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Remove hash sets for counting various classes of CBC, to reduce memor… #430

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Jun 27, 2024
Merged

Remove hash sets for counting various classes of CBC, to reduce memor… #430

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21 changes: 0 additions & 21 deletions src/java/org/broadinstitute/dropseqrna/beadsynthesis/CorrectAndSplitScrnaReadPairs.java
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Original file line number Diff line number Diff line change
Expand Up @@ -130,11 +130,6 @@ protected void splitBAMs() {

if (METRICS != null) {
final MetricsFile<BarcodeCorrectionMetrics, Integer> metricsFile = getMetricsFile();
metrics.NUM_BARCODES_EXACT_MATCH = exactMatchBarcodes.size();
metrics.NUM_BARCODES_CORRECTED_SINGLE_ED1 = singleEd1Barcodes.size();
metrics.NUM_BARCODES_UNCORRECTABLE_NO_ED1_BARCODES = noEd1Barcodes.size();
metrics.NUM_BARCODES_CORRECTED_MULTI_ED1 = multiEd1Barcodes.size();
metrics.NUM_BARCODES_UNCORRECTED_AMBIGUOUS = ambiguousBarcodes.size();
metricsFile.addMetric(metrics);
metricsFile.addHistogram(numCandidatesHist);
metricsFile.write(METRICS);
Expand All @@ -161,7 +156,6 @@ private String getCorrectedCellBarcode(final SAMRecord readWithBarcode) {
log.debug("EXACT_MATCH " + readWithBarcode);
}
++metrics.NUM_READS_EXACT_MATCH;
exactMatchBarcodes.add(cellBarcode);
return cellBarcode;
} else {
List<String> ed1Matches = ed1MatchCache.get(cellBarcode);
Expand All @@ -170,14 +164,12 @@ private String getCorrectedCellBarcode(final SAMRecord readWithBarcode) {
log.debug("UNCORRECTABLE_NO_ED1 " + readWithBarcode);
}
++metrics.NUM_READS_UNCORRECTABLE_NO_ED1_BARCODES;
noEd1Barcodes.add(cellBarcode);
return cellBarcode;
} else if (ed1Matches.size() == 1) {
if (VERBOSITY == Log.LogLevel.DEBUG && metrics.NUM_READS_CORRECTED_SINGLE_ED1 == 0) {
log.debug("CORRECTED_SINGLE_ED1 " + readWithBarcode);
}
++metrics.NUM_READS_CORRECTED_SINGLE_ED1;
singleEd1Barcodes.add(cellBarcode);
numCandidatesHist.increment(1);
return ed1Matches.getFirst();
} else {
Expand All @@ -199,15 +191,13 @@ private String getCorrectedCellBarcode(final SAMRecord readWithBarcode) {
log.debug("CORRECTED_MULTI_ED1 " + readWithBarcode);
}
++metrics.NUM_READS_CORRECTED_MULTI_ED1;
multiEd1Barcodes.add(cellBarcode);
numCandidatesHist.increment(ed1Matches.size());
return bestBarcode;
} else {
if (VERBOSITY == Log.LogLevel.DEBUG && metrics.NUM_READS_UNCORRECTED_AMBIGUOUS == 0) {
log.debug("UNCORRECTED_AMBIGUOUS " + readWithBarcode);
}
++metrics.NUM_READS_UNCORRECTED_AMBIGUOUS;
ambiguousBarcodes.add(cellBarcode);
return cellBarcode;
}
}
Expand Down Expand Up @@ -267,23 +257,12 @@ protected String[] customCommandLineValidation() {
return CustomCommandLineValidationHelper.makeValue(super.customCommandLineValidation(), list);
}

// Sets for counting number of unique barcodes in each category
private final Set<String> exactMatchBarcodes = new HashSet<>();
private final Set<String> singleEd1Barcodes = new HashSet<>();
private final Set<String> multiEd1Barcodes = new HashSet<>();
private final Set<String> noEd1Barcodes = new HashSet<>();
private final Set<String> ambiguousBarcodes = new HashSet<>();
public static class BarcodeCorrectionMetrics extends MetricBase {
public long NUM_READS_EXACT_MATCH;
public long NUM_READS_CORRECTED_SINGLE_ED1;
public long NUM_READS_CORRECTED_MULTI_ED1;
public long NUM_READS_UNCORRECTABLE_NO_ED1_BARCODES;
public long NUM_READS_UNCORRECTED_AMBIGUOUS;
public long NUM_BARCODES_EXACT_MATCH;
public long NUM_BARCODES_CORRECTED_SINGLE_ED1;
public long NUM_BARCODES_CORRECTED_MULTI_ED1;
public long NUM_BARCODES_UNCORRECTABLE_NO_ED1_BARCODES;
public long NUM_BARCODES_UNCORRECTED_AMBIGUOUS;
}

/** Stock main method. */
Expand Down
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