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properly flush the gzip output stream. this was a subtle inheritance bug. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@791 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-05-22 13:57:58 +00:00
parent 63caca31bf
commit 9902ce8073
2 changed files with 24 additions and 5 deletions
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18
java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
View File

@ -315,12 +315,20 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
return contexts;
}
public void onTraversalDone()
public void onTraversalDone(String result)
{
discovery_output_file.flush();
discovery_output_file.close();
individual_output_file.flush();
individual_output_file.close();
System.out.printf("OTD\n");
try
{
discovery_output_file.flush();
discovery_output_file.close();
individual_output_file.flush();
individual_output_file.close();
}
catch (Exception e)
{
e.printStackTrace();
}
return;
}

11
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
View File

@ -65,6 +65,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
public AlleleFrequencyEstimate map(RefMetaDataTracker tracker, char ref, LocusContext context) {
String rodString = getRodString(tracker);
ref = Character.toUpperCase(ref);
if (ref == 'N') { return null; }
if (context.getReads().size() != 0)
@ -252,6 +253,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
return bestAltBaseIndex;
}
private int[] getSecondaryBaseCounts(double[][] probs) {
int[] secondaryBaseCounts = new int[4];
@ -375,6 +377,15 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
return "";
}
public void onTraversalDone()
{
if (callsFileName != null)
{
calls_file.close();
}
}
/*
public String reduce(AlleleFrequencyEstimate alleleFreq, String sum)
{