From 65e30a5dff67bc2ab66779d3aa8f5cbe5fb78d05 Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Mon, 18 Nov 2024 12:03:02 -0800
Subject: [PATCH] GFF3 parsing error -- fixes #1617

---
 src/main/java/org/broad/igv/feature/Exon.java | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/main/java/org/broad/igv/feature/Exon.java b/src/main/java/org/broad/igv/feature/Exon.java
index d23b38dab6..a19521dc51 100644
--- a/src/main/java/org/broad/igv/feature/Exon.java
+++ b/src/main/java/org/broad/igv/feature/Exon.java
@@ -229,12 +229,14 @@ private void computeAminoAcidSequence(Genome genome, Exon prevExon, Exon nextExo
                         // Grab nucleotides from next exon if needed for last codon
                         int phase = (3 - readingFrame) % 3;
                         int diff = 3 - ((readEnd - (codingStart + phase)) % 3);
-                        if (diff > 0 && nextExon != null) {
+                        if (diff > 0 && diff < 3 && nextExon != null && !nextExon.isNonCoding()) {
                             byte[] d = genome.getSequence(chr, nextExon.getCdStart(), nextExon.getCdStart() + diff);
-                            byte[] tmp = new byte[d.length + seqBytes.length];
-                            System.arraycopy(seqBytes, 0, tmp, 0, seqBytes.length);
-                            System.arraycopy(d, 0, tmp, seqBytes.length, d.length);
-                            seqBytes = tmp;
+                            if(d != null) {
+                                byte[] tmp = new byte[d.length + seqBytes.length];
+                                System.arraycopy(seqBytes, 0, tmp, 0, seqBytes.length);
+                                System.arraycopy(d, 0, tmp, seqBytes.length, d.length);
+                                seqBytes = tmp;
+                            }
                         }
 
                     } else {