Using `SamIndexes.asBaiSeekableStreamOrNull()` to support `.cram.crai`.

Updated other IntelliJ IDEA warnings in GATKBAMIndex.
Updated example .cram files to match versions generated by current GATK/HTSJDK.
Bumped HTSJDK and Picard to 1.139 releases.
Added support for using `-SNAPSHOT` of HTSJDK in the future.

pom.xml

@@ -161,6 +161,7 @@
                             <configuration>
                                 <outputDirectory>${gatk.executable.directory}/lib</outputDirectory>
                                 <includeScope>runtime</includeScope>
+                                <useBaseVersion>false</useBaseVersion>
                             </configuration>
                         </execution>
                     </executions>

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java

@@ -25,12 +25,10 @@
 
 package org.broadinstitute.gatk.engine.datasources.reads;
 
-import htsjdk.samtools.Bin;
+import htsjdk.samtools.*;
-import htsjdk.samtools.GATKBin;
-import htsjdk.samtools.GATKChunk;
-import htsjdk.samtools.LinearIndex;
 import htsjdk.samtools.seekablestream.SeekableBufferedStream;
 import htsjdk.samtools.seekablestream.SeekableFileStream;
+import htsjdk.samtools.seekablestream.SeekableStream;
 import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 
@@ -70,10 +68,11 @@ public class GATKBAMIndex {
      */
     public static final int MAX_BINS = 37450;   // =(8^6-1)/7+1
 
+    private final SAMSequenceDictionary sequenceDictionary;
     private final File mFile;
 
     //TODO: figure out a good value for this buffer size
-    private final int BUFFERED_STREAM_BUFFER_SIZE = 8192;
+    private static final int BUFFERED_STREAM_BUFFER_SIZE = 8192;
 
     /**
      * Number of sequences stored in this index.
@@ -86,11 +85,14 @@ public class GATKBAMIndex {
     private final long[] sequenceStartCache;
 
     private SeekableFileStream fileStream;
+    private SeekableStream baiStream;
     private SeekableBufferedStream bufferedStream;
     private long fileLength;
 
-    public GATKBAMIndex(final File file) {
+    public GATKBAMIndex(final File file, final SAMSequenceDictionary sequenceDictionary) {
         mFile = file;
+        this.sequenceDictionary = sequenceDictionary;
+
         // Open the file stream.
         openIndexFile();
 
@@ -127,12 +129,12 @@ public class GATKBAMIndex {
         skipToSequence(referenceSequence);
 
         int binCount = readInteger();
-        List<GATKBin> bins = new ArrayList<GATKBin>();
+        List<GATKBin> bins = new ArrayList<>();
         for (int binNumber = 0; binNumber < binCount; binNumber++) {
             final int indexBin = readInteger();
             final int nChunks = readInteger();
 
-            List<GATKChunk> chunks = new ArrayList<GATKChunk>(nChunks);
+            List<GATKChunk> chunks = new ArrayList<>(nChunks);
             long[] rawChunkData = readLongs(nChunks*2);
             for (int ci = 0; ci < nChunks; ci++) {
                 final long chunkBegin = rawChunkData[ci*2];
@@ -289,7 +291,8 @@ public class GATKBAMIndex {
             final int nBins = readInteger();
             // System.out.println("# nBins: " + nBins);
             for (int j = 0; j < nBins; j++) {
-                final int bin = readInteger();
+                /* final int bin = */
+                readInteger();
                 final int nChunks = readInteger();
                 // System.out.println("# bin[" + j + "] = " + bin + ", nChunks = " + nChunks);
                 skipBytes(16 * nChunks);
@@ -308,7 +311,8 @@ public class GATKBAMIndex {
     private void openIndexFile() {
         try {
             fileStream = new SeekableFileStream(mFile);
-            bufferedStream = new SeekableBufferedStream(fileStream,BUFFERED_STREAM_BUFFER_SIZE);
+            baiStream = SamIndexes.asBaiSeekableStreamOrNull(fileStream, sequenceDictionary);
+            bufferedStream = new SeekableBufferedStream(baiStream, BUFFERED_STREAM_BUFFER_SIZE);
             fileLength=bufferedStream.length();
         }
         catch (IOException exc) {
@@ -319,6 +323,7 @@ public class GATKBAMIndex {
     private void closeIndexFile() {
         try {
             bufferedStream.close();
+            baiStream.close();
             fileStream.close();
             fileLength = -1;
         }

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java

@@ -28,6 +28,7 @@ package org.broadinstitute.gatk.engine.datasources.reads;
 import htsjdk.samtools.MergingSamRecordIterator;
 import htsjdk.samtools.SamFileHeaderMerger;
 import htsjdk.samtools.*;
+import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.samtools.util.CloserUtil;
 import htsjdk.samtools.util.RuntimeIOException;
@@ -372,10 +373,19 @@ public class SAMDataSource {
             originalToMergedReadGroupMappings.put(id,mappingToMerged);
         }
 
+        final SAMSequenceDictionary samSequenceDictionary;
+        if (referenceFile == null) {
+            samSequenceDictionary = mergedHeader.getSequenceDictionary();
+        } else {
+            samSequenceDictionary = ReferenceSequenceFileFactory.
+                    getReferenceSequenceFile(referenceFile).
+                    getSequenceDictionary();
+        }
+
         for(SAMReaderID id: readerIDs) {
             File indexFile = findIndexFile(id.getSamFile());
             if(indexFile != null)
-                bamIndices.put(id,new GATKBAMIndex(indexFile));
+                bamIndices.put(id,new GATKBAMIndex(indexFile, samSequenceDictionary));
         }
 
         resourcePool.releaseReaders(readers);

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java

@@ -50,11 +50,14 @@ public class CramIntegrationTest extends WalkerTest {
                 {"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "2e1b175c9b36154e2bbd1a23ebaf4c22"},
                 {"CountLoci", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
                 {"CountReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
+                {"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "2e1b175c9b36154e2bbd1a23ebaf4c22"},
+                {"CountLoci", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
+                {"CountReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
         };
     }
 
     @Test(dataProvider = "cramData")
-    public void testCRAM(String walker, String input, String args, String ext, String md5) {
+    public void testCram(String walker, String input, String args, String ext, String md5) {
         WalkerTestSpec spec = new WalkerTestSpec(
                 " -T Test" + walker + "Walker" +
                     " -I " + publicTestDir + input +
@@ -64,25 +67,24 @@ public class CramIntegrationTest extends WalkerTest {
                 1, // just one output file
                 Collections.singletonList(ext),
                 Collections.singletonList(md5));
-        executeTest(String.format("testCRAM %s %s -> %s: %s", walker, input, ext, args), spec);
+        executeTest(String.format("testCram %s %s -> %s: %s", walker, input, ext, args), spec);
     }
 
-    @DataProvider(name = "cramNoBaiData")
+    @DataProvider(name = "cramNoIndexData")
-    public Object[][] getCRAMNoBaiData() {
+    public Object[][] getCramNoIndexData() {
         return new Object[][]{
                 {"exampleCRAM-nobai-nocrai.cram"},
-                {"exampleCRAM-nobai-withcrai.cram"},
         };
     }
 
-    @Test(dataProvider = "cramNoBaiData")
+    @Test(dataProvider = "cramNoIndexData")
-    public void testCRAMNoBai(String input) {
+    public void testCramNoIndex(String input) {
         WalkerTestSpec spec = new WalkerTestSpec(
                 " -T TestPrintReadsWalker" +
                         " -I " + publicTestDir + input +
                         " -R " + exampleFASTA,
                 0,
                 UserException.class);
-        executeTest(String.format("testCRAMNoBai %s", input), spec);
+        executeTest(String.format("testCramNoIndex %s", input), spec);
     }
 }

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java

@@ -52,14 +52,19 @@ public class GATKBAMIndexUnitTest extends BaseTest {
      */
     private GATKBAMIndex bamIndex;
 
-    
+    /**
+     * Sequences.
+     */
+    private SAMSequenceDictionary sequenceDictionary;
+
+
     @BeforeClass
     public void init() throws FileNotFoundException {
         SAMFileReader reader = new SAMFileReader(bamFile);
-        SAMSequenceDictionary sequenceDictionary = reader.getFileHeader().getSequenceDictionary();
+        this.sequenceDictionary = reader.getFileHeader().getSequenceDictionary();
         reader.close();
         
-        bamIndex = new GATKBAMIndex(bamIndexFile);
+        bamIndex = new GATKBAMIndex(bamIndexFile, sequenceDictionary);
     }
 
     @Test
@@ -95,13 +100,13 @@ public class GATKBAMIndexUnitTest extends BaseTest {
 
     @Test( expectedExceptions = UserException.MalformedFile.class )
     public void testDetectTruncatedBamIndexWordBoundary() {
-        GATKBAMIndex index = new GATKBAMIndex(new File(privateTestDir + "truncated_at_word_boundary.bai"));
+        GATKBAMIndex index = new GATKBAMIndex(new File(privateTestDir + "truncated_at_word_boundary.bai"), sequenceDictionary);
         index.readReferenceSequence(0);
     }
 
     @Test( expectedExceptions = UserException.MalformedFile.class )
     public void testDetectTruncatedBamIndexNonWordBoundary() {
-        GATKBAMIndex index = new GATKBAMIndex(new File(privateTestDir + "truncated_at_non_word_boundary.bai"));
+        GATKBAMIndex index = new GATKBAMIndex(new File(privateTestDir + "truncated_at_non_word_boundary.bai"), sequenceDictionary);
         index.readReferenceSequence(0);
     }
 

public/gatk-root/pom.xml

@@ -44,8 +44,8 @@
         <test.listeners>org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners>
 
         <!-- Version numbers for picard and htsjdk -->
-        <htsjdk.version>1.138</htsjdk.version>
+        <htsjdk.version>1.139</htsjdk.version>
-        <picard.version>1.138</picard.version>
+        <picard.version>1.139</picard.version>
     </properties>
 
     <!-- Dependency configuration (versions, etc.) -->
@@ -718,6 +718,17 @@
             <name>GATK Public Local Repository</name>
             <url>file:${gatk.basedir}/public/repo</url>
         </repository>
+        <repository>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+            <id>broad.artifactory.snapshots</id>
+            <name>Broad Institute Artifactory SNAPSHOTs</name>
+            <url>https://artifactory.broadinstitute.org/artifactory/libs-snapshot</url>
+        </repository>
     </repositories>
 
 </project>