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CoverageHistogram now sees 0 coverage sites 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1266 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-07-16 20:58:41 +00:00
parent 8bc0832215
commit c5f6ab3dd5
1 changed files with 6 additions and 2 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageHistogram.java
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@ -8,6 +8,8 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate; import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
import org.broadinstitute.sting.playground.utils.*; import org.broadinstitute.sting.playground.utils.*;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
@ -21,6 +23,7 @@ import java.io.*;
// Plot a histogram of depth of coverage // Plot a histogram of depth of coverage
// j.maguire 6-11-2009 // j.maguire 6-11-2009
@By(DataSource.REFERENCE)
public class CoverageHistogram extends LocusWalker<Integer,Integer> public class CoverageHistogram extends LocusWalker<Integer,Integer>
{ {
//@Argument(fullName="start", shortName="start", required=false, doc="start") public Integer START = 0; //@Argument(fullName="start", shortName="start", required=false, doc="start") public Integer START = 0;
@ -59,10 +62,11 @@ public class CoverageHistogram extends LocusWalker<Integer,Integer>
public void onTraversalDone(Integer sum) public void onTraversalDone(Integer sum)
{ {
double mean_coverage = (double)sum_coverage / (double)num_sites; double mean_coverage = (double)sum_coverage / (double)num_sites;
out.printf("# mean:%f num_sites:%d\n\n", mean_coverage, num_sites); out.printf("# all_sites : mean:%f num_sites:%d\n\n", mean_coverage, num_sites);
out.printf("# sites with at least 1 read : mean:%f num_sites:%d\n\n", sum_coverage / ((double)(num_sites - coverage_hist[0])), num_sites - coverage_hist[0]);
out.println("depth count"); out.println("depth count");
for (int i = 1; i < max_depth; i++) for (int i = 0; i < max_depth; i++)
{ {
out.printf("%d %d\n", i, coverage_hist[i]); out.printf("%d %d\n", i, coverage_hist[i]);
} }