diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java
index 02ef42286..4fa6c0c1d 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java
@@ -113,7 +113,11 @@ public class ArtificialPatternedSAMIterator extends ArtificialSAMIterator {
                 return false;
             } else {
                 ++totalReadCount;
-                this.next = ArtificialSAMUtils.createArtificialRead(this.header, String.valueOf(totalReadCount), -1, -1, 50);
+                this.next = ArtificialSAMUtils.createArtificialRead(this.header,
+                        String.valueOf(totalReadCount),
+                        SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX,
+                        SAMRecord.NO_ALIGNMENT_START,
+                        50);
                 --unmappedRemaining;
                 return true;
             }
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java
index 51cbeb154..574a3a781 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java
@@ -139,7 +139,11 @@ public class ArtificialSAMIterator implements StingSAMIterator {
                 return false;
             } else {
                 ++totalReadCount;
-                this.next = ArtificialSAMUtils.createArtificialRead(this.header, String.valueOf(totalReadCount), -1, -1, 50);
+                this.next = ArtificialSAMUtils.createArtificialRead(this.header,
+                        String.valueOf(totalReadCount),
+                        SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX,
+                        SAMRecord.NO_ALIGNMENT_START,
+                        50);
                 --unmappedRemaining;
                 return true;
             }
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
index a311ee5bd..d1f5fe3e7 100755
--- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
@@ -143,7 +143,8 @@ public class ArtificialSAMUtils {
      * @return the artificial read
      */
     public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, int length ) {
-        if (alignmentStart == 0)
+        if( (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart != SAMRecord.NO_ALIGNMENT_START) ||
+            (refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START) )
             throw new StingException("Invalid alignment start for artificial read, start = " + alignmentStart);
         SAMRecord record = new SAMRecord(header);
         record.setReadName(name);
@@ -153,7 +154,7 @@ public class ArtificialSAMUtils {
         elements.add(new CigarElement(length, CigarOperator.characterToEnum('M')));
         record.setCigar(new Cigar(elements));
         record.setProperPairFlag(false);
-        if (refIndex == -1) {
+        if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
             record.setReadUmappedFlag(true);
         }
         return record;
diff --git a/java/src/org/broadinstitute/sting/utils/sam/SAMReadValidator.java b/java/src/org/broadinstitute/sting/utils/sam/SAMReadValidator.java
index b2e590a00..10b091fb8 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/SAMReadValidator.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/SAMReadValidator.java
@@ -79,7 +79,7 @@ public class SAMReadValidator {
         if( read.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START )
             throw new SAMReadValidationException("Read is aligned to nonexistent contig");
         SAMSequenceRecord contigHeader = header.getSequence( read.getReferenceIndex() );
-        if( read.getReadUnmappedFlag() && read.getAlignmentStart() > contigHeader.getSequenceLength() )
+        if( !read.getReadUnmappedFlag() && read.getAlignmentStart() > contigHeader.getSequenceLength() )
             throw new SAMReadValidationException("Read is aligned to a point after the end of the contig");
     }