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Some quick documentation and typo changes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1076 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-06-23 13:40:13 +00:00
parent 6b5560e1e9
commit 9c0dba6979
1 changed files with 6 additions and 7 deletions
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13
java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CountDuplicatesWalker.java
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@ -33,12 +33,12 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import java.util.List; import java.util.List;
/** /**
* a class to store the duplicates information we pass around * a class to store the traversal information we pass around
*/ */
class DuplicateCount { class DuplicateCount {
public int count = 0; public int count = 0; // the count of sites we were given
public int undupDepth = 0; public int undupDepth = 0; // the unique read count
public int depth = 0; public int depth = 0; // the dupplicate read depth
} }
/** /**
@ -96,11 +96,10 @@ public class CountDuplicatesWalker extends DuplicateWalker<DuplicateCount, Dupli
*/ */
public void onTraversalDone(DuplicateCount result) { public void onTraversalDone(DuplicateCount result) {
out.println("[REDUCE RESULT] Traversal result is: "); out.println("[REDUCE RESULT] Traversal result is: ");
out.println("duplicate count = " + result.count); out.println("traversal iterations = " + result.count);
out.println("average depth = " + (double)result.depth / (double)result.count); out.println("average depth = " + (double)result.depth / (double)result.count);
out.println("duplicates seen = " + result.depth); out.println("duplicates seen = " + result.depth);
out.println("average unique depth = " + (double)result.undupDepth / (double)result.undupDepth);
out.println("unique read count = " + result.undupDepth); out.println("unique read count = " + result.undupDepth);
out.println("average unique read depth = " + (double)result.undupDepth / (double)result.count);
} }
} }