The changes to CRAM have introduced an incompatible change to CRAIEnt…

…ry that

affects CramSource in Disq. See the note about incompatible CRAM changes
at https://github.com/samtools/htsjdk/releases/tag/2.17.0.

This commit uses the new CRAIEntry API introduced in samtools/htsjdk#1256

remove use of SAMRecord.getIndexBin() since the method has been removed

Convert catch for EOFException -> RuntimeEOFException

Use htsjdk 2.19.0-rc3-SNAPSHOT

Use htsjdk 2.19.0

pom.xml

@@ -32,7 +32,7 @@
     <properties>
         <maven.compiler.target>1.8</maven.compiler.target>
         <maven.compiler.source>1.8</maven.compiler.source>
-        <htsjdk.version>2.18.2</htsjdk.version>
+        <htsjdk.version>2.19.0</htsjdk.version>
         <hadoop.version>2.7.5</hadoop.version>
         <mockito.version>2.22.0</mockito.version>
         <kryo-serializers.version>0.42</kryo-serializers.version>

src/htsjdk/java/htsjdk/samtools/BAMIndexer2.java

@@ -235,9 +235,7 @@ public int getEnd() {
 
                 @Override
                 public Integer getIndexingBin() {
-                    final Integer binNumber = rec.getIndexingBin();
-                    return (binNumber == null ? rec.computeIndexingBin() : binNumber);
-
+                    return rec.computeIndexingBin();
                 }
 
                 @Override

src/main/java/org/disq_bio/disq/impl/formats/cram/CramSource.java

@@ -152,7 +152,7 @@ private NavigableSet<Long> getContainerOffsetsFromIndex(
       NavigableSet<Long> containerOffsets = new TreeSet<>();
       CRAIIndex index = CRAMCRAIIndexer.readIndex(in);
       for (CRAIEntry entry : index.getCRAIEntries()) {
-        containerOffsets.add(entry.containerStartOffset);
+        containerOffsets.add(entry.getContainerStartByteOffset());
       }
       containerOffsets.add(cramFileLength);
       return containerOffsets;