Merge pull request #299 from edwardkw/ek_fixbai_296

Hooking up the index file to CRAM files in SamReaderFactory

Author: droazen

src/java/htsjdk/samtools/SamReaderFactory.java

@@ -268,11 +268,12 @@ public SamReader open(final SamInputResource resource) {
                             bufferedStream.close();
                             bufferedStream = null;
                         }
-                        // Handle case in which file is a named pipe, e.g. /dev/stdin or created by mkfifo
+
+                        // Always attempt to pass in the index. If it is null, that's fine. If the reference isn't supplied, use the default.
                         if (referenceSource != null) {
-                            primitiveSamReader = new CRAMFileReader(sourceFile, bufferedStream, referenceSource);
+                            primitiveSamReader = new CRAMFileReader(sourceFile, indexMaybe == null ? null : indexMaybe.asFile(), referenceSource);
                         } else {
-                            primitiveSamReader = new CRAMFileReader(sourceFile, bufferedStream);
+                            primitiveSamReader = new CRAMFileReader(sourceFile, indexMaybe == null ? null : indexMaybe.asFile(), new ReferenceSource(Defaults.REFERENCE_FASTA));
                         }
                     } else {
                         if (indexDefined) {

src/tests/java/htsjdk/samtools/SAMFileReaderTest.java

@@ -53,6 +53,40 @@ public Object[][] variousFormatReaderTestCases() {
         return scenarios;
     }
 
+    // tests for CRAM indexing
+
+    @Test(dataProvider = "SmallCRAMTest")
+    public void CRAMIndexTest(final String inputFile) {
+        final File input = new File(TEST_DATA_DIR, inputFile);
+        final SamReader reader = SamReaderFactory.makeDefault().open(input);
+        Assert.assertTrue(reader.hasIndex());
+        CloserUtil.close(reader);
+    }
+
+    @DataProvider(name = "SmallCRAMTest")
+    public Object[][] CRAMIndexTestData() {
+        final Object[][] testFiles = new Object[][]{
+                {"cram/test.cram"},
+        };
+        return testFiles;
+    }
+
+    @Test(dataProvider = "NoIndexCRAMTest")
+    public void CRAMNoIndexTest(final String inputFile) {
+        final File input = new File(TEST_DATA_DIR, inputFile);
+        final SamReader reader = SamReaderFactory.makeDefault().open(input);
+        Assert.assertFalse(reader.hasIndex());
+        CloserUtil.close(reader);
+    }
+
+    @DataProvider(name = "NoIndexCRAMTest")
+    public Object[][] CRAMNoIndexTestData() {
+        final Object[][] testFiles = new Object[][]{
+                {"cram/test2.cram"},
+        };
+        return testFiles;
+    }
+
     // Tests for the SAMRecordFactory usage
     class SAMRecordFactoryTester extends DefaultSAMRecordFactory {
         int samRecordsCreated;

testdata/htsjdk/samtools/cram/auxf.fasta

@@ -0,0 +1,2 @@
+>Sheila
+GCTAGCTCAGAAAAAAAAAA

testdata/htsjdk/samtools/cram/test.cram

@@ -0,0 +1,2 @@
+@HD	VN:1.4	SO:unsorted
+@SQ	SN:Sheila	LN:20	M5:7ddd8a4b4f2c1dec43476a738b1a9b72	UR:file:/Users/edwardk/Documents/htsjdk/testdata/htsjdk/samtools/cram/auxf.fa

testdata/htsjdk/samtools/cram/test.cram.bai

@@ -0,0 +1,2 @@
+>Sheila
+GCTAGCTCAGAAAAAAAAAA

testdata/htsjdk/samtools/cram/test.dict

@@ -0,0 +1 @@
+Sheila	20	8	20	21

testdata/htsjdk/samtools/cram/test.fa

@@ -0,0 +1,2 @@
+>Sheila
+GCTAGCTCAGAAAAAAAAAA