diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index b4c0febec..15d7b8216 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -681,19 +681,19 @@ public class GenomeAnalysisEngine { ShardStrategyFactory.SHATTER_STRATEGY.LINEAR; shardStrategy = ShardStrategyFactory.shatter(readsDataSource, referenceDataSource, - argCollection.experimentalSharding ? ShardStrategyFactory.SHATTER_STRATEGY.LOCUS_EXPERIMENTAL : shardType, + !argCollection.disableExperimentalSharding ? ShardStrategyFactory.SHATTER_STRATEGY.LOCUS_EXPERIMENTAL : shardType, drivingDataSource.getSequenceDictionary(), SHARD_SIZE, intervals, maxIterations); } else shardStrategy = ShardStrategyFactory.shatter(readsDataSource, referenceDataSource, - argCollection.experimentalSharding ? ShardStrategyFactory.SHATTER_STRATEGY.LOCUS_EXPERIMENTAL : ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, + !argCollection.disableExperimentalSharding ? ShardStrategyFactory.SHATTER_STRATEGY.LOCUS_EXPERIMENTAL : ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, drivingDataSource.getSequenceDictionary(), SHARD_SIZE, maxIterations); } else if (walker instanceof ReadWalker || walker instanceof DuplicateWalker) { - if(argCollection.experimentalSharding) + if(!argCollection.disableExperimentalSharding) shardType = ShardStrategyFactory.SHATTER_STRATEGY.READS_EXPERIMENTAL; else shardType = ShardStrategyFactory.SHATTER_STRATEGY.READS; @@ -740,7 +740,7 @@ public class GenomeAnalysisEngine { return null; SAMDataSource dataSource = null; - if(argCollection.experimentalSharding) + if(!argCollection.disableExperimentalSharding) dataSource = new BlockDrivenSAMDataSource(reads); else dataSource = new IndexDrivenSAMDataSource(reads); diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index af18171a9..f742901f1 100755 --- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -155,8 +155,8 @@ public class GATKArgumentCollection { // public boolean enableRodWalkers = false; @Element(required = false) - @Argument(fullName = "experimental_sharding",shortName="es", doc="Use the experimental sharding strategy. Will not work for all traversal types.", required = false) - public boolean experimentalSharding = false; + @Argument(fullName = "disable_experimental_sharding",shortName="ds", doc="Disable the experimental sharding strategy.", required = false) + public boolean disableExperimentalSharding = false; /** * marshal the data out to a object