From bbc028b64e16605fa71fed496702f404e3098e61 Mon Sep 17 00:00:00 2001
From: George Grant <ggrant@broadinstitute.org>
Date: Wed, 7 Feb 2024 13:50:06 -0500
Subject: [PATCH] Parameterize the logging frequency for ProgressLogger in
 GatherVcfsCloud. (#8662)

---
 .../hellbender/tools/GatherVcfsCloud.java             | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/GatherVcfsCloud.java b/src/main/java/org/broadinstitute/hellbender/tools/GatherVcfsCloud.java
index 1751baece73..2fe45cc2e52 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/GatherVcfsCloud.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/GatherVcfsCloud.java
@@ -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;
@@ -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.");
@@ -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;