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Trival refactoring in preparation for on-the-fly indexing 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4409 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-10-01 22:32:59 +00:00
parent 399e6f1463
commit 7551ba8249
1 changed files with 7 additions and 4 deletions
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11
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
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@ -201,7 +201,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
// 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
if (dictFromIndex.size() == 0 && dict != null) { if (dictFromIndex.size() == 0 && dict != null) {
File indexFile = new File(inputFile.getAbsoluteFile() + indexExtension); File indexFile = indexFileForFile(inputFile);
setIndexSequenceDictionary(index,dict,indexFile,true); setIndexSequenceDictionary(index,dict,indexFile,true);
dictFromIndex = getSequenceDictionaryFromProperties(index); dictFromIndex = getSequenceDictionaryFromProperties(index);
} }
@ -218,6 +218,10 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
return reader; return reader;
} }
public static File indexFileForFile(File inputFile) {
return new File(inputFile.getAbsoluteFile() + indexExtension);
}
/** /**
* create an index for the input file * create an index for the input file
* @param inputFile the input file * @param inputFile the input file
@ -226,9 +230,8 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @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 static 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 = new File(inputFile.getAbsoluteFile() + indexExtension); File indexFile = indexFileForFile(inputFile);
FSLockWithShared lock = new FSLockWithShared(indexFile); FSLockWithShared lock = new FSLockWithShared(indexFile);
// acquire a lock on the file // acquire a lock on the file
@ -309,7 +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 {
locked = lock.exclusiveLock(); 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));