A few more unit tests plus some extra

functionality for BAM index visualization.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5222 348d0f76-0448-11de-a6fe-93d51630548a

build.xml

@@ -321,6 +321,7 @@
             <fileset dir="${java.classes}" includes="**/sting/datasources/**/*.class"/>
             <fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
             <fileset dir="${java.classes}" includes="net/sf/picard/**/*.class"/>
+            <fileset dir="${java.classes}" includes="net/sf/samtools/**/*.class"/>
             <manifest>
                 <attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
             </manifest>

java/src/net/sf/samtools/GATKBAMFileSpan.java

@@ -56,4 +56,15 @@ public class GATKBAMFileSpan extends BAMFileSpan {
     public GATKBAMFileSpan(final List<GATKChunk> chunks) {
         super(new ArrayList<Chunk>(chunks));
     }
+
+    /**
+     * Gets the constituent chunks stored in this span.
+     * @return An unmodifiable list of chunks.
+     */
+    public List<GATKChunk> getGATKChunks() {
+        List<GATKChunk> gatkChunks = new ArrayList<GATKChunk>();
+        for(Chunk chunk: getChunks())
+            gatkChunks.add(new GATKChunk(chunk));
+        return gatkChunks;
+    }
 }

java/src/net/sf/samtools/GATKBin.java

@@ -62,4 +62,9 @@ public class GATKBin extends Bin {
     public void setGATKChunkList(List<GATKChunk> chunks) {
         super.setChunkList(new ArrayList<Chunk>(chunks));
     }
+
+    @Override
+    public String toString() {
+        return String.format("Bin %d in contig %d",getBinNumber(),getReferenceSequence());
+    }
 }

java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java

@@ -0,0 +1,133 @@
+/*
+ * Copyright (c) 2011, 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 org.broadinstitute.sting.gatk.datasources.reads;
+
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+import org.apache.commons.lang.ArrayUtils;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+import java.nio.channels.FileChannel;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: mhanna
+ * Date: Feb 7, 2011
+ * Time: 2:46:34 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class BAMBlockStartIterator implements Iterator<Long> {
+    /**
+     * How large is a BGZF header?
+     */
+    private static int BGZF_HEADER_SIZE = 18;
+
+    /**
+     * Where within the header does the BLOCKSIZE actually live?
+     */
+    private static int BLOCK_SIZE_HEADER_POSITION = BGZF_HEADER_SIZE - 2;
+
+    private FileChannel bamInputChannel;
+    private ByteBuffer headerByteBuffer;
+
+    private long nextLocation = 0;
+
+    public BAMBlockStartIterator(File bamFile) {
+        try {
+            FileInputStream bamInputStream = new FileInputStream(bamFile);
+            bamInputChannel = bamInputStream.getChannel();
+
+            headerByteBuffer = ByteBuffer.allocate(BGZF_HEADER_SIZE);
+            headerByteBuffer.order(ByteOrder.LITTLE_ENDIAN);
+
+        }
+        catch(IOException ex) {
+            throw new StingException("Could not open file",ex);
+        }
+    }
+
+    public boolean hasNext() {
+        return nextLocation != -1;
+    }
+
+    public Long next() {
+        long currentLocation = nextLocation;
+        advance();
+        return currentLocation;
+    }
+
+    public void remove() {
+        throw new UnsupportedOperationException("Cannot remove from a BAMBlockStartIterator");
+    }
+
+    private void advance() {
+        int readStatus;
+
+        headerByteBuffer.clear();
+        try {
+            readStatus = bamInputChannel.read(headerByteBuffer);
+        }
+        catch(IOException ex) {
+            throw new StingException("Could not read header data",ex);
+        }
+
+        if(readStatus == -1) {
+            nextLocation = -1;
+            try {
+                bamInputChannel.close();
+            }
+            catch(IOException ex) {
+                throw new StingException("Could not close input file",ex);
+            }
+            return;
+        }
+
+        headerByteBuffer.position(BLOCK_SIZE_HEADER_POSITION);
+        int blockSize = headerByteBuffer.getShort();
+
+        try {
+            bamInputChannel.position(bamInputChannel.position()+blockSize-BGZF_HEADER_SIZE+1);
+            nextLocation = bamInputChannel.position();
+        }
+        catch(IOException ex) {
+            throw new StingException("Could not reposition input stream",ex);
+        }
+    }
+
+    public static void main(String argv[]) throws IOException {
+        BAMBlockStartIterator blockStartIterator = new BAMBlockStartIterator(new File("/Users/mhanna/testdata/reads/MV1994.bam"));
+        int i = 0;
+        while(blockStartIterator.hasNext())
+            System.out.printf("%d -> %d%n",i++,blockStartIterator.next());
+    }
+}

java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java

@@ -126,8 +126,8 @@ public class GATKBAMIndex implements BAMIndex, BrowseableBAMIndex {
      * @return The size (number of possible bins) of the given level.
      */
     public int getLevelSize(final int levelNumber) {
-        if(levelNumber == getNumIndexLevels())
-            return MAX_BINS+1-LEVEL_STARTS[levelNumber];
+        if(levelNumber == getNumIndexLevels()-1)
+            return MAX_BINS-LEVEL_STARTS[levelNumber];
         else
             return LEVEL_STARTS[levelNumber+1]-LEVEL_STARTS[levelNumber];
     }
@@ -331,6 +331,31 @@ public class GATKBAMIndex implements BAMIndex, BrowseableBAMIndex {
         return new GATKBAMFileSpan(chunkList);
     }
 
+    public GATKBAMFileSpan getContentsOfBin(final Bin bin) {
+        if(bin == null)
+            return null;
+
+        GATKBin gatkBin = new GATKBin(bin);
+
+        BAMIndexContent indexQuery = getQueryResults(gatkBin.getReferenceSequence());
+
+        if(indexQuery == null)
+            return null;
+
+        GATKBin queriedBin = indexQuery.getBins().getBin(gatkBin.getBinNumber());
+
+        return queriedBin != null ? new GATKBAMFileSpan(queriedBin.getGATKChunkList()) : null;
+    }
+
+    /**
+     * Retrieves the linear index for the given reference sequence.
+     * @param referenceSequence Reference sequence number for which to retrieve the reference.
+     * @return The linear index for the given reference sequence.
+     */
+    public LinearIndex getLinearIndex(int referenceSequence) {
+        return getQueryResults(referenceSequence).getLinearIndex();
+    }
+
     /**
      * Get a list of bins in the BAM file that may contain SAMRecords for the given range.
      * @param referenceIndex sequence of desired SAMRecords

java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java

@@ -0,0 +1,94 @@
+/*
+ * Copyright (c) 2011, 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 org.broadinstitute.sting.gatk.datasources.reads;
+
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMSequenceDictionary;
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+
+/**
+ * Test basic functionality in the GATK's implementation of the BAM index classes.
+ */
+public class GATKBAMIndexUnitTest extends BaseTest {
+    private static File bamFile = new File(validationDataLocation+"MV1994.selected.bam");
+
+    /**
+     * Index file forming the source of all unit tests.
+     */
+    private static File bamIndexFile = new File(validationDataLocation+"MV1994.selected.bam.bai");
+
+    /**
+     * Storage for the index itself.
+     */
+    private GATKBAMIndex bamIndex;
+
+    
+    @BeforeClass
+    public void init() throws FileNotFoundException {
+        SAMFileReader reader = new SAMFileReader(bamFile);
+        SAMSequenceDictionary sequenceDictionary = reader.getFileHeader().getSequenceDictionary();
+        reader.close();
+        
+        bamIndex = new GATKBAMIndex(bamIndexFile,sequenceDictionary);
+    }
+
+    @Test
+    public void testNumberAndSizeOfIndexLevels() {
+        // The correct values for this test are pulled directly from the
+        // SAM Format Specification v1.3-r882, Section 4.1.1, last paragraph.
+        Assert.assertEquals(GATKBAMIndex.getNumIndexLevels(),6,"Incorrect number of levels in BAM index");
+
+        // Level 0
+        Assert.assertEquals(GATKBAMIndex.getFirstBinInLevel(0),0);
+        Assert.assertEquals(bamIndex.getLevelSize(0),1);
+
+        // Level 1
+        Assert.assertEquals(GATKBAMIndex.getFirstBinInLevel(1),1);
+        Assert.assertEquals(bamIndex.getLevelSize(1),8-1+1);
+
+        // Level 2
+        Assert.assertEquals(GATKBAMIndex.getFirstBinInLevel(2),9);
+        Assert.assertEquals(bamIndex.getLevelSize(2),72-9+1);
+
+        // Level 3
+        Assert.assertEquals(GATKBAMIndex.getFirstBinInLevel(3),73);
+        Assert.assertEquals(bamIndex.getLevelSize(3),584-73+1);
+
+        // Level 4
+        Assert.assertEquals(GATKBAMIndex.getFirstBinInLevel(4),585);
+        Assert.assertEquals(bamIndex.getLevelSize(4),4680-585+1);
+
+        // Level 5                                
+        Assert.assertEquals(GATKBAMIndex.getFirstBinInLevel(5),4681);
+        Assert.assertEquals(bamIndex.getLevelSize(5),37449-4681+1);
+    }
+
+}