From 64b7b3f83be3dc9f241f91242d9b41fbbca4233e Mon Sep 17 00:00:00 2001 From: aaron Date: Sat, 2 Oct 2010 04:35:11 +0000 Subject: [PATCH] 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 --- .../sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java index c4c8a727b..c4e139ca8 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java @@ -312,7 +312,7 @@ public class RMDTrackBuilder extends PluginManager { private static Index writeIndexToDisk(Index index, File indexFile, FSLockWithShared lock) throws IOException { boolean locked = false; // could we exclusive lock the file? 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) { logger.info("Writing Tribble index to disk for file " + indexFile); LittleEndianOutputStream stream = new LittleEndianOutputStream(new FileOutputStream(indexFile)); @@ -320,7 +320,7 @@ public class RMDTrackBuilder extends PluginManager { stream.close(); } 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; } catch(FileSystemInabilityToLockException ex) {