From 76584da65ab5ca8e7d8c48140ba41af88a53c11a Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Sun, 8 Dec 2024 19:36:46 -0800
Subject: [PATCH] Disable memory-mapped index files.  This is not needed for
 IGV, and can result rare but obscure errors.

---
 src/main/java/org/broad/igv/sam/reader/SAMReader.java     | 6 ++++--
 src/main/java/org/broad/igv/sam/reader/SamReaderPool.java | 3 ++-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/main/java/org/broad/igv/sam/reader/SAMReader.java b/src/main/java/org/broad/igv/sam/reader/SAMReader.java
index 84ceeebdc2..ab87e569c7 100644
--- a/src/main/java/org/broad/igv/sam/reader/SAMReader.java
+++ b/src/main/java/org/broad/igv/sam/reader/SAMReader.java
@@ -69,7 +69,7 @@ public SAMReader(String samFile) throws IOException {
         this(samFile, true);
     }
 
-    public SAMReader(String samFile, boolean requireIndex) throws IOException {
+    public SAMReader(String samFile, boolean requireIndex) {
         this.samFile = samFile;
         if (requireIndex) {
             featureIndex = SamUtils.getIndexFor(samFile);
@@ -78,7 +78,9 @@ public SAMReader(String samFile, boolean requireIndex) throws IOException {
             }
         }
         factory = SamReaderFactory.makeDefault().
-                validationStringency(ValidationStringency.SILENT);
+                validationStringency(ValidationStringency.SILENT).
+                referenceSource(new IGVReferenceSource()).
+                enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX);
         loadHeader();
     }
 
diff --git a/src/main/java/org/broad/igv/sam/reader/SamReaderPool.java b/src/main/java/org/broad/igv/sam/reader/SamReaderPool.java
index e18395cc3b..1c163badd5 100644
--- a/src/main/java/org/broad/igv/sam/reader/SamReaderPool.java
+++ b/src/main/java/org/broad/igv/sam/reader/SamReaderPool.java
@@ -84,7 +84,8 @@ private SamReader createReader(int bufferSize) throws IOException {
         boolean isLocal = locator.isLocal();
         final SamReaderFactory factory = SamReaderFactory.makeDefault().
                 referenceSource(new IGVReferenceSource()).
-                validationStringency(ValidationStringency.SILENT);
+                validationStringency(ValidationStringency.SILENT).
+                enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX);
         SamInputResource resource;
 
         if (isLocal) {