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
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hanna
parent
8de83725f9
commit
e75366f738
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@ -68,4 +68,11 @@ public class GATKBAMFileSpan extends BAMFileSpan {
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gatkChunks.add(new GATKChunk(chunk));
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return gatkChunks;
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}
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public String toString() {
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StringBuilder builder = new StringBuilder();
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for(GATKChunk chunk: getGATKChunks())
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builder.append(String.format("%s;",chunk));
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return builder.toString();
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}
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}
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@ -110,8 +110,6 @@ public class BAMIndexBinIterator {
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binPositionBuffer.putLong(position);
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binPositionBuffer.flip();
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System.out.printf("Writing bin number %d to position %d: coordinate = %d%n",indexBin,indexBin*Long.SIZE*8,position);
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metaIndexChannel.write(binPositionBuffer);
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binPositionBuffer.flip();
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@ -182,12 +182,16 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
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for(GATKBin bin: binTree.getBins()) {
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if(bin == null)
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continue;
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chunks.addAll(Arrays.asList(bin.getChunkList()));
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// The optimizer below will mutate the chunk list. Make sure each element is a clone of the reference sequence.
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for(GATKChunk chunk: bin.getChunkList())
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chunks.add(chunk.clone());
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}
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// Optimize the chunk list with a linear index optimization
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chunks = index.optimizeChunkList(chunks,index.getLinearIndex(initialRegion.getContigIndex()).getMinimumOffset(initialRegion.getStart()));
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return new GATKBAMFileSpan(chunks.toArray(new GATKChunk[chunks.size()]));
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GATKBAMFileSpan fileSpan = new GATKBAMFileSpan(chunks.toArray(new GATKChunk[chunks.size()]));
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return fileSpan;
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}
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}
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@ -0,0 +1,115 @@
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/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.datasources.reads.utilities;
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import net.sf.samtools.GATKBAMFileSpan;
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import net.sf.samtools.GATKChunk;
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import net.sf.samtools.SAMFileReader;
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import net.sf.samtools.SAMRecordIterator;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.CommandLineProgram;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import java.io.File;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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/**
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* Created by IntelliJ IDEA.
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* User: mhanna
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* Date: Feb 25, 2011
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* Time: 3:25:13 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class PrintBAMRegion extends CommandLineProgram {
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@Argument(fullName="input",shortName="I",doc="Input file to process",required=true)
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private File input = null;
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@Argument(fullName="region",shortName="R",doc="BAM region to process, in chunk format (mmmm:nn-xxxx:yy)",required=true)
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private String region;
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private static final long MIN_BLOCK_SIZE = 0;
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private static final long MAX_BLOCK_SIZE = (long)Math.pow(2,48)-1;
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private static final int MIN_OFFSET_SIZE = 0;
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private static final int MAX_OFFSET_SIZE = (int)Math.pow(2,16)-1;
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public int execute() {
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SAMFileReader reader = new SAMFileReader(input);
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reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
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Pattern regionPattern = Pattern.compile("(\\d+):(\\d+)-(\\d+):(\\d+)");
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Matcher matcher = regionPattern.matcher(region);
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if(!matcher.matches())
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throw new UserException("BAM region to process must be in chunk format (mmmm:nn-xxxx:yy)");
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long firstBlock = Long.parseLong(matcher.group(1));
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int firstOffset = Integer.parseInt(matcher.group(2));
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long lastBlock = Long.parseLong(matcher.group(3));
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int lastOffset = Integer.parseInt(matcher.group(4));
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if(firstBlock < MIN_BLOCK_SIZE || firstBlock > MAX_BLOCK_SIZE)
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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));
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if(lastBlock < MIN_BLOCK_SIZE || lastBlock > MAX_BLOCK_SIZE)
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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));
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if(firstOffset < MIN_OFFSET_SIZE || firstOffset > MAX_OFFSET_SIZE)
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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));
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if(lastOffset < MIN_OFFSET_SIZE || lastOffset > MAX_OFFSET_SIZE)
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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));
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GATKChunk chunk = new GATKChunk(firstBlock<<16 | firstOffset,lastBlock<<16 | lastOffset);
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GATKBAMFileSpan fileSpan = new GATKBAMFileSpan(chunk);
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SAMRecordIterator iterator = reader.iterator(fileSpan);
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long readCount = 0;
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while(iterator.hasNext()) {
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System.out.printf("%s%n",iterator.next().format());
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readCount++;
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}
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System.out.printf("%d reads shown.",readCount);
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iterator.close();
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reader.close();
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return 0;
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}
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/**
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* Required main method implementation.
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* @param argv Command-line argument text.
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* @throws Exception on error.
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*/
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public static void main(String[] argv) throws Exception {
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try {
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PrintBAMRegion instance = new PrintBAMRegion();
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start(instance, argv);
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System.exit(0);
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}
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catch(Exception ex) {
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ex.printStackTrace();
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System.exit(1);
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}
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}
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}
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