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Be explicit about when VariantContexts are biallelic #8332

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Jun 12, 2023
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eachBase -< base
davidbenjamin committed Jun 12, 2023

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This commit was created on GitHub.com and signed with GitHub’s verified signature.
commit dc3ee2b7f23eac35608bc438b156931be64af936
Original file line number Diff line number Diff line change
@@ -88,14 +88,14 @@ public static Pair<Set<Event>, Set<Event>> goodAndBadPileupEvents(final List<Ali
Map<Byte, int[]> SNPCounts = new HashMap<>();

for (PileupElement element : pileup) {
final byte eachBase = element.getBase();
final byte base = element.getBase();

// Subtract out low quality bases to mimic the reading active region determination //TODO this might need to also ignore the qual basees
if (element.getQual() < minBaseQualityScore) {
pileupDepth.decrement();
}

final boolean SNPFound = !onlyTrackDeletions && refBase != eachBase && eachBase != 'D' && element.getQual() > args.qualityForSnpsInPileupDetection;
final boolean SNPFound = !onlyTrackDeletions && refBase != base && base != 'D' && element.getQual() > args.qualityForSnpsInPileupDetection;
final boolean insertionFound = !onlyTrackDeletions && args.detectIndels && element.isBeforeInsertion();
final boolean deletionFound = args.detectIndels && element.isBeforeDeletionStart();

@@ -104,7 +104,7 @@ public static Pair<Set<Event>, Set<Event>> goodAndBadPileupEvents(final List<Ali
final boolean badAssembly = isBadAssemblyRead(element.getRead(), args);

if (SNPFound) {
incrementCounts(eachBase, SNPCounts, badPileup, badAssembly);
incrementCounts(base, SNPCounts, badPileup, badAssembly);
}

if (insertionFound) {