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Fail fast if users try to parallelize a read walker. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3484 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2010-06-03 18:14:33 +00:00
parent 7d79848f40
commit 3d055e3d16
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -83,7 +83,9 @@ public abstract class MicroScheduler {
public static MicroScheduler create(GenomeAnalysisEngine engine, Walker walker, SAMDataSource reads, IndexedFastaSequenceFile reference, Collection<ReferenceOrderedDataSource> rods, int nThreadsToUse) { public static MicroScheduler create(GenomeAnalysisEngine engine, Walker walker, SAMDataSource reads, IndexedFastaSequenceFile reference, Collection<ReferenceOrderedDataSource> rods, int nThreadsToUse) {
if (walker instanceof TreeReducible && nThreadsToUse > 1) { if (walker instanceof TreeReducible && nThreadsToUse > 1) {
if(walker.isReduceByInterval()) if(walker.isReduceByInterval())
throw new StingException(String.format("The analysis %s aggregates results by interval. Due to a current limitation of the GATK, analyses of this type do not support parallel execution. Please run your analysis without the -nt option.", engine.getWalkerName(walker.getClass()))); throw new StingException(String.format("The analysis %s aggregates results by interval. Due to a current limitation of the GATK, analyses of this type do not currently support parallel execution. Please run your analysis without the -nt option.", engine.getWalkerName(walker.getClass())));
if(walker instanceof ReadWalker)
throw new StingException(String.format("The analysis %s is a read walker. Due to a current limitation of the GATK, analyses of this type do not currently support parallel execution. Please run your analysis without the -nt option.", engine.getWalkerName(walker.getClass())));
logger.info(String.format("Running the GATK in parallel mode with %d concurrent threads",nThreadsToUse)); logger.info(String.format("Running the GATK in parallel mode with %d concurrent threads",nThreadsToUse));
return new HierarchicalMicroScheduler(engine, walker, reads, reference, rods, nThreadsToUse); return new HierarchicalMicroScheduler(engine, walker, reads, reference, rods, nThreadsToUse);
} else { } else {