Fixed performance issue in protosharding code -- turns out that the index

optimizer was mutating the data stored in the indices.  Protosharding still
disabled by default.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5334 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -68,4 +68,11 @@ public class GATKBAMFileSpan extends BAMFileSpan {
             gatkChunks.add(new GATKChunk(chunk));
         return gatkChunks;
     }
+
+    public String toString() {
+        StringBuilder builder = new StringBuilder();
+        for(GATKChunk chunk: getGATKChunks())
+            builder.append(String.format("%s;",chunk));
+        return builder.toString();
+    }
 }

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

@@ -110,8 +110,6 @@ public class BAMIndexBinIterator {
                 binPositionBuffer.putLong(position);
                 binPositionBuffer.flip();
 
-                System.out.printf("Writing bin number %d to position %d: coordinate = %d%n",indexBin,indexBin*Long.SIZE*8,position);
-
                 metaIndexChannel.write(binPositionBuffer);
                 binPositionBuffer.flip();
 

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

@@ -182,12 +182,16 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
         for(GATKBin bin: binTree.getBins()) {
             if(bin == null)
                 continue;
-            chunks.addAll(Arrays.asList(bin.getChunkList()));
+            // The optimizer below will mutate the chunk list.  Make sure each element is a clone of the reference sequence.
+            for(GATKChunk chunk: bin.getChunkList())
+                chunks.add(chunk.clone());
         }
 
         // Optimize the chunk list with a linear index optimization
         chunks = index.optimizeChunkList(chunks,index.getLinearIndex(initialRegion.getContigIndex()).getMinimumOffset(initialRegion.getStart()));
         
-        return new GATKBAMFileSpan(chunks.toArray(new GATKChunk[chunks.size()]));
+        GATKBAMFileSpan fileSpan = new GATKBAMFileSpan(chunks.toArray(new GATKChunk[chunks.size()]));
+
+        return fileSpan;
     }
 }

java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java

@@ -0,0 +1,115 @@
+/*
+ * 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.utilities;
+
+import net.sf.samtools.GATKBAMFileSpan;
+import net.sf.samtools.GATKChunk;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecordIterator;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
+import java.io.File;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: mhanna
+ * Date: Feb 25, 2011
+ * Time: 3:25:13 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class PrintBAMRegion extends CommandLineProgram {
+    @Argument(fullName="input",shortName="I",doc="Input file to process",required=true)
+    private File input = null;
+
+    @Argument(fullName="region",shortName="R",doc="BAM region to process, in chunk format (mmmm:nn-xxxx:yy)",required=true)
+    private String region;
+
+    private static final long MIN_BLOCK_SIZE = 0;
+    private static final long MAX_BLOCK_SIZE = (long)Math.pow(2,48)-1;
+    private static final int MIN_OFFSET_SIZE = 0;
+    private static final int MAX_OFFSET_SIZE = (int)Math.pow(2,16)-1;
+
+    public int execute() {
+        SAMFileReader reader = new SAMFileReader(input);
+        reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+
+        Pattern regionPattern = Pattern.compile("(\\d+):(\\d+)-(\\d+):(\\d+)");
+        Matcher matcher = regionPattern.matcher(region);
+        if(!matcher.matches())
+            throw new UserException("BAM region to process must be in chunk format (mmmm:nn-xxxx:yy)");
+
+        long firstBlock = Long.parseLong(matcher.group(1));
+        int firstOffset = Integer.parseInt(matcher.group(2));
+        long lastBlock = Long.parseLong(matcher.group(3));
+        int lastOffset = Integer.parseInt(matcher.group(4));
+
+        if(firstBlock < MIN_BLOCK_SIZE || firstBlock > MAX_BLOCK_SIZE)
+            throw new UserException(String.format("First block is invalid; must be between %d and %d; actually is %d",MIN_BLOCK_SIZE,MAX_BLOCK_SIZE,firstBlock));
+        if(lastBlock < MIN_BLOCK_SIZE || lastBlock > MAX_BLOCK_SIZE)
+            throw new UserException(String.format("Last block is invalid; must be between %d and %d; actually is %d",MIN_BLOCK_SIZE,MAX_BLOCK_SIZE,lastBlock));
+        if(firstOffset < MIN_OFFSET_SIZE || firstOffset > MAX_OFFSET_SIZE)
+            throw new UserException(String.format("First offset is invalid; must be between %d and %d; actually is %d",MIN_OFFSET_SIZE,MAX_OFFSET_SIZE,firstOffset));
+        if(lastOffset < MIN_OFFSET_SIZE || lastOffset > MAX_OFFSET_SIZE)
+            throw new UserException(String.format("Last offset is invalid; must be between %d and %d; actually is %d",MIN_OFFSET_SIZE,MAX_OFFSET_SIZE,lastOffset));
+
+        GATKChunk chunk = new GATKChunk(firstBlock<<16 | firstOffset,lastBlock<<16 | lastOffset);
+        GATKBAMFileSpan fileSpan = new GATKBAMFileSpan(chunk);
+
+        SAMRecordIterator iterator = reader.iterator(fileSpan);
+        long readCount = 0;
+        while(iterator.hasNext()) {
+            System.out.printf("%s%n",iterator.next().format());
+            readCount++;
+        }
+        System.out.printf("%d reads shown.",readCount);
+
+        iterator.close();
+        reader.close();
+
+        return 0;
+    }
+
+
+    /**
+     * Required main method implementation.
+     * @param argv Command-line argument text.
+     * @throws Exception on error.
+     */
+    public static void main(String[] argv) throws Exception {
+        try {
+            PrintBAMRegion instance = new PrintBAMRegion();
+            start(instance, argv);
+            System.exit(0);
+        }
+        catch(Exception ex) {
+            ex.printStackTrace();
+            System.exit(1);
+        }
+    }
+}