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Bugfix for bad nt / nct argument detection in MicroScheduler

This commit is contained in:
Mark DePristo 2012-10-18 10:19:21 -04:00
parent b57df6cac8
commit 97abb98c0b
1 changed files with 9 additions and 5 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -157,18 +157,22 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
if ( ! (walker instanceof TreeReducible) ) { if ( ! (walker instanceof TreeReducible) ) {
throw badNT("nt", engine, walker); throw badNT("nt", engine, walker);
} else {
return new HierarchicalMicroScheduler(engine, walker, reads, reference, rods, threadAllocation);
} }
}
if ( threadAllocation.getNumCPUThreadsPerDataThread() > 1 && ! (walker instanceof NanoSchedulable) ) {
throw badNT("nct", engine, walker);
}
if ( threadAllocation.getNumDataThreads() > 1 ) {
return new HierarchicalMicroScheduler(engine, walker, reads, reference, rods, threadAllocation);
} else { } else {
if ( threadAllocation.getNumCPUThreadsPerDataThread() > 1 && ! (walker instanceof NanoSchedulable) )
throw badNT("nct", engine, walker);
return new LinearMicroScheduler(engine, walker, reads, reference, rods, threadAllocation); return new LinearMicroScheduler(engine, walker, reads, reference, rods, threadAllocation);
} }
} }
private static UserException badNT(final String parallelArg, final GenomeAnalysisEngine engine, final Walker walker) { private static UserException badNT(final String parallelArg, final GenomeAnalysisEngine engine, final Walker walker) {
throw new UserException.BadArgumentValue("nt", throw new UserException.BadArgumentValue(parallelArg,
String.format("The analysis %s currently does not support parallel execution with %s. " + String.format("The analysis %s currently does not support parallel execution with %s. " +
"Please run your analysis without the %s option.", engine.getWalkerName(walker.getClass()), parallelArg, parallelArg)); "Please run your analysis without the %s option.", engine.getWalkerName(walker.getClass()), parallelArg, parallelArg));
} }