From 6b4a1e3b9fce86461910f19729805439404ac513 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 9 Aug 2010 00:12:09 +0000
Subject: [PATCH] Reenabling code that was commented out after it was confirmed
 to work by many participating in this thread:
 http://getsatisfaction.com/gsa/topics/error_thrown_when_reading_reference_file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3981 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../ReferenceDataSource.java                  | 64 +++++++++----------
 1 file changed, 32 insertions(+), 32 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
index b9c848c6b..ab6b7502d 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
@@ -143,39 +143,39 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
          * but is incomplete). To avoid this, obtain shared locks on both files before creating IndexedFastaSequenceFile.
          */
 
-//        FSLockWithShared dictLock = new FSLockWithShared(dictFile,true);
-//        FSLockWithShared indexLock = new FSLockWithShared(indexFile,true);
-//        try {
-//            try {
-//                if (!dictLock.sharedLock()) {
-//                    throw new StingException("Could not open dictionary file because a lock could not be obtained.");
-//                }
-//            }
-//            catch(FileSystemInabilityToLockException ex) {
-//                logger.info(String.format("Unable to create a lock on dictionary file: %s",ex.getMessage()));
-//                logger.info("Treating existing dictionary file as complete.");
-//            }
-//
-//            try {
-//                if (!indexLock.sharedLock()) {
-//                    throw new StingException("Could not open index file because a lock could not be obtained.");
-//                }
-//            }
-//            catch(FileSystemInabilityToLockException ex) {
-//                logger.info(String.format("Unable to create a lock on index file: %s",ex.getMessage()));
-//                logger.info("Treating existing index file as complete.");
-//            }
+        FSLockWithShared dictLock = new FSLockWithShared(dictFile,true);
+        FSLockWithShared indexLock = new FSLockWithShared(indexFile,true);
+        try {
+            try {
+                if (!dictLock.sharedLock()) {
+                    throw new StingException("Could not open dictionary file because a lock could not be obtained.");
+                }
+            }
+            catch(FileSystemInabilityToLockException ex) {
+                logger.info(String.format("Unable to create a lock on dictionary file: %s",ex.getMessage()));
+                logger.info("Treating existing dictionary file as complete.");
+            }
 
-        index = new IndexedFastaSequenceFile(fastaFile);
-//
-//        }
-//        catch (Exception e) {
-//            throw new StingException(String.format("Error reading fasta file %s.", fastaFile.getAbsolutePath()), e);
-//        }
-//        finally {
-//            dictLock.unlock();
-//            indexLock.unlock();
-//        }
+            try {
+                if (!indexLock.sharedLock()) {
+                    throw new StingException("Could not open index file because a lock could not be obtained.");
+                }
+            }
+            catch(FileSystemInabilityToLockException ex) {
+                logger.info(String.format("Unable to create a lock on index file: %s",ex.getMessage()));
+                logger.info("Treating existing index file as complete.");
+            }
+
+            index = new IndexedFastaSequenceFile(fastaFile);
+
+        }
+        catch (Exception e) {
+            throw new StingException(String.format("Error reading fasta file %s.", fastaFile.getAbsolutePath()), e);
+        }
+        finally {
+            dictLock.unlock();
+            indexLock.unlock();
+        }
     }
 
     /**