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Use an LRU cache with CorrectAndSplitScrnaReadPairs to reduce mem #427

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Jun 10, 2024
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Use an LRU cache with CorrectAndSplitScrnaReadPairs to reduce mem #427

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2 changes: 1 addition & 1 deletion gradle/wrapper/gradle-wrapper.properties
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
distributionUrl=https\://services.gradle.org/distributions/gradle-8.8-bin.zip
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Java 21 cannot run Gradle 8.4: via https://docs.gradle.org/current/userguide/compatibility.html#java

Makes it difficult to debug in IntelliJ.

networkTimeout=10000
validateDistributionUrl=true
zipStoreBase=GRADLE_USER_HOME
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28 changes: 24 additions & 4 deletions src/java/org/broadinstitute/dropseqrna/beadsynthesis/CorrectAndSplitScrnaReadPairs.java
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Expand Up @@ -79,11 +79,26 @@ public class CorrectAndSplitScrnaReadPairs
public String BARCODE_QUALS_TAG;

private Map<String, Double> allowedBarcodeNormalizedOccurences;
private final Map<String, List<String>> ed1MatchCache = new HashMap<>();

private final ResourceLimitedMap<String, List<String>> ed1MatchCache =
new ResourceLimitedMap<>(
1_000_000,
new ResourceLimitedMapFunctor<>() {
@Override
public List<String> makeValue(final String key) {
return CorrectAndSplitScrnaReadPairs.this.getEd1Matches(key);
}

@Override
public void finalizeValue(final String key, final List<String> strings) {
}
}
);

private List<BaseRange> baseRanges;

private BarcodeCorrectionMetrics metrics = new BarcodeCorrectionMetrics();
private Histogram<Integer> numCandidatesHist = new Histogram<>("NUM_ED1_CANDIDATES", "NUM_READS");
private final BarcodeCorrectionMetrics metrics = new BarcodeCorrectionMetrics();
private final Histogram<Integer> numCandidatesHist = new Histogram<>("NUM_ED1_CANDIDATES", "NUM_READS");

@Override
protected void splitBAMs() {
Expand Down Expand Up @@ -146,7 +161,7 @@ private String getCorrectedCellBarcode(final SAMRecord readWithBarcode) {
exactMatchBarcodes.add(cellBarcode);
return cellBarcode;
} else {
List<String> ed1Matches = ed1MatchCache.computeIfAbsent(cellBarcode, this::getEd1Matches);
List<String> ed1Matches = ed1MatchCache.get(cellBarcode);
if (ed1Matches.isEmpty()) {
if (VERBOSITY == Log.LogLevel.DEBUG && metrics.NUM_READS_UNCORRECTABLE_NO_ED1_BARCODES == 0) {
log.debug("UNCORRECTABLE_NO_ED1 " + readWithBarcode);
Expand Down Expand Up @@ -267,4 +282,9 @@ public static class BarcodeCorrectionMetrics extends MetricBase {
public long NUM_BARCODES_UNCORRECTABLE_NO_ED1_BARCODES;
public long NUM_BARCODES_UNCORRECTED_AMBIGUOUS;
}

/** Stock main method. */
public static void main(final String[] args) {
System.exit(new CorrectAndSplitScrnaReadPairs().instanceMain(args));
}
}
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