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New sharding system is live. Disable with -ds. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3016 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-17 03:32:45 +00:00
parent 1fd909cdaf
commit 2cc040aa1c
2 changed files with 6 additions and 6 deletions
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8
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -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);

4
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
View File

@ -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