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restore GFF_OUTPUT_FILE to a required argument. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@255 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-04-02 14:34:08 +00:00
parent 2cd9a1597f
commit f42b75da72
1 changed files with 3 additions and 9 deletions
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12
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
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@ -19,9 +19,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
{ {
@Argument public int N; @Argument public int N;
@Argument public int DOWNSAMPLE; @Argument public int DOWNSAMPLE;
@Argument(required=false,defaultValue="") @Argument public String GFF_OUTPUT_FILE;
public String GFF_OUTPUT_FILE;
protected static Logger logger = Logger.getLogger(AlleleFrequencyWalker.class); protected static Logger logger = Logger.getLogger(AlleleFrequencyWalker.class);
@ -457,10 +455,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
try try
{ {
this.random = new java.util.Random(0); this.random = new java.util.Random(0);
if ( GFF_OUTPUT_FILE == null ) this.output = new PrintStream(GFF_OUTPUT_FILE);
this.output = out;
else
this.output = new PrintStream(GFF_OUTPUT_FILE);
} }
catch (Exception e) catch (Exception e)
{ {
@ -480,8 +475,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
try try
{ {
this.output.flush(); this.output.flush();
if ( GFF_OUTPUT_FILE != null ) this.output.close();
this.output.close();
} }
catch (Exception e) catch (Exception e)
{ {