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re-enable the check for up-to-date versions in the Tribble index. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4039 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-08-16 12:47:58 +00:00
parent 37586d3a43
commit b23545fafa
1 changed files with 7 additions and 2 deletions
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9
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
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@ -196,7 +196,12 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
public synchronized static Index loadIndex(File inputFile, FeatureCodec codec, boolean onDisk) throws IOException { public synchronized static Index loadIndex(File inputFile, FeatureCodec codec, boolean onDisk) 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 = new File(inputFile.getAbsoluteFile() + indexExtension); File indexFile = null;
if (useLinearIndex)
indexFile = new File(inputFile.getAbsoluteFile() + indexExtension);
else
indexFile = new File(inputFile.getAbsoluteFile() + ".tdx");
FSLockWithShared lock = new FSLockWithShared(indexFile); FSLockWithShared lock = new FSLockWithShared(indexFile);
// acquire a lock on the file // acquire a lock on the file
@ -251,7 +256,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
Index index = IndexFactory.loadIndex(indexFile.getAbsolutePath()); Index index = IndexFactory.loadIndex(indexFile.getAbsolutePath());
// check if the file is up-to date (filestamp and version check) // check if the file is up-to date (filestamp and version check)
if (/*index.isCurrentVersion() && */ indexFile.lastModified() > inputFile.lastModified()) if (index.isCurrentVersion() && indexFile.lastModified() > inputFile.lastModified())
return index; return index;
else if (indexFile.lastModified() < inputFile.lastModified()) else if (indexFile.lastModified() < inputFile.lastModified())
logger.warn("Index file " + indexFile + " is out of date (index older than input file), deleting and updating the index file"); logger.warn("Index file " + indexFile + " is out of date (index older than input file), deleting and updating the index file");