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Added sharding strat. code that picks the right kind of shard, based on the traversal engine 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@644 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-05-08 21:55:10 +00:00
parent 6e394490cb
commit 517f27f331
1 changed files with 8 additions and 5 deletions
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13
java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource; import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource;
import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.traversals.TraversalEngine; import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
import org.broadinstitute.sting.gatk.traversals.TraverseByReads; import org.broadinstitute.sting.gatk.traversals.TraverseReads;
import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference; import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
@ -69,7 +69,7 @@ public abstract class MicroScheduler {
*/ */
protected MicroScheduler( Walker walker, List<File> reads, File refFile, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods ) { protected MicroScheduler( Walker walker, List<File> reads, File refFile, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods ) {
if (walker instanceof ReadWalker) { if (walker instanceof ReadWalker) {
traversalEngine = new TraverseByReads(reads, refFile, rods); traversalEngine = new TraverseReads(reads, refFile, rods);
} else { } else {
traversalEngine = new TraverseLociByReference(reads, refFile, rods); traversalEngine = new TraverseLociByReference(reads, refFile, rods);
} }
@ -102,13 +102,16 @@ public abstract class MicroScheduler {
*/ */
protected ShardStrategy getShardStrategy( ReferenceSequenceFile drivingDataSource, List<GenomeLoc> intervals ) { protected ShardStrategy getShardStrategy( ReferenceSequenceFile drivingDataSource, List<GenomeLoc> intervals ) {
ShardStrategy shardStrategy = null; ShardStrategy shardStrategy = null;
if( intervals != null ) ShardStrategyFactory.SHATTER_STRATEGY shardType = (traversalEngine instanceof TraverseReads) ?
shardStrategy = ShardStrategyFactory.shatter( ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, ShardStrategyFactory.SHATTER_STRATEGY.READS : ShardStrategyFactory.SHATTER_STRATEGY.LINEAR;
if( intervals != null && shardType != ShardStrategyFactory.SHATTER_STRATEGY.READS)
shardStrategy = ShardStrategyFactory.shatter( shardType,
drivingDataSource.getSequenceDictionary(), drivingDataSource.getSequenceDictionary(),
SHARD_SIZE, SHARD_SIZE,
intervals ); intervals );
else else
shardStrategy = ShardStrategyFactory.shatter( ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, shardStrategy = ShardStrategyFactory.shatter( shardType,
drivingDataSource.getSequenceDictionary(), drivingDataSource.getSequenceDictionary(),
SHARD_SIZE ); SHARD_SIZE );