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fix for a recent change to the indexing code where we ignore the results of locking the file (this is bad), and as a result don't write the index; this should fix the build. 

Off to Yosemite in 4 hours, enjoy the week gsa folks!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4410 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-10-02 04:35:11 +00:00
parent 7551ba8249
commit 64b7b3f83b
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
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@ -312,7 +312,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
private static Index writeIndexToDisk(Index index, File indexFile, FSLockWithShared lock) throws IOException { private static Index writeIndexToDisk(Index index, File indexFile, FSLockWithShared lock) throws IOException {
boolean locked = false; // could we exclusive lock the file? boolean locked = false; // could we exclusive lock the file?
try { try {
lock.exclusiveLock(); // handle the case where we aren't locking anything locked = lock.exclusiveLock(); // handle the case where we aren't locking anything
if (locked) { if (locked) {
logger.info("Writing Tribble index to disk for file " + indexFile); logger.info("Writing Tribble index to disk for file " + indexFile);
LittleEndianOutputStream stream = new LittleEndianOutputStream(new FileOutputStream(indexFile)); LittleEndianOutputStream stream = new LittleEndianOutputStream(new FileOutputStream(indexFile));
@ -320,7 +320,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
stream.close(); stream.close();
} }
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.info("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");
return index; return index;
} }
catch(FileSystemInabilityToLockException ex) { catch(FileSystemInabilityToLockException ex) {