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Additional logging of the temp file creation, management, and merging process 

for VCF files.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5234 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-02-11 22:07:25 +00:00
parent 5f10fffa47
commit 8d6db5d188
1 changed files with 12 additions and 1 deletions
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13
java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.io.storage; package org.broadinstitute.sting.gatk.io.storage;
import org.apache.log4j.Logger;
import org.broad.tribble.source.BasicFeatureSource; import org.broad.tribble.source.BasicFeatureSource;
import org.broad.tribble.vcf.*; import org.broad.tribble.vcf.*;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
@ -18,6 +19,11 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
* @version 0.1 * @version 0.1
*/ */
public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter { public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
/**
* our log, which we want to capture anything from this class
*/
private static Logger logger = Logger.getLogger(VCFWriterStorage.class);
protected final File file; protected final File file;
protected OutputStream stream; protected OutputStream stream;
protected final VCFWriter writer; protected final VCFWriter writer;
@ -70,6 +76,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
* @param tempFile File into which to direct the output data. * @param tempFile File into which to direct the output data.
*/ */
public VCFWriterStorage(VCFWriterStub stub, File tempFile) { public VCFWriterStorage(VCFWriterStub stub, File tempFile) {
logger.debug("Creating temporary VCF file " + tempFile.getAbsolutePath() + " for VCF output.");
this.file = tempFile; this.file = tempFile;
this.writer = vcfWriterToFile(stub, file, false); this.writer = vcfWriterToFile(stub, file, false);
writer.writeHeader(stub.getVCFHeader()); writer.writeHeader(stub.getVCFHeader());
@ -92,12 +99,16 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
* Close the VCF storage object. * Close the VCF storage object.
*/ */
public void close() { public void close() {
if(file != null)
logger.debug("Closing temporary file " + file.getAbsolutePath());
writer.close(); writer.close();
} }
public void mergeInto(VCFWriterStorage target) { public void mergeInto(VCFWriterStorage target) {
try { try {
//System.out.printf("merging %s%n", file); String sourceFilePath = file.getAbsolutePath();
String targetFilePath = target.file != null ? target.file.getAbsolutePath() : "/dev/stdin";
logger.debug(String.format("Merging %s into %s",sourceFilePath,targetFilePath));
BasicFeatureSource<VariantContext> source = BasicFeatureSource.getFeatureSource(file.getAbsolutePath(), new VCFCodec(), false); BasicFeatureSource<VariantContext> source = BasicFeatureSource.getFeatureSource(file.getAbsolutePath(), new VCFCodec(), false);
for ( VariantContext vc : source.iterator() ) { for ( VariantContext vc : source.iterator() ) {