Support bgzipped SAM files in SAMFileReader.

src/java/net/sf/samtools/SAMFileReader.java

@@ -27,6 +27,7 @@ package net.sf.samtools;
 import net.sf.samtools.util.*;
 
 import java.io.*;
+import java.util.Arrays;
 import java.util.zip.GZIPInputStream;
 import java.net.URL;
 
@@ -133,7 +134,7 @@ public class SAMFileReader implements Iterable<SAMRecord>, Closeable {
      * @param eagerDecode if true, decode SAM record entirely when reading it.
      */
     public SAMFileReader(final InputStream stream, final boolean eagerDecode) {
-        init(stream, eagerDecode, defaultValidationStringency);
+        init(stream, null, null, eagerDecode, defaultValidationStringency);
     }
 
     /**
@@ -144,7 +145,7 @@ public class SAMFileReader implements Iterable<SAMRecord>, Closeable {
      * @param eagerDecode if true, decode SAM record entirely when reading it.
      */
     public SAMFileReader(final File file, final boolean eagerDecode) {
-        init(file, null, eagerDecode, defaultValidationStringency);
+        this(file, null, eagerDecode);
     }
 
     /**
@@ -156,7 +157,7 @@ public class SAMFileReader implements Iterable<SAMRecord>, Closeable {
      * @param eagerDecode eagerDecode if true, decode SAM record entirely when reading it.
      */
     public SAMFileReader(final File file, final File indexFile, final boolean eagerDecode){
-        init(file, indexFile, eagerDecode, defaultValidationStringency);
+        init(null, file, indexFile, eagerDecode, defaultValidationStringency);
     }
 
     /**
@@ -446,27 +447,6 @@ public class SAMFileReader implements Iterable<SAMRecord>, Closeable {
         }
     }
 
-    private void init(final InputStream stream, final boolean eagerDecode, final ValidationStringency validationStringency) {
-
-        try {
-            final BufferedInputStream bufferedStream = IOUtil.toBufferedStream(stream);
-            if (isBAMFile(bufferedStream)) {
-                mIsBinary = true;
-                mReader = new BAMFileReader(bufferedStream, null, eagerDecode, validationStringency);
-            } else if (isGzippedSAMFile(bufferedStream)) {
-                mIsBinary = false;
-                mReader = new SAMTextReader(new GZIPInputStream(bufferedStream), validationStringency);
-            } else if (isSAMFile(bufferedStream)) {
-                mIsBinary = false;
-                mReader = new SAMTextReader(bufferedStream, validationStringency);
-            } else {
-                throw new SAMFormatException("Unrecognized file format");
-            }
-            setValidationStringency(validationStringency);
-        } catch (IOException e) {
-            throw new RuntimeIOException(e);
-        }
-    }
 
 
     private void init(final SeekableStream strm, final File indexFile, final boolean eagerDecode,
@@ -489,21 +469,26 @@ public class SAMFileReader implements Iterable<SAMRecord>, Closeable {
     }
 
 
-    private void init(final File file, File indexFile, final boolean eagerDecode, final ValidationStringency validationStringency) {
+    private void init(final InputStream stream, final File file, File indexFile, final boolean eagerDecode, final ValidationStringency validationStringency) {
+        if (stream != null && file != null) throw new IllegalArgumentException("stream and file are mutually exclusive");
         this.samFile = file;
 
         try {
-            final BufferedInputStream bufferedStream = new BufferedInputStream(new FileInputStream(file));
+            final BufferedInputStream bufferedStream;
+            if (file != null) bufferedStream = new BufferedInputStream(new FileInputStream(file));
+            else bufferedStream = IOUtil.toBufferedStream(stream);
             if (isBAMFile(bufferedStream)) {
                 mIsBinary = true;
-                if (!file.isFile()) {
+                if (file == null || !file.isFile()) {
                     // Handle case in which file is a named pipe, e.g. /dev/stdin or created by mkfifo
                     mReader = new BAMFileReader(bufferedStream, indexFile, eagerDecode, validationStringency);
                 } else {
                     bufferedStream.close();
-                    final BAMFileReader reader = new BAMFileReader(file, indexFile, eagerDecode, validationStringency);
-                    mReader = reader;
+                    mReader = new BAMFileReader(file, indexFile, eagerDecode, validationStringency);
                 }
+            } else if (BlockCompressedInputStream.isValidFile(bufferedStream)) {
+                mIsBinary = false;
+                mReader = new SAMTextReader(new BlockCompressedInputStream(bufferedStream), validationStringency);
             } else if (isGzippedSAMFile(bufferedStream)) {
                 mIsBinary = false;
                 mReader = new SAMTextReader(new GZIPInputStream(bufferedStream), validationStringency);
@@ -531,7 +516,30 @@ public class SAMFileReader implements Iterable<SAMRecord>, Closeable {
      */
     private boolean isBAMFile(final InputStream stream)
             throws IOException {
-        return BlockCompressedInputStream.isValidFile(stream);
+        if (!BlockCompressedInputStream.isValidFile(stream)) {
+          return false;
+        }
+        final int buffSize = BlockCompressedStreamConstants.MAX_COMPRESSED_BLOCK_SIZE;
+        stream.mark(buffSize);
+        final byte[] buffer = new byte[buffSize];
+        readBytes(stream, buffer, 0, buffSize);
+        stream.reset();
+        final byte[] magicBuf = new byte[4];
+        final int magicLength = readBytes(new BlockCompressedInputStream(new ByteArrayInputStream(buffer)), magicBuf, 0, 4);
+        return magicLength == BAMFileConstants.BAM_MAGIC.length && Arrays.equals(BAMFileConstants.BAM_MAGIC, magicBuf);
+    }
+
+    private static int readBytes(final InputStream stream, final byte[] buffer, final int offset, final int length)
+        throws IOException {
+        int bytesRead = 0;
+        while (bytesRead < length) {
+            final int count = stream.read(buffer, offset + bytesRead, length - bytesRead);
+            if (count <= 0) {
+                break;
+            }
+            bytesRead += count;
+        }
+        return bytesRead;
     }
 
     /**

src/tests/java/net/sf/samtools/SAMFileReaderTest.java

+/*
+ * The MIT License
+ *
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+package net.sf.samtools;
+
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.File;
+
+public class SAMFileReaderTest {
+    private static final File TEST_DATA_DIR = new File("testdata/net/sf/samtools");
+
+    @Test(dataProvider = "variousFormatReaderTestCases")
+    public void variousFormatReaderTest(final String inputFile) {
+        final File input = new File(TEST_DATA_DIR, inputFile);
+        final SAMFileReader reader = new SAMFileReader(input);
+        for (final SAMRecord rec: reader) {}
+        reader.close();
+    }
+
+    @DataProvider(name = "variousFormatReaderTestCases")
+    public Object[][] variousFormatReaderTestCases() {
+        final Object[][] scenarios = new Object[][] {
+                { "block_compressed.sam.gz"},
+                { "uncompressed.sam"},
+                { "compressed.sam.gz"},
+                { "compressed.bam"},
+        };
+        return scenarios;
+    }
+
+}

testdata/net/sf/samtools/uncompressed.sam

+@HD	VN:1.0	SO:unsorted
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr2	LN:101
+@SQ	SN:chr3	LN:101
+@RG	ID:0	SM:Hi,Mom!
+A	73	chr2	1	255	10M	*	0	0	CAACAGAAGC	)'.*.+2,))	RG:Z:0
+A	133	*	0	0	*	chr2	1	0	CAACAGAAGC	)'.*.+2,))	RG:Z:0
+B	99	chr1	1	255	10M	=	26	35	CAACAGAAGC	)'.*.+2,))	RG:Z:0
+B	147	chr1	26	255	10M	=	1	-35	CAACAGAAGC	)'.*.+2,))	RG:Z:0
+C	99	chr2	1	255	10M	=	26	35	CAACAGAAGC	)'.*.+2,))	RG:Z:0
+C	147	chr2	26	255	10M	=	1	-35	CAACAGAAGC	)'.*.+2,))	RG:Z:0
+D	99	chr3	1	255	10M	=	25	35	CAACAGAAGC	)'.*.+2,))	RG:Z:0
+D	147	chr3	26	255	10M	=	1	-35	CAACAGAAGC	)'.*.+2,))	RG:Z:0
+E	99	chr1	2	255	10M	=	15	30	CAACAGAAGC	)'.*.+2,))	RG:Z:0
+E	147	chr1	15	255	10M	=	2	-30	CAACAGAAGC	)'.*.+2,))	RG:Z:0