/*
* Copyright (c) 2012 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.gatk.engine.datasources.reads.utilities;
import htsjdk.samtools.BAMIndex;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.instrumentation.Sizeof;
import java.io.File;
import java.lang.reflect.Field;
import java.util.List;
import java.util.Map;
/**
*
*
* @author mhanna
* @version 0.1
*/
public class BAMFileStat extends CommandLineProgram {
public enum CommandType { ShowBlocks, ShowIndex }
@Argument(doc="Which operation to run.",required=true)
private CommandType command;
@Argument(doc="The BAM file to inspect.",required=true)
private String bamFileName;
@Argument(doc="The range to inspect.",required=false)
private String range;
public int execute() {
switch(command) {
case ShowBlocks:
throw new ReviewedGATKException("The BAM block inspector has been disabled.");
case ShowIndex:
showIndexBins(new File(bamFileName),range);
break;
}
return 0;
}
/**
* Required main method implementation.
* @param argv Command-line arguments.
*/
public static void main(String[] argv) {
try {
BAMFileStat instance = new BAMFileStat();
start(instance, argv);
System.exit(CommandLineProgram.result);
} catch (Exception e) {
exitSystemWithError(e);
}
}
private void showIndexBins(File bamFile,String contigName) {
SAMFileReader reader;
BAMIndex index;
reader = new SAMFileReader(bamFile);
reader.setValidationStringency(ValidationStringency.SILENT);
reader.enableIndexCaching(true);
index = reader.getIndex();
reader.queryOverlapping(contigName,1,reader.getFileHeader().getSequence(contigName).getSequenceLength()).close();
int numBins = 0;
int numChunks = 0;
int numLinearIndexEntries = 0;
try {
Field[] fields = index.getClass().getDeclaredFields();
for(Field field: fields) {
if(field.getName().equals("mLastReferenceRetrieved")) {
field.setAccessible(true);
Integer lastReferenceRetrieved = (Integer)field.get(index);
System.out.printf("Last reference retrieved: %d%n", lastReferenceRetrieved);
}
if(field.getName().equals("mQueriesByReference")) {
field.setAccessible(true);
Map<Integer,Object> cachedQueries = (Map<Integer,Object>)field.get(index);
for(Object bamIndexContent: cachedQueries.values()) {
List<Object> bins = null;
Map<Object,Object> binToChunkMap = null;
Object linearIndex = null;
Field[] indexContentFields = bamIndexContent.getClass().getDeclaredFields();
for(Field indexContentField: indexContentFields) {
if(indexContentField.getName().equals("mReferenceSequence")) {
indexContentField.setAccessible(true);
System.out.printf("Reference sequence: %d%n", indexContentField.getInt(bamIndexContent));
}
if(indexContentField.getName().equals("mBins")) {
indexContentField.setAccessible(true);
bins = (List<Object>)indexContentField.get(bamIndexContent);
}
if(indexContentField.getName().equals("mBinToChunks")) {
indexContentField.setAccessible(true);
binToChunkMap = (Map<Object,Object>)indexContentField.get(bamIndexContent);
}
if(indexContentField.getName().equals("mLinearIndex")) {
indexContentField.setAccessible(true);
linearIndex = indexContentField.get(bamIndexContent);
}
}
numBins = bins.size();
for(Object bin: bins) {
int binNumber;
Field[] binFields = bin.getClass().getDeclaredFields();
for(Field binField: binFields) {
if(binField.getName().equals("binNumber")) {
binField.setAccessible(true);
binNumber = binField.getInt(bin);
List<Object> chunks = (List<Object>)binToChunkMap.get(bin);
System.out.printf("\tBin: %d, number of chunks: %d%n",binNumber,chunks.size());
for(Object chunk: chunks)
System.out.printf("\t\tChunk: %s%n",chunk);
numChunks += chunks.size();
}
}
}
Field[] linearIndexFields = linearIndex.getClass().getDeclaredFields();
for(Field linearIndexField: linearIndexFields) {
if(linearIndexField.getName().equals("mIndexEntries")) {
linearIndexField.setAccessible(true);
long[] linearIndexEntries = (long[])linearIndexField.get(linearIndex);
System.out.printf("\t\tIndex entries: %d", linearIndexEntries.length);
for(long indexEntry: linearIndexEntries)
System.out.printf("%d,",indexEntry);
System.out.printf("%n");
numLinearIndexEntries = linearIndexEntries.length;
}
}
}
}
}
}
catch(IllegalAccessException ex) {
throw new ReviewedGATKException("Unable to examine cached index",ex);
}
System.out.printf("%nOverall: %d bins, %d chunks, %d linear index entries",numBins,numChunks,numLinearIndexEntries);
if(Sizeof.isEnabled())
System.out.printf(", total index size in bytes: %d",Sizeof.getObjectGraphSize(index));
System.out.println();
reader.close();
}
}