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Trivial update for data processing paper: change syntax of output argument for Beagle by depth walker to update to new GATK format. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4724 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-11-24 01:45:44 +00:00
parent e15d18129c
commit 9cdc341be5
1 changed files with 2 additions and 4 deletions
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6
java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
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@ -54,10 +54,8 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
public static final String INPUT_COMP_ROD_NAME = "comp"; public static final String INPUT_COMP_ROD_NAME = "comp";
@Output @Output
public PrintStream out; protected PrintStream outputWriter = null;
@Argument(fullName = "output_file", shortName = "output", doc = "File to output results", required = true)
public PrintStream outputWriter = null;
public void initialize() { public void initialize() {
@ -211,7 +209,7 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
* @param result the number of loci seen. * @param result the number of loci seen.
*/ */
public void onTraversalDone(Integer result) { public void onTraversalDone(Integer result) {
out.printf("Processed %d loci.\n", result); System.out.printf("Processed %d loci.\n", result);
} }