From c0c46b0b126cef4e55b695d1e7054a80aaf33b7e Mon Sep 17 00:00:00 2001
From: tfenne <tfenne@tfenne.com>
Date: Tue, 18 May 2021 16:44:54 -0600
Subject: [PATCH] Minor fixes to IlluminaBasecallsToSam and related classes.

---
 src/main/java/picard/illumina/IlluminaBasecallsToSam.java   | 5 +++--
 src/main/java/picard/illumina/SortedBasecallsConverter.java | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java
index 271d298c81..acbd73ee26 100644
--- a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java
+++ b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java
@@ -312,7 +312,8 @@ private void initialize() {
                 .withApplyEamssFiltering(APPLY_EAMSS_FILTER)
                 .withIncludeNonPfReads(INCLUDE_NON_PF_READS)
                 .withIgnoreUnexpectedBarcodes(IGNORE_UNEXPECTED_BARCODES)
-                .withBclQualityEvaluationStrategy(bclQualityEvaluationStrategy);
+                .withBclQualityEvaluationStrategy(bclQualityEvaluationStrategy)
+                .withMaxRecordsInRam(this.MAX_RECORDS_IN_RAM);
 
         if (SORT) {
             converterBuilder = converterBuilder
@@ -551,7 +552,7 @@ protected String[] customCommandLineValidation() {
         // Remove once deprecated parameter is deleted.
         if (MAX_READS_IN_RAM_PER_TILE != -1) {
             log.warn("Setting deprecated parameter `MAX_READS_IN_RAM_PER_TILE` use ` MAX_RECORDS_IN_RAM` instead");
-            MAX_RECORDS_IN_RAM = MAX_READS_IN_RAM_PER_TILE;
+            MAX_RECORDS_IN_RAM = MAX_READS_IN_RAM_PER_TILE * NUM_PROCESSORS;
         }
 
         final ArrayList<String> messages = new ArrayList<>();
diff --git a/src/main/java/picard/illumina/SortedBasecallsConverter.java b/src/main/java/picard/illumina/SortedBasecallsConverter.java
index 9b22ee3dea..46af4a071c 100644
--- a/src/main/java/picard/illumina/SortedBasecallsConverter.java
+++ b/src/main/java/picard/illumina/SortedBasecallsConverter.java
@@ -104,7 +104,7 @@ protected SortedBasecallsConverter(
         this.codecPrototype = codecPrototype;
         this.outputRecordComparator = outputRecordComparator;
         this.outputRecordClass = outputRecordClass;
-        tileWriteExecutor = new ThreadPoolExecutorWithExceptions(barcodeRecordWriterMap.keySet().size());
+        tileWriteExecutor = new ThreadPoolExecutorWithExceptions(numThreads);
         tileReadExecutor = new ThreadPoolExecutorWithExceptions(numThreads);
     }