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No longer writes the index to disk twice. But fixes for closing VCFWriters throughout the codebase 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4488 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-10-13 14:26:06 +00:00
parent 28a1020c89
commit da29fcdb68
2 changed files with 16 additions and 4 deletions
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19
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
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@ -40,8 +40,10 @@ import org.broadinstitute.sting.gatk.AbstractGenomeAnalysisEngine;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.file.FSLockWithShared; import org.broadinstitute.sting.utils.file.FSLockWithShared;
import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException; import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException;
import org.broadinstitute.sting.utils.instrumentation.Sizeof;
import java.io.*; import java.io.*;
import java.util.*; import java.util.*;
@ -194,6 +196,9 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
Pair<BasicFeatureSource, SAMSequenceDictionary> reader; Pair<BasicFeatureSource, SAMSequenceDictionary> reader;
try { try {
Index index = loadIndex(inputFile, createCodec(targetClass, name)); Index index = loadIndex(inputFile, createCodec(targetClass, name));
try { logger.info(String.format(" Index for %s has size in bytes %d", inputFile, Sizeof.getObjectGraphSize(index))); }
catch ( ReviewedStingException e) { }
SAMSequenceDictionary dictFromIndex = getSequenceDictionaryFromProperties(index); SAMSequenceDictionary dictFromIndex = getSequenceDictionaryFromProperties(index);
// if we don't have a dictionary in the Tribble file, and we've set a dictionary for this builder, set it in the file if they match // if we don't have a dictionary in the Tribble file, and we've set a dictionary for this builder, set it in the file if they match
@ -222,7 +227,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @return a linear index for the specified type * @return a linear index for the specified type
* @throws IOException if we cannot write the index file * @throws IOException if we cannot write the index file
*/ */
public synchronized static Index loadIndex(File inputFile, FeatureCodec codec) throws IOException { public synchronized Index loadIndex(File inputFile, FeatureCodec codec) throws IOException {
// create the index file name, locking on the index file name // create the index file name, locking on the index file name
File indexFile = Tribble.indexFile(inputFile); File indexFile = Tribble.indexFile(inputFile);
FSLockWithShared lock = new FSLockWithShared(indexFile); FSLockWithShared lock = new FSLockWithShared(indexFile);
@ -248,7 +253,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @return an index, or null if we couldn't load one * @return an index, or null if we couldn't load one
* @throws IOException if we fail for FS issues * @throws IOException if we fail for FS issues
*/ */
protected static Index attemptIndexFromDisk(File inputFile, FeatureCodec codec, File indexFile, FSLockWithShared lock) throws IOException { protected Index attemptIndexFromDisk(File inputFile, FeatureCodec codec, File indexFile, FSLockWithShared lock) throws IOException {
boolean locked; boolean locked;
try { try {
locked = lock.sharedLock(); locked = lock.sharedLock();
@ -314,6 +319,10 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
} }
else // we can't write it to disk, just store it in memory, tell them this else // we can't write it to disk, just store it in memory, tell them this
logger.warn("Unable to write to " + indexFile + " for the index file, creating index in memory only"); logger.warn("Unable to write to " + indexFile + " for the index file, creating index in memory only");
try { logger.info(String.format(" Index for %s has size in bytes %d", indexFile, Sizeof.getObjectGraphSize(index))); }
catch ( ReviewedStingException e) { }
return index; return index;
} }
catch(FileSystemInabilityToLockException ex) { catch(FileSystemInabilityToLockException ex) {
@ -332,10 +341,12 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @return a LinearIndex, given the file location * @return a LinearIndex, given the file location
* @throws IOException when unable to create the index in memory * @throws IOException when unable to create the index in memory
*/ */
private static Index createIndexInMemory(File inputFile, FeatureCodec codec) { private Index createIndexInMemory(File inputFile, FeatureCodec codec) {
// this can take a while, let them know what we're doing // this can take a while, let them know what we're doing
logger.info("Creating Tribble index in memory for file " + inputFile); logger.info("Creating Tribble index in memory for file " + inputFile);
return IndexFactory.createIndex(inputFile, codec, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); Index idx = IndexFactory.createIndex(inputFile, codec, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
setIndexSequenceDictionary(idx, dict, null, false);
return idx;
} }
/** /**

1
java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
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@ -105,6 +105,7 @@ public class VCF4WriterTestWalker extends RodWalker<Integer, Integer> {
} }
} }
vcfWriter.close();
} }