Returning index dumping functionality in BAMFileStat to a useable state.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3880 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna
parent
19ad44d332
commit
8b072b59e2
|
|
@ -23,7 +23,7 @@
|
|||
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.sting.gatk.datasources.utilities;
|
||||
package org.broadinstitute.sting.gatk.datasources;
|
||||
|
||||
import org.broadinstitute.sting.commandline.CommandLineProgram;
|
||||
import org.broadinstitute.sting.commandline.Argument;
|
||||
|
|
@ -31,6 +31,11 @@ import org.broadinstitute.sting.utils.StingException;
|
|||
|
||||
import java.io.File;
|
||||
import java.io.PrintStream;
|
||||
import java.lang.reflect.Field;
|
||||
import java.util.Map;
|
||||
import java.util.List;
|
||||
|
||||
import net.sf.samtools.*;
|
||||
|
||||
/**
|
||||
*
|
||||
|
|
@ -47,28 +52,15 @@ public class BAMFileStat extends CommandLineProgram {
|
|||
@Argument(doc="The BAM file to inspect.",required=true)
|
||||
private String bamFileName;
|
||||
|
||||
@Argument(doc="The range of blocks to inspect.",required=false)
|
||||
@Argument(doc="The range to inspect.",required=false)
|
||||
private String range;
|
||||
|
||||
public int execute() {
|
||||
Integer startPosition = null, stopPosition = null;
|
||||
if(range != null) {
|
||||
int dashPosition = range.indexOf('-');
|
||||
if(dashPosition > 0) {
|
||||
if(dashPosition > 0)
|
||||
startPosition = Integer.valueOf(range.substring(0,dashPosition));
|
||||
if(dashPosition < range.length()-1)
|
||||
stopPosition = Integer.valueOf(range.substring(dashPosition+1));
|
||||
}
|
||||
else
|
||||
startPosition = Integer.valueOf(range);
|
||||
}
|
||||
|
||||
switch(command) {
|
||||
case ShowBlocks:
|
||||
throw new StingException("The BAM block inspector has been disabled.");
|
||||
case ShowIndex:
|
||||
showIndexBins(new File(bamFileName+".bai"));
|
||||
showIndexBins(new File(bamFileName),range);
|
||||
break;
|
||||
}
|
||||
return 0;
|
||||
|
|
@ -88,36 +80,102 @@ public class BAMFileStat extends CommandLineProgram {
|
|||
}
|
||||
}
|
||||
|
||||
private void showIndexBins(File bamFile) {
|
||||
BAMFileIndexContentInspector inspector = new BAMFileIndexContentInspector(bamFile);
|
||||
inspector.inspect(System.out,null,null);
|
||||
}
|
||||
private void showIndexBins(File bamFile,String contigName) {
|
||||
SAMFileReader reader;
|
||||
BAMIndex index;
|
||||
|
||||
private class BAMFileIndexContentInspector /*extends CachingBAMFileIndex*/ {
|
||||
public BAMFileIndexContentInspector(File bamFileIndex) {
|
||||
// super(bamFileIndex);
|
||||
}
|
||||
reader = new SAMFileReader(bamFile);
|
||||
reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
|
||||
reader.enableIndexCaching(true);
|
||||
index = reader.getIndex();
|
||||
|
||||
public void inspect(PrintStream outputStream, Integer startPosition, Integer stopPosition) {
|
||||
/*
|
||||
outputStream.printf("Number of reference sequences: %d%n", this.referenceToBins.size());
|
||||
for(int referenceSequence: referenceToBins.keySet()) {
|
||||
Bin[] bins = referenceToBins.get(referenceSequence);
|
||||
outputStream.printf("Reference sequence: %d%n",referenceSequence);
|
||||
outputStream.printf("number of bins: %d%n",bins.length);
|
||||
for(Bin bin: bins) {
|
||||
List<Chunk> chunks = binToChunks.get(bin);
|
||||
outputStream.printf("\tBin: %d, number of chunks: %d%n", bin.binNumber, chunks.size());
|
||||
for(Chunk chunk: chunks)
|
||||
outputStream.printf("\t\tChunk: %s%n", chunk);
|
||||
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;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
LinearIndex linearIndex = referenceToLinearIndices.get(referenceSequence);
|
||||
outputStream.printf("\t\tIndex entries: %d", linearIndex.indexEntries.length);
|
||||
for(long indexEntry: linearIndex.indexEntries)
|
||||
outputStream.printf("%d,",indexEntry);
|
||||
outputStream.printf("%n");
|
||||
}
|
||||
*/
|
||||
}
|
||||
catch(IllegalAccessException ex) {
|
||||
throw new StingException("Unable to examine cached index",ex);
|
||||
}
|
||||
|
||||
System.out.printf("%nOverall: %d bins, %d chunks, %d linear index entries",numBins,numChunks,numLinearIndexEntries);
|
||||
|
||||
reader.close();
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue