Misc CRAM cleanup

src/main/java/htsjdk/samtools/BAMSBIIndexer.java

@@ -28,8 +28,8 @@
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.BlockCompressedInputStream;
 import htsjdk.samtools.util.IOUtil;
+import htsjdk.samtools.util.RuntimeEOFException;
 
-import java.io.EOFException;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.nio.ByteBuffer;
@@ -80,7 +80,7 @@ public static void createIndex(final SeekableStream in, final OutputStream out,
                     // Process the record start position, then skip to the start of the next BAM record
                     indexWriter.processRecord(recordStart);
                     InputStreamUtils.skipFully(blockIn, blockSize);
-                } catch (EOFException e) {
+                } catch (RuntimeEOFException e) {
                     break;
                 }
             }

src/main/java/htsjdk/samtools/CRAMBAIIndexer.java

@@ -115,56 +115,51 @@ public CRAMBAIIndexer(final OutputStream output, final SAMFileHeader fileHeader)
      * @param container container to be indexed
      */
     public void processContainer(final Container container, final ValidationStringency validationStringency) {
-        try {
-            if (container == null || container.isEOF()) {
-                return;
-            }
+        if (container == null || container.isEOF()) {
+            return;
+        }
 
-            int sliceIndex = 0;
-            for (final Slice slice : container.slices) {
+        int sliceIndex = 0;
+        for (final Slice slice : container.slices) {
+            slice.containerOffset = container.offset;
+            slice.index = sliceIndex++;
+            if (slice.isMultiref()) {
+                final ContainerParser parser = new ContainerParser(indexBuilder.bamHeader);
+                final Map<Integer, AlignmentSpan> refSet = parser.getReferences(container, validationStringency);
+                final Slice fakeSlice = new Slice();
                 slice.containerOffset = container.offset;
                 slice.index = sliceIndex++;
-                if (slice.isMultiref()) {
-                    final ContainerParser parser = new ContainerParser(indexBuilder.bamHeader);
-                    final Map<Integer, AlignmentSpan> refSet = parser.getReferences(container, validationStringency);
-                    final Slice fakeSlice = new Slice();
-                    slice.containerOffset = container.offset;
-                    slice.index = sliceIndex++;
-                    /**
-                     * Unmapped span must be processed after mapped spans:
-                     */
-                    AlignmentSpan unmappedSpan = refSet.remove(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
-                    for (final int refId : new TreeSet<>(refSet.keySet())) {
-                        final AlignmentSpan span = refSet.get(refId);
-                        fakeSlice.sequenceId = refId;
-                        fakeSlice.containerOffset = slice.containerOffset;
-                        fakeSlice.offset = slice.offset;
-                        fakeSlice.index = slice.index;
-
-                        fakeSlice.alignmentStart = span.getStart();
-                        fakeSlice.alignmentSpan = span.getSpan();
-                        fakeSlice.nofRecords = span.getCount();
-                        processSingleReferenceSlice(fakeSlice);
-                    }
-                    if (unmappedSpan != null) {
-                        final AlignmentSpan span = unmappedSpan;
-                        fakeSlice.sequenceId = SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX;
-                        fakeSlice.containerOffset = slice.containerOffset;
-                        fakeSlice.offset = slice.offset;
-                        fakeSlice.index = slice.index;
-
-                        fakeSlice.alignmentStart = SAMRecord.NO_ALIGNMENT_START;
-                        fakeSlice.alignmentSpan = 0;
-                        fakeSlice.nofRecords = span.getCount();
-                        processSingleReferenceSlice(fakeSlice);
-                    }
-                } else {
-                    processSingleReferenceSlice(slice);
+                /**
+                 * Unmapped span must be processed after mapped spans:
+                 */
+                AlignmentSpan unmappedSpan = refSet.remove(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
+                for (final int refId : new TreeSet<>(refSet.keySet())) {
+                    final AlignmentSpan span = refSet.get(refId);
+                    fakeSlice.sequenceId = refId;
+                    fakeSlice.containerOffset = slice.containerOffset;
+                    fakeSlice.offset = slice.offset;
+                    fakeSlice.index = slice.index;
+
+                    fakeSlice.alignmentStart = span.getStart();
+                    fakeSlice.alignmentSpan = span.getSpan();
+                    fakeSlice.nofRecords = span.getCount();
+                    processSingleReferenceSlice(fakeSlice);
+                }
+                if (unmappedSpan != null) {
+                    final AlignmentSpan span = unmappedSpan;
+                    fakeSlice.sequenceId = SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX;
+                    fakeSlice.containerOffset = slice.containerOffset;
+                    fakeSlice.offset = slice.offset;
+                    fakeSlice.index = slice.index;
+
+                    fakeSlice.alignmentStart = SAMRecord.NO_ALIGNMENT_START;
+                    fakeSlice.alignmentSpan = 0;
+                    fakeSlice.nofRecords = span.getCount();
+                    processSingleReferenceSlice(fakeSlice);
                 }
+            } else {
+                processSingleReferenceSlice(slice);
             }
-
-        } catch (final IOException e) {
-            throw new RuntimeIOException("Failed to read cram container", e);
         }
     }
 

src/main/java/htsjdk/samtools/CRAMFileReader.java

@@ -315,13 +315,10 @@ public SAMRecordIterator iterator(final SAMFileSpan fileSpan) {
         // get the file coordinates for the span:
         final long[] coordinateArray = ((BAMFileSpan) fileSpan).toCoordinateArray();
         if (coordinateArray == null || coordinateArray.length == 0) return emptyIterator;
-        try {
-            // create an input stream that reads the source cram stream only within the coordinate pairs:
-            final SeekableStream seekableStream = getSeekableStreamOrFailWithRTE();
-            return new CRAMIterator(seekableStream, referenceSource, coordinateArray, validationStringency);
-        } catch (final IOException e) {
-            throw new RuntimeException(e);
-        }
+
+        // create an input stream that reads the source cram stream only within the coordinate pairs:
+        final SeekableStream seekableStream = getSeekableStreamOrFailWithRTE();
+        return new CRAMIterator(seekableStream, referenceSource, coordinateArray, validationStringency);
     }
 
     @Override
@@ -508,16 +505,14 @@ public CRAMIntervalIterator(final QueryInterval[] queries, final boolean contain
             super(queries, contained);
 
             if (coordinates != null && coordinates.length != 0) {
-                try {
-                    unfilteredIterator = new CRAMIterator(
-                            getSeekableStreamOrFailWithRTE(),
-                            referenceSource,
-                            coordinates,
-                            validationStringency
-                    );
-                } catch (final IOException e) {
-                    throw new RuntimeEOFException(e);
-                }
+
+                unfilteredIterator = new CRAMIterator(
+                        getSeekableStreamOrFailWithRTE(),
+                        referenceSource,
+                        coordinates,
+                        validationStringency
+                );
+
                 getNextRecord(); // advance to the first record that matches the filter criteria
             }
         }

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

@@ -29,17 +29,15 @@
 import htsjdk.samtools.cram.structure.CramHeader;
 import htsjdk.samtools.cram.structure.Slice;
 import htsjdk.samtools.seekablestream.SeekableStream;
-import htsjdk.samtools.util.Log;
 
-import java.io.IOException;
 import java.io.InputStream;
 import java.math.BigInteger;
 import java.util.*;
 
 import htsjdk.samtools.cram.CRAMException;
+import htsjdk.samtools.util.RuntimeIOException;
 
 public class CRAMIterator implements SAMRecordIterator {
-    private static final Log log = Log.getInstance(CRAMIterator.class);
     private final CountingInputStream countingInputStream;
     private final CramHeader cramHeader;
     private final ArrayList<SAMRecord> records;
@@ -63,8 +61,7 @@ public ValidationStringency getValidationStringency() {
         return validationStringency;
     }
 
-    public void setValidationStringency(
-            final ValidationStringency validationStringency) {
+    public void setValidationStringency(final ValidationStringency validationStringency) {
         this.validationStringency = validationStringency;
     }
 
@@ -75,11 +72,13 @@ public void setValidationStringency(
     private long samRecordIndex;
     private ArrayList<CramCompressionRecord> cramRecords;
 
-    public CRAMIterator(final InputStream inputStream, final CRAMReferenceSource referenceSource, final ValidationStringency validationStringency)
-            throws IOException {
+    public CRAMIterator(final InputStream inputStream,
+                        final CRAMReferenceSource referenceSource,
+                        final ValidationStringency validationStringency) {
         if (null == referenceSource) {
             throw new CRAMException("A reference source is required for CRAM files");
         }
+
         this.countingInputStream = new CountingInputStream(inputStream);
         this.referenceSource = referenceSource;
         this.validationStringency = validationStringency;
@@ -88,17 +87,20 @@ public CRAMIterator(final InputStream inputStream, final CRAMReferenceSource ref
         this.containerIterator = containerIterator;
 
         firstContainerOffset = this.countingInputStream.getCount();
-        records = new ArrayList<SAMRecord>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE);
+        records = new ArrayList<>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE);
         normalizer = new CramNormalizer(cramHeader.getSamFileHeader(),
                 referenceSource);
         parser = new ContainerParser(cramHeader.getSamFileHeader());
     }
 
-    public CRAMIterator(final SeekableStream seekableStream, final CRAMReferenceSource referenceSource, final long[] coordinates, final ValidationStringency validationStringency)
-            throws IOException {
+    public CRAMIterator(final SeekableStream seekableStream,
+                        final CRAMReferenceSource referenceSource,
+                        final long[] coordinates,
+                        final ValidationStringency validationStringency) {
         if (null == referenceSource) {
             throw new CRAMException("A reference source is required for CRAM files");
         }
+
         this.countingInputStream = new CountingInputStream(seekableStream);
         this.referenceSource = referenceSource;
         this.validationStringency = validationStringency;
@@ -107,24 +109,24 @@ public CRAMIterator(final SeekableStream seekableStream, final CRAMReferenceSour
         this.containerIterator = containerIterator;
 
         firstContainerOffset = containerIterator.getFirstContainerOffset();
-        records = new ArrayList<SAMRecord>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE);
+        records = new ArrayList<>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE);
         normalizer = new CramNormalizer(cramHeader.getSamFileHeader(),
                 referenceSource);
         parser = new ContainerParser(cramHeader.getSamFileHeader());
     }
 
     @Deprecated
-    public CRAMIterator(final SeekableStream seekableStream, final CRAMReferenceSource referenceSource, final long[] coordinates)
-            throws IOException {
+    public CRAMIterator(final SeekableStream seekableStream,
+                        final CRAMReferenceSource referenceSource,
+                        final long[] coordinates) {
         this(seekableStream, referenceSource, coordinates, ValidationStringency.DEFAULT_STRINGENCY);
     }
 
     public CramHeader getCramHeader() {
         return cramHeader;
     }
 
-    void nextContainer() throws IOException, IllegalArgumentException,
-            IllegalAccessException, CRAMException {
+    void nextContainer() throws IllegalArgumentException, CRAMException {
 
         if (containerIterator != null) {
             if (!containerIterator.hasNext()) {
@@ -149,7 +151,7 @@ void nextContainer() throws IOException, IllegalArgumentException,
 
         records.clear();
         if (cramRecords == null)
-            cramRecords = new ArrayList<CramCompressionRecord>(container.nofRecords);
+            cramRecords = new ArrayList<>(container.nofRecords);
         else
             cramRecords.clear();
 
@@ -250,11 +252,7 @@ public boolean advanceToAlignmentInContainer(final int refIndex, final int pos)
     public boolean hasNext() {
         if (container != null && container.isEOF()) return false;
         if (!iterator.hasNext()) {
-            try {
-                nextContainer();
-            } catch (IOException | IllegalAccessException e) {
-                throw new SAMException(e);
-            }
+            nextContainer();
         }
 
         return !records.isEmpty();
@@ -287,10 +285,10 @@ public void close() {
         records.clear();
         //noinspection EmptyCatchBlock
         try {
-            if (countingInputStream != null)
+            if (countingInputStream != null) {
                 countingInputStream.close();
-        } catch (final IOException e) {
-        }
+            }
+        } catch (final RuntimeIOException e) { }
     }
 
     @Override

src/main/java/htsjdk/samtools/cram/CRAIEntry.java

@@ -50,7 +50,7 @@ public CRAIEntry(final int sequenceId,
      * @param line string formatted as a CRAI index entry
      * @throws CRAIIndex.CRAIIndexException
      */
-    public CRAIEntry(final String line) throws CRAIIndex.CRAIIndexException {
+    public CRAIEntry(final String line) {
         final String[] chunks = line.split("\t");
         if (chunks.length != CRAI_INDEX_COLUMNS) {
             throw new CRAIIndex.CRAIIndexException(

src/main/java/htsjdk/samtools/cram/CRAIIndex.java

@@ -8,6 +8,7 @@
 import htsjdk.samtools.seekablestream.SeekableMemoryStream;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.ValidationStringency;
+import htsjdk.samtools.util.RuntimeIOException;
 
 import java.io.*;
 import java.util.*;
@@ -70,11 +71,16 @@ public void processContainer(final Container container) {
         }
     }
 
-    public static SeekableStream openCraiFileAsBaiStream(final File cramIndexFile, final SAMSequenceDictionary dictionary) throws IOException {
-        return openCraiFileAsBaiStream(new FileInputStream(cramIndexFile), dictionary);
+    public static SeekableStream openCraiFileAsBaiStream(final File cramIndexFile, final SAMSequenceDictionary dictionary) {
+        try {
+            return openCraiFileAsBaiStream(new FileInputStream(cramIndexFile), dictionary);
+        }
+        catch (final FileNotFoundException e) {
+            throw new RuntimeIOException(e);
+        }
     }
 
-    public static SeekableStream openCraiFileAsBaiStream(final InputStream indexStream, final SAMSequenceDictionary dictionary) throws IOException, CRAIIndexException {
+    public static SeekableStream openCraiFileAsBaiStream(final InputStream indexStream, final SAMSequenceDictionary dictionary) {
         final List<CRAIEntry> full = CRAMCRAIIndexer.readIndex(indexStream).getCRAIEntries();
         Collections.sort(full);
 

src/main/java/htsjdk/samtools/cram/build/ContainerFactory.java

@@ -24,7 +24,6 @@
 import htsjdk.samtools.cram.compression.ExternalCompressor;
 import htsjdk.samtools.cram.encoding.writer.CramRecordWriter;
 import htsjdk.samtools.cram.io.DefaultBitOutputStream;
-import htsjdk.samtools.cram.io.ExposedByteArrayOutputStream;
 import htsjdk.samtools.cram.structure.block.ExternalBlock;
 import htsjdk.samtools.cram.structure.block.Block;
 import htsjdk.samtools.cram.structure.CompressionHeader;