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documenting this walker as it may be useful to others in the future. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5899 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-05-27 21:58:51 +00:00
parent 2524216d4b
commit 69d9b5989f
1 changed files with 4 additions and 7 deletions
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11
java/src/org/broadinstitute/sting/oneoffprojects/walkers/Percent20xCoverage.java
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@ -11,8 +11,7 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import java.io.PrintStream; import java.io.PrintStream;
/** /**
* Walks over the input data set, calculating the total number of covered loci for diagnostic purposes. * Walks over the input data set, calculating the percentage of loci covered by at least 20 reads.
* Simplest example of a locus walker.
*/ */
public class Percent20xCoverage extends LocusWalker<Integer, Long> implements TreeReducible<Long> { public class Percent20xCoverage extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
@Output(doc="Write count to this file instead of STDOUT") @Output(doc="Write count to this file instead of STDOUT")
@ -39,16 +38,14 @@ public class Percent20xCoverage extends LocusWalker<Integer, Long> implements Tr
return 0; return 0;
} }
public Long reduceInit() { return 0l; } public Long reduceInit() {
return 0l;
}
public Long reduce(Integer value, Long sum) { public Long reduce(Integer value, Long sum) {
return value + sum; return value + sum;
} }
/**
* Reduces two subtrees together. In this case, the implementation of the tree reduce
* is exactly the same as the implementation of the single reduce.
*/
public Long treeReduce(Long lhs, Long rhs) { public Long treeReduce(Long lhs, Long rhs) {
return lhs + rhs; return lhs + rhs;
} }