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

8
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java
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@ -42,23 +42,21 @@ public class GATKReportGatherer extends Gatherer {
try { try {
o = new PrintStream(output); o = new PrintStream(output);
} catch (FileNotFoundException e) { } 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(); GATKReport current = new GATKReport();
boolean isFirst = true; boolean isFirst = true;
for (File input : inputs) { for (File input : inputs) {
// If the table is empty
if (isFirst) { if (isFirst) {
current = new GATKReport(input); current = new GATKReport(input);
isFirst = false; isFirst = false;
} else { } else {
GATKReport toAdd = new GATKReport(input); current.concat(new GATKReport(input));
current.concat(toAdd);
} }
} }
current.print(o); current.print(o);
o.close();
} }
} }