Protect more calculated end positions from integer overflow. See issue …

…#977
igvteam · Jul 13, 2021 · 40b16d0 · 40b16d0
1 parent 5fd66df
commit 40b16d0
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Showing 5 changed files with 14 additions and 1 deletion.
diff --git a/src/main/java/org/broad/igv/methyl/MethylTrack.java b/src/main/java/org/broad/igv/methyl/MethylTrack.java
@@ -106,6 +106,9 @@ public void load(ReferenceFrame frame) {
         int width = (end - start) / 2;
         int expandedStart = Math.max(0, start - width);
         int expandedEnd = end + width;
+        if(expandedEnd < 0) {
+            expandedEnd = Integer.MAX_VALUE;  // Overflow
+        }
 
         List<MethylScore> scores = new ArrayList<MethylScore>(1000);
         Iterator<MethylScore> iter = dataSource.query(chr, expandedStart, expandedEnd);

diff --git a/src/main/java/org/broad/igv/sam/AlignmentDataManager.java b/src/main/java/org/broad/igv/sam/AlignmentDataManager.java
@@ -360,6 +360,9 @@ public void load(ReferenceFrame frame,
             if (expandEnds) {
                 adjustedStart = Math.max(0, Math.min(start, center - expand));
                 adjustedEnd = Math.max(end, center + expand);
+                if(adjustedEnd < 0) {
+                    adjustedEnd = Integer.MAX_VALUE;  // Overflow
+                }
             }
 
             AlignmentInterval loadedInterval = loadInterval(chr, adjustedStart, adjustedEnd, renderOptions);

diff --git a/src/main/java/org/broad/igv/track/DataTrack.java b/src/main/java/org/broad/igv/track/DataTrack.java
@@ -141,6 +141,10 @@ public synchronized void load(ReferenceFrame referenceFrame) {
         int delta = multiLocus ? 1 : (end - start) / 2;
         int expandedStart = Math.max(0, start - delta);
         int expandedEnd = Math.min(maxEnd, end + delta);
+        if(expandedEnd < 0) {
+            // overflow
+            expandedEnd = Integer.MAX_VALUE;
+        }
         LoadedDataInterval<List<LocusScore>> interval = getSummaryScores(queryChr, expandedStart, expandedEnd, zoom);
         loadedIntervalCache.put(referenceFrame.getName(), interval);
 

diff --git a/src/main/java/org/broad/igv/track/FeatureTrack.java b/src/main/java/org/broad/igv/track/FeatureTrack.java
@@ -685,6 +685,9 @@ protected void loadFeatures(final String chr, final int start, final int end, fi
             int delta = (end - start) / 2;
             int expandedStart = start - delta;
             int expandedEnd = end + delta;
+            if(expandedEnd < 0) {
+                expandedEnd = Integer.MAX_VALUE;  // overflow
+            }
 
             //Make sure we are only querying within the chromosome we allow for somewhat pathological cases of start
             //being negative and end being outside, but only if directly queried. Our expansion should not

diff --git a/src/test/java/org/broad/igv/sam/ByteSubarrayTest.java b/src/test/java/org/broad/igv/sam/ByteSubarrayTest.java
@@ -11,7 +11,7 @@ public void testReverseComplement()  {
         byte [] forwardSeq = "AAAAATCGAAAA".getBytes();
         byte [] expected = "CGAT".getBytes();
 
-        ByteSubarray subarray = new ByteSubarray(forwardSeq, 4, 4);
+        ByteSubarray subarray = new ByteSubarray(forwardSeq, 4, 4, (byte) 0);
         ByteSubarray reverse = AlignmentUtils.reverseComplementCopy(subarray);
         for(int i=0; i<4; i++) {
             byte b = reverse.getByte(i);