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Ensure that the gene summary has a header line

This commit is contained in:
Christopher Hartl 2012-07-19 21:24:04 -04:00
parent e4db8dde91
commit af383c30b5
1 changed files with 32 additions and 0 deletions
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32
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -507,6 +507,38 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
}
PrintStream geneSummaryOut = getCorrectStream(DoCOutputType.Partition.sample, DoCOutputType.Aggregation.gene, DoCOutputType.FileType.summary);
StringBuilder summaryHeader = new StringBuilder();
summaryHeader.append("Gene");
summaryHeader.append(separator);
summaryHeader.append("total_coverage");
summaryHeader.append(separator);
summaryHeader.append("average_coverage");
for ( String s : statsByTarget.get(0).second.getCoverageByAggregationType(DoCOutputType.Partition.sample).getAllSamples() ) {
summaryHeader.append(separator);
summaryHeader.append(s);
summaryHeader.append("_total_cvg");
summaryHeader.append(separator);
summaryHeader.append(s);
summaryHeader.append("_mean_cvg");
summaryHeader.append(separator);
summaryHeader.append(s);
summaryHeader.append("_granular_Q1");
summaryHeader.append(separator);
summaryHeader.append(s);
summaryHeader.append("_granular_median");
summaryHeader.append(separator);
summaryHeader.append(s);
summaryHeader.append("_granular_Q3");
for ( int thresh : coverageThresholds ) {
summaryHeader.append(separator);
summaryHeader.append(s);
summaryHeader.append("_%_above_");
summaryHeader.append(thresh);
}
}
geneSummaryOut.printf("%s%n",summaryHeader);
for ( Pair<String,DepthOfCoverageStats> geneStats : statsByGene ) {
printTargetSummary(geneSummaryOut,geneStats);