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don't be tricked by multiple read groups with the same sample id! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@730 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-05-16 15:28:55 +00:00
parent 947bac5cdc
commit 3b57a35009
1 changed files with 6 additions and 4 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
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@ -14,9 +14,7 @@ import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import java.util.ArrayList; import java.util.*;
import java.util.List;
import java.util.Random;
import java.io.*; import java.io.*;
// Draft iterative pooled caller // Draft iterative pooled caller
@ -65,9 +63,13 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
random = new Random(42); random = new Random(42);
HashSet<String> unique_sample_names = new HashSet<String>();
for (int i = 0; i < read_groups.size(); i++) for (int i = 0; i < read_groups.size(); i++)
{ {
String sample_name = read_groups.get(i).getSample(); String sample_name = read_groups.get(i).getSample();
if (unique_sample_names.contains(sample_name)) { continue; }
unique_sample_names.add(sample_name);
sample_names.add(sample_name); sample_names.add(sample_name);
System.out.println("SAMPLE: " + sample_name); System.out.println("SAMPLE: " + sample_name);
@ -77,7 +79,7 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
caller.lodThreshold = lodThreshold; caller.lodThreshold = lodThreshold;
caller.fourBaseMode = false; caller.fourBaseMode = false;
caller.printMetrics = false; caller.printMetrics = false;
//caller.initialize(); caller.initialize();
callers.add(caller); callers.add(caller);
} }
} }