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Fix mismatching number of columns in report 

Quick fix the missing column header in the QualifyMissingIntervals
report.

Adding a QScript for the tool as well as a few minor updates to the
GATKReportGatherer.
This commit is contained in:
Mauricio Carneiro 2013-10-09 14:38:15 -04:00
parent e9a93d23c3
commit 5d6421494b
2 changed files with 9 additions and 10 deletions
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11
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
View File

@ -47,16 +47,15 @@
package org.broadinstitute.sting.gatk.walkers.diagnostics.missing;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Gather;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
import org.broadinstitute.sting.gatk.report.GATKReportGatherer;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
@ -109,10 +108,12 @@ import java.util.List;
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@By(DataSource.REFERENCE)
@PartitionBy(PartitionType.INTERVAL)
public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics> implements NanoSchedulable {
/**
* A single GATKReport table with the qualifications on why the intervals passed by the -L argument were missing.
*/
@Gather(GATKReportGatherer.class)
@Output
protected PrintStream out;
@ -194,7 +195,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
if (cdsFile == null)
cdsFile = targetsFile;
simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "DP", "TP", "CD", "LN", "DS");
simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "DP", "TP", "TS", "CD", "LN", "DS");
final GenomeLocParser parser = getToolkit().getGenomeLocParser();
target = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
cds = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, cdsFile));

8
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java
View File

@ -42,23 +42,21 @@ public class GATKReportGatherer extends Gatherer {
try {
o = new PrintStream(output);
} catch (FileNotFoundException e) {
throw new UserException("File to be output by CoverageByRG Gather function was not found");
throw new UserException(String.format("File %s to be output by GATKReportGatherer function was not found", output));
}
GATKReport current = new GATKReport();
boolean isFirst = true;
for (File input : inputs) {
// If the table is empty
if (isFirst) {
current = new GATKReport(input);
isFirst = false;
} else {
GATKReport toAdd = new GATKReport(input);
current.concat(toAdd);
current.concat(new GATKReport(input));
}
}
current.print(o);
o.close();
}
}