diff --git a/src/main/java/htsjdk/samtools/cram/build/CRAMReferenceRegion.java b/src/main/java/htsjdk/samtools/cram/build/CRAMReferenceRegion.java
index 514aeee6dd..8fc1c32bde 100644
--- a/src/main/java/htsjdk/samtools/cram/build/CRAMReferenceRegion.java
+++ b/src/main/java/htsjdk/samtools/cram/build/CRAMReferenceRegion.java
@@ -27,6 +27,7 @@
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.samtools.cram.CRAMException;
 import htsjdk.samtools.cram.ref.CRAMReferenceSource;
 import htsjdk.samtools.cram.ref.ReferenceContext;
 
@@ -73,7 +74,7 @@ public byte[] getReferenceBases(final int referenceIndex) {
                 final SAMSequenceRecord sequence = samFileHeader.getSequence(referenceIndex);
                 referenceBases = referenceSource.getReferenceBases(sequence, true);
                 if (referenceBases == null) {
-                    throw new IllegalArgumentException(
+                    throw new CRAMException(
                             String.format(
                                     "A reference must be supplied (reference sequence %s not found).",
                                     sequence));
@@ -92,5 +93,4 @@ public void setEmbeddedReference(final byte[] embeddedReferenceBytes, final int
         referenceBasesContextID = embeddedReferenceIndex;
         referenceBases = embeddedReferenceBytes;
     }
-
 }
diff --git a/src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java b/src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java
index 19375e745b..a6cebf3392 100644
--- a/src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java
+++ b/src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java
@@ -17,6 +17,7 @@
  */
 package htsjdk.samtools.cram.build;
 
+import htsjdk.samtools.cram.CRAMException;
 import htsjdk.samtools.cram.common.MutableInt;
 import htsjdk.samtools.cram.compression.ExternalCompressor;
 import htsjdk.samtools.cram.encoding.*;
@@ -422,7 +423,7 @@ private EncodingDetails buildEncodingForTag(final List<CRAMCompressionRecord> re
                         new ExternalByteArrayEncoding(tagID)).toEncodingDescriptor();
                 return details;
             default:
-                throw new IllegalArgumentException("Unknown tag type: " + (char) type);
+                throw new CRAMException("Unknown tag type: " + (char) type);
         }
     }
 
@@ -468,9 +469,9 @@ static int getTagValueByteSize(final byte type, final Object value) {
                 if (value instanceof long[]) {
                     return 1 + 4 + ((long[]) value).length * 4;
                 }
-                throw new RuntimeException("Unknown tag array class: " + value.getClass());
+                throw new CRAMException("Unknown tag array class: " + value.getClass());
             default:
-                throw new RuntimeException("Unknown tag type: " + (char) type);
+                throw new CRAMException("Unknown tag type: " + (char) type);
         }
     }
 }
diff --git a/src/main/java/htsjdk/samtools/cram/build/CramContainerIterator.java b/src/main/java/htsjdk/samtools/cram/build/CramContainerIterator.java
index 848b6feec1..6ce897a316 100644
--- a/src/main/java/htsjdk/samtools/cram/build/CramContainerIterator.java
+++ b/src/main/java/htsjdk/samtools/cram/build/CramContainerIterator.java
@@ -1,6 +1,7 @@
 package htsjdk.samtools.cram.build;
 
 import htsjdk.samtools.SAMFileHeader;
+import htsjdk.samtools.cram.CRAMException;
 import htsjdk.samtools.cram.io.CountingInputStream;
 import htsjdk.samtools.cram.structure.Container;
 import htsjdk.samtools.cram.structure.CramHeader;
@@ -71,7 +72,7 @@ public Container next() {
 
     @Override
     public void remove() {
-        throw new RuntimeException("Read only iterator.");
+        throw new CRAMException("Read only iterator.");
     }
 
     public CramHeader getCramHeader() {
diff --git a/src/main/java/htsjdk/samtools/cram/build/CramIO.java b/src/main/java/htsjdk/samtools/cram/build/CramIO.java
index b0783426b4..7fcc36b2a8 100644
--- a/src/main/java/htsjdk/samtools/cram/build/CramIO.java
+++ b/src/main/java/htsjdk/samtools/cram/build/CramIO.java
@@ -19,6 +19,7 @@
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMTextHeaderCodec;
+import htsjdk.samtools.cram.CRAMException;
 import htsjdk.samtools.cram.common.CramVersions;
 import htsjdk.samtools.cram.common.CRAMVersion;
 import htsjdk.samtools.cram.structure.*;
@@ -26,6 +27,7 @@
 import htsjdk.samtools.util.Log;
 import htsjdk.samtools.util.RuntimeIOException;
 
+import javax.security.auth.login.CredentialException;
 import java.io.*;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
@@ -88,7 +90,7 @@ public static long writeCramEOF(final CRAMVersion cramVersion, final OutputStrea
             throw new RuntimeIOException(e);
         }
 
-        throw new IllegalArgumentException(String.format("Unrecognized CRAM version %s", cramVersion));
+        throw new CRAMException(String.format("Unrecognized CRAM version %s", cramVersion));
     }
 
     /**
@@ -123,13 +125,13 @@ public static CramHeader readCramHeader(final InputStream inputStream) {
         try {
             for (final byte magicByte : CramHeader.MAGIC) {
                 if (magicByte != inputStream.read()) {
-                    throw new RuntimeException("Input does not have a valid CRAM header.");
+                    throw new CRAMException("Input does not have a valid CRAM header.");
                 }
             }
 
             final CRAMVersion cramVersion = new CRAMVersion(inputStream.read(), inputStream.read());
             if (!CramVersions.isSupportedVersion(cramVersion)) {
-                throw new RuntimeException(String.format("CRAM version %s is not supported", cramVersion));
+                throw new CRAMException(String.format("CRAM version %s is not supported", cramVersion));
             }
 
             final CramHeader header = new CramHeader(cramVersion, null);
diff --git a/src/main/java/htsjdk/samtools/cram/build/CramSpanContainerIterator.java b/src/main/java/htsjdk/samtools/cram/build/CramSpanContainerIterator.java
index b7457ea1de..61792d9f15 100644
--- a/src/main/java/htsjdk/samtools/cram/build/CramSpanContainerIterator.java
+++ b/src/main/java/htsjdk/samtools/cram/build/CramSpanContainerIterator.java
@@ -1,5 +1,6 @@
 package htsjdk.samtools.cram.build;
 
+import htsjdk.samtools.cram.CRAMException;
 import htsjdk.samtools.cram.structure.Container;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.RuntimeIOException;
@@ -19,7 +20,7 @@ public final class CramSpanContainerIterator extends CramContainerIterator {
     private Iterator<Boundary> containerBoundaries;
     private Boundary currentBoundary;
 
-    private CramSpanContainerIterator(final SeekableStream seekableStream, final long[] coordinates) throws IOException {
+    private CramSpanContainerIterator(final SeekableStream seekableStream, final long[] coordinates) throws CRAMException {
         super(seekableStream);
         this.seekableStream = seekableStream;
         final List<Boundary> boundaries = new ArrayList<>();
@@ -70,7 +71,7 @@ public Boundary(final long start, final long end) {
             this.start = start;
             this.end = end;
             if (start >= end) {
-                throw new RuntimeException("Boundary start is greater than end.");
+                throw new CRAMException("Boundary start is greater than end.");
             }
         }
 
@@ -91,7 +92,7 @@ public Container next() {
                 }
 
                 if (!hasNext()) {
-                    throw new RuntimeException("No more containers in this boundary.");
+                    throw new CRAMException("No more containers in this boundary.");
                 }
 
                 return new Container(getCramHeader().getCRAMVersion(), seekableStream, seekableStream.position());