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Renaming -cnt to -nct for consistency

This commit is contained in:
Mark DePristo 2012-09-05 21:13:19 -04:00
parent e77abfa82d
commit 1b064805ed
3 changed files with 6 additions and 6 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -307,7 +307,7 @@ public class GATKArgumentCollection {
* the benefit of not requiring X times as much memory per thread as data threads do, but rather * the benefit of not requiring X times as much memory per thread as data threads do, but rather
* only a constant overhead. * only a constant overhead.
*/ */
@Argument(fullName="num_cpu_threads_per_data_thread", shortName = "cnt", doc="How many CPU threads should be allocated per data thread to running this analysis?", required = false) @Argument(fullName="num_cpu_threads_per_data_thread", shortName = "nct", doc="How many CPU threads should be allocated per data thread to running this analysis?", required = false)
public int numberOfCPUThreadsPerDataThread = 1; public int numberOfCPUThreadsPerDataThread = 1;
@Argument(fullName="num_io_threads", shortName = "nit", doc="How many of the given threads should be allocated to IO", required = false) @Argument(fullName="num_io_threads", shortName = "nit", doc="How many of the given threads should be allocated to IO", required = false)

2
public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -117,7 +117,7 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
} }
} else { } else {
if ( threadAllocation.getNumCPUThreadsPerDataThread() > 1 && ! (walker instanceof NanoSchedulable) ) if ( threadAllocation.getNumCPUThreadsPerDataThread() > 1 && ! (walker instanceof NanoSchedulable) )
throw badNT("cnt", engine, walker); throw badNT("nct", engine, walker);
return new LinearMicroScheduler(engine, walker, reads, reference, rods, threadAllocation); return new LinearMicroScheduler(engine, walker, reads, reference, rods, threadAllocation);
} }
} }

8
public/java/test/org/broadinstitute/sting/WalkerTest.java
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@ -280,11 +280,11 @@ public class WalkerTest extends BaseTest {
results = executeTest(name + "-nt-" + nt, spec); results = executeTest(name + "-nt-" + nt, spec);
} }
for ( int cnt : cpuThreads ) { for ( int nct : cpuThreads ) {
if ( cnt != 1 ) { if ( nct != 1 ) {
String extra = " -cnt " + cnt; String extra = " -nct " + nct;
spec.args = originalArgs + extra; spec.args = originalArgs + extra;
results = executeTest(name + "-cnt-" + cnt, spec); results = executeTest(name + "-cnt-" + nct, spec);
} }
} }