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Making the GATK unpredictably random... 

through an option! 

set -ndrs if you want the GATK to be really random (non-deterministic). Engine option, available to every walker.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5715 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-04-29 19:29:08 +00:00
parent f97e7d2fb4
commit 36ac8beee1
2 changed files with 10 additions and 2 deletions
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7
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -189,9 +189,9 @@ public class GenomeAnalysisEngine {
private static final long GATK_RANDOM_SEED = 47382911L;
private static Random randomGenerator = new Random(GATK_RANDOM_SEED);
public static final Random getRandomGenerator() { return randomGenerator; }
public static Random getRandomGenerator() { return randomGenerator; }
public static void resetRandomGenerator() { randomGenerator.setSeed(GATK_RANDOM_SEED); }
public static void resetRandomGenerator(long seed) { randomGenerator.setSeed(seed); }
/**
* Actually run the GATK with the specified walker.
*
@ -211,6 +211,9 @@ public class GenomeAnalysisEngine {
if (this.walker == null)
throw new ReviewedStingException("The walker passed to GenomeAnalysisEngine can not be null.");
if (this.getArguments().nonDeterministicRandomSeed)
resetRandomGenerator(System.currentTimeMillis());
// Prepare the data for traversal.
initializeDataSources();

5
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
View File

@ -114,6 +114,11 @@ public class GATKArgumentCollection {
@Argument(fullName = "BTI_merge_rule", shortName = "BTIMR", doc = "Indicates the merging approach the interval parser should use to combine the BTI track with other -L options", required = false)
public IntervalSetRule BTIMergeRule = IntervalSetRule.UNION;
@Element(required = false)
@Argument(fullName = "nonDeterministicRandomSeed", shortName = "ndrs", doc = "Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run", required = false)
public boolean nonDeterministicRandomSeed = false;
@Element(required = false)
@Input(fullName = "DBSNP", shortName = "D", doc = "DBSNP file", required = false)
public String DBSNPFile = null;