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stick headers on the output tables 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@782 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-05-21 20:35:50 +00:00
parent 83e1454a11
commit b5ad5176f7
3 changed files with 16 additions and 3 deletions
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11
java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
View File

@ -15,6 +15,7 @@ import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import java.util.*;
import java.util.zip.*;
import java.io.*;
// Draft iterative pooled caller
@ -45,7 +46,8 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
try
{
discovery_output_file = new PrintStream(DISCOVERY_OUTPUT);
individual_output_file = new PrintStream(INDIVIDUAL_OUTPUT);
individual_output_file = new PrintStream(new GZIPOutputStream(new FileOutputStream(INDIVIDUAL_OUTPUT)));
individual_output_file.println(AlleleFrequencyEstimate.asTabularStringHeader());
}
catch (Exception e)
{
@ -324,6 +326,7 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
public String reduceInit()
{
discovery_output_file.printf("loc ref alt EM_alt_freq discovery_posterior discovery_null discovery_lod\n");
for (int i = 0; i < callers.size(); i++)
{
callers.get(i).reduceInit();
@ -333,8 +336,14 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
public String reduce(AlleleFrequencyEstimate alleleFreq, String sum)
{
if (calls == null) { return ""; }
for (int i = 0; i < callers.size(); i++)
{
if (calls == null) { System.err.printf("calls == null\n"); }
if (calls[i] == null) { System.err.printf("calls[%d] == null\n", i); }
if (caller_sums == null) { System.err.printf("caller_sums == null\n"); }
if (callers.get(i) == null) { System.err.printf("callers[%d] == null\n", i); }
if (caller_sums.get(i) == null) { System.err.printf("caller_sums[%d] == null\n", i); }
caller_sums.set(i, callers.get(i).reduce(calls[i], caller_sums.get(i)));
}
return "";

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

@ -49,7 +49,11 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
{
sample_name = null;
if (metricsFileName != null) { metrics = new AlleleMetrics(metricsFileName, lodThreshold); }
if (callsFileName != null) { calls_file = new PrintStream(callsFileName); }
if (callsFileName != null)
{
calls_file = new PrintStream(callsFileName);
calls_file.println(AlleleFrequencyEstimate.asTabularStringHeader());
}
}
catch (Exception e)
{

2
java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
View File

@ -147,7 +147,7 @@ public class AlleleFrequencyEstimate {
return s;
}
public String asTabularStringHeader()
public static String asTabularStringHeader()
{
return "location sample_name ref alt genotype qhat qstar lodVsRef lodVsNextBest depth bases";
}