From 3e7d61e4d25b692543a97252f82a361c70bf841d Mon Sep 17 00:00:00 2001
From: Yossi Farjoun <farjoun@gmail.com>
Date: Sun, 6 Dec 2015 13:29:03 -0500
Subject: [PATCH] investigate issue 316 in htsjdk. added a test.

---
 src/java/htsjdk/samtools/SAMRecord.java       |  9 ++++++++-
 .../htsjdk/samtools/SAMRecordUnitTest.java    | 20 ++++++++++++++++++-
 2 files changed, 27 insertions(+), 2 deletions(-)

diff --git a/src/java/htsjdk/samtools/SAMRecord.java b/src/java/htsjdk/samtools/SAMRecord.java
index cfa922f74a..9826fe8c2c 100644
--- a/src/java/htsjdk/samtools/SAMRecord.java
+++ b/src/java/htsjdk/samtools/SAMRecord.java
@@ -32,6 +32,7 @@
 import java.lang.reflect.Array;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -1712,7 +1713,13 @@ public List<SAMValidationError> validateCigar(final long recordNumber) {
         List<SAMValidationError> ret = null;
 
         if (null != getHeader() && getValidationStringency() != ValidationStringency.SILENT && !this.getReadUnmappedFlag()) {
-            ret = SAMUtils.validateCigar(this, getCigar(), getReferenceIndex(), getAlignmentBlocks(), recordNumber, "Read CIGAR");
+            try {
+                //make sure that the cashed version is good
+                //wrapped in a try to catch an un-parsable string
+                return SAMUtils.validateCigar(this, getCigar(), getReferenceIndex(), getAlignmentBlocks(), recordNumber, "Read CIGAR");
+            } catch( final IllegalArgumentException e){
+                return Collections.singletonList(new SAMValidationError(SAMValidationError.Type.INVALID_CIGAR,e.getMessage(),getReadName(),recordNumber));
+            }
         }
         return ret;
     }
diff --git a/src/tests/java/htsjdk/samtools/SAMRecordUnitTest.java b/src/tests/java/htsjdk/samtools/SAMRecordUnitTest.java
index a3c3e68086..380e77010d 100644
--- a/src/tests/java/htsjdk/samtools/SAMRecordUnitTest.java
+++ b/src/tests/java/htsjdk/samtools/SAMRecordUnitTest.java
@@ -31,6 +31,7 @@
 import org.testng.annotations.Test;
 
 import java.io.*;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
@@ -456,7 +457,7 @@ record = new SAMRecord(header);
             Assert.fail("Unexpected exception", e);
         }
 
-        record.setAttribute(tag, (long)Integer.MIN_VALUE-1L);
+        record.setAttribute(tag, (long) Integer.MIN_VALUE - 1L);
     }
 
     @Test(expectedExceptions = SAMException.class)
@@ -777,6 +778,23 @@ public void testNullHeaderSerialization(final File inputFile) throws Exception {
         Assert.assertEquals(deserializedSAMRecord, initialSAMRecord, "Deserialized SAMRecord not equal to original SAMRecord");
     }
 
+
+    @Test
+    public void testValidateNonsenseCigar(){
+        // Create nonsense record
+        SAMRecord rec = createTestRecordHelper();
+        rec.setCigarString("nonsense");
+
+        //The default validationStringency of a sam record is SILENT.
+        rec.setValidationStringency(ValidationStringency.STRICT);
+        // Validate record
+        List<SAMValidationError> err = rec.validateCigar(-1);
+
+        Assert.assertNotNull(err);
+        Assert.assertEquals(err.size(), 1);
+        Assert.assertEquals(err.get(0).getType(), SAMValidationError.Type.INVALID_CIGAR);
+    }
+
     @Test
     public void testNullHeaderRecordValidation() {
         final SAMRecord sam = createTestRecordHelper();