh thats a nasty issue i see...

if (collectedSORs.get(sorIndices[i])>SOR_THRESHOLD){
if (!result.contains(alleles.get(sorIndices[i]))) {
result.add(alleles.get(sorIndices[i]));
}
}
}
logger.debug(() -> String.format("SHA:: Have %d candidates with high SOR", result.size() - rplCount));
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