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Re-allow running the GATK with experimental downsampling 

It's now possible to run with experimental downsampling enabled
using the --enable_experimental_downsampling engine argument.

This is scheduled to become the GATK-wide default next week after
diff engine output for failing tests has been examined.
This commit is contained in:
David Roazen 2012-09-21 22:27:45 -04:00
parent 34eed20aa6
commit e077347cc2
1 changed files with 0 additions and 5 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -445,11 +445,6 @@ public class GenomeAnalysisEngine {
GATKArgumentCollection argCollection = this.getArguments(); GATKArgumentCollection argCollection = this.getArguments();
boolean useExperimentalDownsampling = argCollection.enableExperimentalDownsampling; boolean useExperimentalDownsampling = argCollection.enableExperimentalDownsampling;
// until the file pointer bug with the experimental downsamplers is fixed, disallow running with experimental downsampling
if ( useExperimentalDownsampling ) {
throw new UserException("The experimental downsampling implementation is currently crippled by a file-pointer-related bug. Until this bug is fixed, it's not safe (or possible) for anyone to use the experimental implementation!");
}
DownsamplingMethod commandLineMethod = argCollection.getDownsamplingMethod(); DownsamplingMethod commandLineMethod = argCollection.getDownsamplingMethod();
DownsamplingMethod walkerMethod = WalkerManager.getDownsamplingMethod(walker, useExperimentalDownsampling); DownsamplingMethod walkerMethod = WalkerManager.getDownsamplingMethod(walker, useExperimentalDownsampling);
DownsamplingMethod defaultMethod = DownsamplingMethod.getDefaultDownsamplingMethod(walker, useExperimentalDownsampling); DownsamplingMethod defaultMethod = DownsamplingMethod.getDefaultDownsamplingMethod(walker, useExperimentalDownsampling);