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DoC now does not require a -o argument. (Change for Matt) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3157 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-04-13 13:58:17 +00:00
parent 2183f10a1d
commit 7b05091c04
1 changed files with 4 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -102,7 +102,8 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<String,int[]>, Covera
}
if ( getToolkit().getArguments().outFileName == null ) {
throw new StingException("This walker requires that you specify an output file (-o)");
logger.warn("This walker creates many output files from one input file; you may wish to specify an input file rather "+
"than defaulting all output to stdout.");
}
if ( ! omitDepthOutput ) { // print header
@ -299,7 +300,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<String,int[]>, Covera
printIntervalTable(statsOut,nTargetsByAvgCvgBySample,firstStats.getEndpoints());
if ( ! getToolkit().getArguments().outFileName.contains("stdout")) {
if ( getToolkit().getArguments().outErrFileName != null && ! getToolkit().getArguments().outFileName.contains("stdout")) {
summaryOut.close();
statsOut.close();
}
@ -490,7 +491,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<String,int[]>, Covera
public File deriveFromStream(String append) {
String name = getToolkit().getArguments().outFileName;
if ( name.contains("stdout") || name.contains("Stdout") || name.contains("STDOUT")) {
if ( name == null || name.contains("stdout") || name.contains("Stdout") || name.contains("STDOUT")) {
return null;
} else {
return new File(name+"."+append);