From c5f6ab3dd515d11adc56243a9f7f8ed8db51396e Mon Sep 17 00:00:00 2001 From: depristo Date: Thu, 16 Jul 2009 20:58:41 +0000 Subject: [PATCH] CoverageHistogram now sees 0 coverage sites git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1266 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/playground/gatk/walkers/CoverageHistogram.java | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageHistogram.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageHistogram.java index d39ad43b4..f2cb27401 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageHistogram.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageHistogram.java @@ -8,6 +8,8 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; 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.*; import org.broadinstitute.sting.utils.*; @@ -21,6 +23,7 @@ import java.io.*; // Plot a histogram of depth of coverage // j.maguire 6-11-2009 +@By(DataSource.REFERENCE) public class CoverageHistogram extends LocusWalker { //@Argument(fullName="start", shortName="start", required=false, doc="start") public Integer START = 0; @@ -59,10 +62,11 @@ public class CoverageHistogram extends LocusWalker public void onTraversalDone(Integer sum) { 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"); - 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]); }