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Low-memory sharding is now enabled by default. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5643 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-04-15 14:22:07 +00:00
parent 2830dc70b7
commit be3bad1f61
3 changed files with 5 additions and 5 deletions
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3
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -907,7 +907,8 @@ public class GenomeAnalysisEngine {
getWalkerBAQApplicationTime() == BAQ.ApplicationTime.ON_INPUT ? argCollection.BAQMode : BAQ.CalculationMode.OFF, getWalkerBAQApplicationTime() == BAQ.ApplicationTime.ON_INPUT ? argCollection.BAQMode : BAQ.CalculationMode.OFF,
getWalkerBAQQualityMode(), getWalkerBAQQualityMode(),
refReader, refReader,
argCollection.defaultBaseQualities,argCollection.enableLowMemorySharding); argCollection.defaultBaseQualities,
!argCollection.disableLowMemorySharding);
return dataSource; return dataSource;
} }

6
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -243,8 +243,8 @@ public class GATKArgumentCollection {
public boolean allowIntervalsWithUnindexedBAM = false; public boolean allowIntervalsWithUnindexedBAM = false;
@Element(required = 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) @Argument(fullName="disable_experimental_low_memory_sharding",doc="Enable experimental low-memory sharding functionality. Use at your own risk.",required=false)
public boolean enableLowMemorySharding = false; public boolean disableLowMemorySharding = false;
// -------------------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------------------
// //
@ -432,7 +432,7 @@ public class GATKArgumentCollection {
if (allowIntervalsWithUnindexedBAM != other.allowIntervalsWithUnindexedBAM) if (allowIntervalsWithUnindexedBAM != other.allowIntervalsWithUnindexedBAM)
return false; return false;
if (enableLowMemorySharding != other.enableLowMemorySharding) if (disableLowMemorySharding != other.disableLowMemorySharding)
return false; return false;
return true; return true;

1
java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
View File

@ -45,7 +45,6 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
private final GenomeLocParser parser; private final GenomeLocParser parser;
public LowMemoryIntervalSharder(final SAMDataSource dataSource, final GenomeLocSortedSet loci) { public LowMemoryIntervalSharder(final SAMDataSource dataSource, final GenomeLocSortedSet loci) {
System.out.println("Low memory interval sharding enabled");
wrappedIterator = new PeekableIterator<FilePointer>(new BAMScheduler(dataSource,loci)); wrappedIterator = new PeekableIterator<FilePointer>(new BAMScheduler(dataSource,loci));
parser = loci.getGenomeLocParser(); parser = loci.getGenomeLocParser();
} }