Add support for CRAM in SamSequenceDictionaryExtractor (#1305)

src/main/java/htsjdk/samtools/CRAMIterator.java

@@ -32,12 +32,24 @@
 
 import java.io.InputStream;
 import java.math.BigInteger;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.*;
 
 import htsjdk.samtools.cram.CRAMException;
+import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.RuntimeIOException;
 
 public class CRAMIterator implements SAMRecordIterator {
+
+    /** A CRAMReferenceSource that is never invoked . It's used in {@link #extractDictionary(Path)}*/
+    private static final CRAMReferenceSource NIL_CRAM_REFERENCE_SRC = new CRAMReferenceSource() {
+        @Override
+        public byte[] getReferenceBases(final SAMSequenceRecord sequenceRecord, boolean tryNameVariants) {
+            throw new IllegalStateException("CRAMReferenceSource.getReferenceBases shouldn't be called");
+            }
+    };
+
     private final CountingInputStream countingInputStream;
     private final CramHeader cramHeader;
     private final ArrayList<SAMRecord> records;
@@ -303,4 +315,18 @@ public SAMFileHeader getSAMFileHeader() {
         return cramHeader.getSamFileHeader();
     }
 
+    /** extracts a {@link SAMSequenceDictionary} from a cram file.
+     * @return the dictionary of the cram file
+     * @throws SAMException if a dictionary cannot be extracted
+     */
+    public static SAMSequenceDictionary extractDictionary(final Path cramPath) {
+        IOUtil.assertFileIsReadable(cramPath);
+        try (final InputStream in = Files.newInputStream(cramPath)) {
+            try(final CRAMIterator iter= new CRAMIterator(in, NIL_CRAM_REFERENCE_SRC, ValidationStringency.SILENT)) {
+                return iter.getSAMFileHeader().getSequenceDictionary();
+            }
+        } catch (final Exception err) {
+           throw new SAMException("Cannot extract dictionary from "+cramPath, err);
+        }
+    }
 }

src/main/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.java

@@ -25,6 +25,7 @@
 package htsjdk.variant.utils;
 
 import htsjdk.samtools.*;
+import htsjdk.samtools.cram.build.CramIO;
 import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
 import htsjdk.samtools.util.BufferedLineReader;
 import htsjdk.samtools.util.CollectionUtil;
@@ -49,7 +50,7 @@ enum TYPE {
         FASTA(ReferenceSequenceFileFactory.FASTA_EXTENSIONS) {
 
             @Override
-            SAMSequenceDictionary extractDictionary(Path reference) {
+            SAMSequenceDictionary extractDictionary(final Path reference) {
                 final SAMSequenceDictionary dict = ReferenceSequenceFileFactory.getReferenceSequenceFile(reference).getSequenceDictionary();
                 if (dict == null)
                     throw new SAMException("Could not find dictionary next to reference file " + reference.toUri().toString());
@@ -70,17 +71,24 @@ SAMSequenceDictionary extractDictionary(final Path dictionary) {
                 }
             }
         },
+        CRAM(CramIO.CRAM_FILE_EXTENSION) {
+
+            @Override
+            SAMSequenceDictionary extractDictionary(final Path cram) {
+                    return CRAMIterator.extractDictionary(cram);
+            }
+        },
         SAM(IOUtil.SAM_FILE_EXTENSION, BamFileIoUtils.BAM_FILE_EXTENSION) {
 
             @Override
-            SAMSequenceDictionary extractDictionary(Path sam) {
+            SAMSequenceDictionary extractDictionary(final Path sam) {
                 return SamReaderFactory.makeDefault().getFileHeader(sam).getSequenceDictionary();
             }
         },
         VCF(IOUtil.VCF_EXTENSIONS) {
 
             @Override
-            SAMSequenceDictionary extractDictionary(Path vcf) {
+            SAMSequenceDictionary extractDictionary(final Path vcf) {
                 try (VCFFileReader vcfPathReader = new VCFFileReader(vcf, false)){
                     return vcfPathReader.getFileHeader().getSequenceDictionary();
                 }
@@ -89,7 +97,7 @@ SAMSequenceDictionary extractDictionary(Path vcf) {
         INTERVAL_LIST(IOUtil.INTERVAL_LIST_FILE_EXTENSION) {
 
             @Override
-            SAMSequenceDictionary extractDictionary(Path intervalList) {
+            SAMSequenceDictionary extractDictionary(final Path intervalList) {
                 return IntervalList.fromPath(intervalList).getHeader().getSequenceDictionary();
             }
         };

src/test/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractorTest.java

@@ -31,12 +31,14 @@
 import org.testng.Assert;
 
 import java.io.File;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 
 /**
  * @author farjoun on 4/9/14.
  */
 public class SAMSequenceDictionaryExtractorTest extends HtsjdkTest {
-    String path = "src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/";
+    final String path = "src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/";
 
     @DataProvider(name = "testExtractDictionaries")
     public Object[][] dictionaries() {
@@ -49,13 +51,14 @@ public Object[][] dictionaries() {
                 new Object[]{"test2_comp.interval_list", "Homo_sapiens_assembly18.trimmed.dict"},
                 new Object[]{"ScreenSamReads.100.input.sam", "test3_comp.interval_list"},
                 new Object[]{"ScreenSamReads.100.input.sam", "test4_comp.interval_list"},
+                new Object[]{"toy.cram", "toy.dict"}
         };
     }
 
     @Test(dataProvider = "testExtractDictionaries")
     public void testExtractDictionary(final String dictSource, final String dictExpected) throws Exception {
-        final File dictSourceFile = new File(path, dictSource);
-        final File dictExpectedFile = new File(path, dictExpected);
+        final Path dictSourceFile = Paths.get(path, dictSource);
+        final Path dictExpectedFile = Paths.get(path, dictExpected);
         final SAMSequenceDictionary dict1 = SAMSequenceDictionaryExtractor.extractDictionary(dictSourceFile);
         final SAMSequenceDictionary dict2 = SAMSequenceDictionaryExtractor.extractDictionary(dictExpectedFile);
 

src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/toy.dict

@@ -0,0 +1,3 @@
+@HD	VN:1.5	SO:unsorted
+@SQ	SN:ref	LN:45	M5:7a66cae8ab14aef8d635bc80649e730b
+@SQ	SN:ref2	LN:40	M5:1636753510ec27476fdd109a6684680e