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Added an auxiliary table to DepthOfCoverage, which is the cumulative equivalent of the locus table (got tired of doing the calculation by hand). Also took care of a trailing tab in the per-locus output table. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3138 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-04-08 19:37:17 +00:00
parent fab31e1d53
commit 7025f5b51d
4 changed files with 32 additions and 14 deletions
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12
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
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@ -274,4 +274,16 @@ public class DepthOfCoverageStats {
return totalDepthOfCoverage;
}
public double[] getCoverageProportions(String sample) {
int[] hist = granularHistogramBySample.get(sample);
double[] distribution = new double[hist.length];
long count = 0;
for ( int i = hist.length-1; i >= 0; i -- ) {
count += hist[i];
distribution[i] = ( (double) count) / nLoci;
}
return distribution;
}
}

23
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
View File

@ -476,12 +476,14 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<String,int[]>, Covera
logger.info("Printing locus summary");
if ( ! useReadGroup || useBoth ) {
File perLocusStatisticsFile = deriveFromStream("sample_locus_statistics");
printPerLocus(perLocusStatisticsFile,coverageProfiles.getCoverageBySample());
File perLocusCoverageFile = deriveFromStream("sample_coverage_statistics");
printPerLocus(perLocusStatisticsFile,perLocusCoverageFile,coverageProfiles.getCoverageBySample());
}
if ( useReadGroup || useBoth ) {
File perLocusRGStats = deriveFromStream("read_group_locus_statistics");
printPerLocus(perLocusRGStats,coverageProfiles.getCoverageByReadGroup());
File perLocusRGCoverage = deriveFromStream("read_group_locus_coverage");
printPerLocus(perLocusRGStats,perLocusRGCoverage,coverageProfiles.getCoverageByReadGroup());
}
}
}
@ -521,8 +523,9 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<String,int[]>, Covera
}
}
private void printPerLocus(File locusFile, DepthOfCoverageStats stats) {
private void printPerLocus(File locusFile, File coverageFile, DepthOfCoverageStats stats) {
PrintStream output = getCorrectStream(out,locusFile);
PrintStream coverageOut = getCorrectStream(out,coverageFile);
if ( output == null ) {
return;
}
@ -543,14 +546,24 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<String,int[]>, Covera
header.append(String.format("%n"));
output.print(header);
coverageOut.print(header);
for ( int row = 0; row < samples; row ++ ) {
output.printf("%s_%d\t","NSamples",row+1);
output.printf("%s_%d","NSamples",row+1);
for ( int depthBin = 0; depthBin < baseCoverageCumDist[0].length; depthBin ++ ) {
output.printf("%d\t",baseCoverageCumDist[row][depthBin]);
output.printf("\t%d",baseCoverageCumDist[row][depthBin]);
}
output.printf("%n");
}
for ( String sample : stats.getAllSamples() ) {
coverageOut.printf("%s",sample);
double[] coverageDistribution = stats.getCoverageProportions(sample);
for ( int bin = 0; bin < coverageDistribution.length; bin ++ ) {
coverageOut.printf("\t%.2f",coverageDistribution[bin]);
}
coverageOut.printf("%n");
}
}
private PrintStream getCorrectStream(PrintStream out, File optionalFile) {

7
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java
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@ -10,13 +10,6 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.cmdLine.Argument;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: Jan 27, 2010
* Time: 10:40:44 AM
* To change this template use File | Settings | File Templates.
*/
/*
* Calculates per-sample concordance metrics across two multi-sample VCF files; outputs simple counts of concordant
* variant and genotype calls, genotyping errors, and call errors. Requires a VCF binding with the name 'truth' and

4
java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java
View File

@ -60,12 +60,12 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
spec.addAuxFile("959937a9b0ace520b4b7d9915d708003", baseOutputFile);
spec.addAuxFile("aff2349d6dc221c08f6c469379aeaedf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
spec.addAuxFile("6476ed0c54a4307a618aa6d3268b050f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("50870dad272f03f77befb0075baed1cd", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_locus_statistics"));
spec.addAuxFile("faf63982622764299c734299ffeb3c63", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_locus_statistics"));
spec.addAuxFile("65318c1e73d98a59cc6f817cde12d3d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary_statistics"));
spec.addAuxFile("ef8c3e2ba3fc0da829e10e2d487c00d2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("223377e07b35e81a394b75b38d8e72ee", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
spec.addAuxFile("096f4ed94020327288ea76245ebd6942", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
spec.addAuxFile("06ed004c86f8b2ad8e64a3b42a0d85c5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_locus_statistics"));
spec.addAuxFile("8e391b7b84fc19dff83002b6dd9773d8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_locus_statistics"));
spec.addAuxFile("43c160ff9d754744728c142709011993", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
spec.addAuxFile("a374410efe20609c5c4b87a6da7f4d51", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));