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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1195 348d0f76-0448-11de-a6fe-93d51630548a
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jmaguire 2009-07-08 16:59:36 +00:00
parent d8fbb2b62c
commit 0a67386525
1 changed files with 67 additions and 0 deletions
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67
java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintHapmapGenotypes.java 100644
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package org.broadinstitute.sting.playground.gatk.walkers;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.playground.gatk.walkers.varianteval.Histogram;
import java.util.*;
import java.io.*;
// Sanity check to test HapmapGenotypeROD
// Compute %dbsnp and transition/transversion rate.
@By(DataSource.REFERENCE)
@Requires(DataSource.REFERENCE)
@Allows(DataSource.REFERENCE)
public class PrintHapmapGenotypes extends RefWalker<Integer, Integer>
{
//@Argument(required=false, shortName="n_frequency_bins", doc="") public int n_frequency_bins = 20;
public void initialize()
{
}
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context)
{
// Iterate over each analysis, and update it
//rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbsnp", null);
HapMapGenotypeROD A = (HapMapGenotypeROD)tracker.lookup("A", null);
if (A != null)
{
GenomeLoc loc = A.getLocation();
String[] sample_ids = A.getSampleIDs();
String[] genotypes = A.getGenotypes();
for (int i = 0; i < sample_ids.length; i++)
{
out.printf("%s %s %s\n", loc, sample_ids[i], genotypes[i]);
}
out.printf("\n");
}
return 1;
}
// Given result of map function
public Integer reduceInit() { return 0; }
public Integer reduce(Integer value, Integer sum)
{
return treeReduce(sum,value);
}
public Integer treeReduce(Integer lhs, Integer rhs)
{
return lhs + rhs;
}
public void onTraversalDone(Integer result)
{
}
}