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Parameterize the logging frequency for ProgressLogger. #8662

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merged 1 commit into from
Feb 7, 2024
Merged

Parameterize the logging frequency for ProgressLogger. #8662

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11 changes: 8 additions & 3 deletions src/main/java/org/broadinstitute/hellbender/tools/GatherVcfsCloud.java
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Original file line number Diff line number Diff line change
Expand Up @@ -129,6 +129,10 @@ public final class GatherVcfsCloud extends CommandLineProgram {
"AUTOMATIC chooses BLOCK if possible and CONVENTIONAL otherwise.")
public GatherType gatherType = GatherType.AUTOMATIC;

@Argument(fullName = "progress-logger-frequency",
doc = "The frequency with which the progress is logged to output (i.e. every N records)")
public Integer progressLoggerFrequency = 10000;

@Advanced
@Argument(fullName = IGNORE_SAFETY_CHECKS_LONG_NAME, doc = "Disable sanity checks to improve performance, may result in silently creating corrupted outputs data")
public boolean ignoreSafetyChecks = false;
Expand Down Expand Up @@ -188,7 +192,7 @@ protected Object doWork() {
break;
case CONVENTIONAL:
log.info("Gathering by conventional means.");
gatherConventionally(sequenceDictionary, createIndex, inputPaths, output, cloudPrefetchBuffer, disableContigOrderingCheck);
gatherConventionally(sequenceDictionary, createIndex, inputPaths, output, cloudPrefetchBuffer, disableContigOrderingCheck, progressLoggerFrequency);
break;
default:
throw new GATKException.ShouldNeverReachHereException("Invalid gather type: " + gatherType + ". Please report this bug to the developers.");
Expand Down Expand Up @@ -299,13 +303,14 @@ private static void gatherConventionally(final SAMSequenceDictionary sequenceDic
final List<Path> inputFiles,
final File outputFile,
final int cloudPrefetchBuffer,
final boolean disableContigOrderingCheck) {
final boolean disableContigOrderingCheck,
final int progressLoggerFrequency) {
final EnumSet<Options> options = EnumSet.copyOf(VariantContextWriterBuilder.DEFAULT_OPTIONS);
if (createIndex) options.add(Options.INDEX_ON_THE_FLY); else options.remove(Options.INDEX_ON_THE_FLY);
try (final VariantContextWriter out = new VariantContextWriterBuilder().setOutputFile(outputFile)
.setReferenceDictionary(sequenceDictionary).setOptions(options).build()) {

final ProgressLogger progress = new ProgressLogger(log, 10000);
final ProgressLogger progress = new ProgressLogger(log, progressLoggerFrequency);
VariantContext lastContext = null;
Path lastFile = null;
VCFHeader firstHeader = null;
Expand Down
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