zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

use boolean instead of String for flag to suppress printing in map 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@236 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-03-31 15:14:00 +00:00
parent 907c183242
commit 234137dee8
1 changed files with 3 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
View File

@ -14,11 +14,11 @@ import java.util.List;
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>> { public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>> {
@Argument(fullName="printall",required=false,defaultValue="true") @Argument(fullName="suppressLocusPrinting",required=false,defaultValue="false")
public String printAllLoci; // booleans don't work public boolean suppressPrinting;
public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) { public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
if (printAllLoci.equals("true")) if ( !suppressPrinting )
out.printf("%s: %d%n", context.getLocation(), context.getReads().size() ); out.printf("%s: %d%n", context.getLocation(), context.getReads().size() );
return context.getReads().size(); return context.getReads().size();
} }