Add hidden command-line argument for low-memory sharding.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5355 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -836,6 +836,9 @@ public class GenomeAnalysisEngine {
         if ( getWalkerBAQApplicationTime() == BAQ.ApplicationTime.FORBIDDEN && argCollection.BAQMode != BAQ.CalculationMode.OFF)
             throw new UserException.BadArgumentValue("baq", "Walker cannot accept BAQ'd base qualities, and yet BAQ mode " + argCollection.BAQMode + " was requested.");
 
+        // TEMPORARY: Force low-memory sharding to be available.
+        SAMDataSource.enableLowMemorySharding(argCollection.enableLowMemorySharding);
+
         return new SAMDataSource(
                 samReaderIDs,
                 genomeLocParser,

java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -238,10 +238,14 @@ public class GATKArgumentCollection {
     public int processTrackerID = -1;
 
     @Element(required = false)
-    @Argument(fullName="allow_intervals_with_unindexed_bam",doc="Allow interval processing with an unsupported BAM.  NO INTEGRATION TESTS are available.  Use at your own risk.")
+    @Argument(fullName="allow_intervals_with_unindexed_bam",doc="Allow interval processing with an unsupported BAM.  NO INTEGRATION TESTS are available.  Use at your own risk.",required=false)
     @Hidden
     public boolean allowIntervalsWithUnindexedBAM = false;
 
+    @Element(required = false)
+    @Argument(fullName="enable_experimental_low_memory_sharding",doc="Enable experimental low-memory sharding functionality.  Use at your own risk.",required=false)
+    public boolean enableLowMemorySharding = false;
+
     // --------------------------------------------------------------------------------------------------------------
     //
     // methods
@@ -428,6 +432,9 @@ public class GATKArgumentCollection {
         if (allowIntervalsWithUnindexedBAM != other.allowIntervalsWithUnindexedBAM)
             return false;
 
+        if (enableLowMemorySharding != other.enableLowMemorySharding)
+            return false;
+
         return true;
     }
 

java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java

@@ -83,7 +83,7 @@ public class LocusShardStrategy implements ShardStrategy {
             else
                 intervals = locations;
 
-            if(SAMDataSource.TRY_LOW_MEMORY_SHARDING)
+            if(SAMDataSource.isLowMemoryShardingEnabled())
                 this.filePointerIterator = new LowMemoryIntervalSharder(this.reads,intervals);
             else
                 this.filePointerIterator = IntervalSharder.shardIntervals(this.reads,intervals);

java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java

@@ -96,7 +96,7 @@ public class ReadShardStrategy implements ShardStrategy {
         this.locations = locations;
 
         if(locations != null)
-            filePointerIterator = SAMDataSource.TRY_LOW_MEMORY_SHARDING ? new LowMemoryIntervalSharder(this.dataSource,locations) : IntervalSharder.shardIntervals(this.dataSource,locations);
+            filePointerIterator = SAMDataSource.isLowMemoryShardingEnabled() ? new LowMemoryIntervalSharder(this.dataSource,locations) : IntervalSharder.shardIntervals(this.dataSource,locations);
         else
             filePointerIterator = filePointers.iterator();
 

java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java

@@ -128,7 +128,10 @@ public class SAMDataSource {
      */
     private final SAMResourcePool resourcePool;
 
-    static final boolean TRY_LOW_MEMORY_SHARDING = false;
+    /**
+     * Whether to enable the new low-memory sharding mechanism.
+     */
+    private static boolean enableLowMemorySharding = false;
 
     /**
      * Create a new SAM data source given the supplied read metadata.
@@ -281,7 +284,7 @@ public class SAMDataSource {
             originalToMergedReadGroupMappings.put(id,mappingToMerged);
         }
 
-        if(TRY_LOW_MEMORY_SHARDING) {
+        if(enableLowMemorySharding) {
             for(SAMReaderID id: readerIDs) {
                 File indexFile = findIndexFile(id.samFile);
                 if(indexFile != null) {
@@ -302,6 +305,22 @@ public class SAMDataSource {
      */
     public ReadProperties getReadsInfo() { return readProperties; }
 
+    /**
+     * Enable experimental low-memory sharding.
+     * @param enable True to enable sharding.  False otherwise.
+     */
+    public static void enableLowMemorySharding(final boolean enable) {
+        enableLowMemorySharding = enable;
+    }
+
+    /**
+     * Returns whether low-memory sharding is enabled.
+     * @return True if enabled, false otherwise.
+     */
+    public static boolean isLowMemoryShardingEnabled() {
+        return enableLowMemorySharding;
+    }
+
     /**
      * Checks to see whether any reads files are supplying data.
      * @return True if no reads files are supplying data to the traversal; false otherwise.
@@ -389,7 +408,7 @@ public class SAMDataSource {
      * @return True if all readers have an index.
      */
     public boolean hasIndex() {
-        if(TRY_LOW_MEMORY_SHARDING)
+        if(enableLowMemorySharding)
             return readerIDs.size() == bamIndices.size();
         else {
             for(SAMFileReader reader: resourcePool.getReadersWithoutLocking()) {
@@ -406,7 +425,7 @@ public class SAMDataSource {
      * @return The index.  Will preload the index if necessary.
      */
     public BrowseableBAMIndex getIndex(final SAMReaderID id) {
-        if(TRY_LOW_MEMORY_SHARDING)
+        if(enableLowMemorySharding)
             return bamIndices.get(id);
         else {
             SAMReaders readers = resourcePool.getReadersWithoutLocking();
@@ -729,7 +748,7 @@ public class SAMDataSource {
             for(SAMReaderID readerID: readerIDs) {
                 SAMFileReader reader = new SAMFileReader(readerID.samFile);
                 reader.enableFileSource(true);
-                if(!TRY_LOW_MEMORY_SHARDING)
+                if(!enableLowMemorySharding)
                     reader.enableIndexCaching(true);
                 reader.setValidationStringency(validationStringency);