From 907726c2985cdf9e44217b4da1f7cb2af57cf27d Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Wed, 25 Sep 2024 14:24:44 -0400
Subject: [PATCH] Fix for 2bit reference crash when reading the end of the
 reference (#1586)

* Clip requests for sequence to not go over the length of the chromosome.
* fixes https://github.com/igvteam/igv/issues/1583
---
 src/main/java/org/broad/igv/ucsc/twobit/TwoBitSequence.java | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/main/java/org/broad/igv/ucsc/twobit/TwoBitSequence.java b/src/main/java/org/broad/igv/ucsc/twobit/TwoBitSequence.java
index d491d997f..27368ad83 100644
--- a/src/main/java/org/broad/igv/ucsc/twobit/TwoBitSequence.java
+++ b/src/main/java/org/broad/igv/ucsc/twobit/TwoBitSequence.java
@@ -133,6 +133,9 @@ public byte[] readSequence(String seqName, int regionStart, int regionEnd) {
                 throw new RuntimeException("regionStart cannot be less than 0");
             }
 
+            //don't run off the end of the genome
+            regionEnd = Math.min(record.getDnaSize(), regionEnd);
+
             Queue<Block> nBlocks = _getOverlappingBlocks(regionStart, regionEnd, record.nBlocks);
             Queue<Block> maskBlocks = _getOverlappingBlocks(regionStart, regionEnd, record.maskBlocks);