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Merge pull request #300 from broadinstitute/mc_move_qualify_intervals_to_protected 

Few bug fixes to this tool now that it is in protected
This commit is contained in:
Mark DePristo 2013-06-24 09:35:45 -07:00
parent d8ca4d3e6d 1d67d07cf1
commit 191e4ca251
1 changed files with 5 additions and 3 deletions
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8
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
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@ -87,7 +87,7 @@ import java.util.List;
* *
* <h3>Input</h3> * <h3>Input</h3>
* <p> * <p>
* A reference file * A reference file (for GC content), the input bam file (for base and mapping quality calculation), the missing intervals (in the -L), the baits/targets used to sequence (in the -targets) and a bed file with the coding sequence intervals of the genome (in the -cds)
* </p> * </p>
* *
* <h3>Output</h3> * <h3>Output</h3>
@ -100,6 +100,7 @@ import java.util.List;
* java -Xmx2g -jar GenomeAnalysisTK.jar \ * java -Xmx2g -jar GenomeAnalysisTK.jar \
* -T QualifyMissingIntervals \ * -T QualifyMissingIntervals \
* -R ref.fasta \ * -R ref.fasta \
* -I input.bam \
* -o output.grp \ * -o output.grp \
* -L input.intervals \ * -L input.intervals \
* -cds cds.intervals \ * -cds cds.intervals \
@ -117,7 +118,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
public File targetsFile; public File targetsFile;
@Argument(shortName = "cds", required = false) @Argument(shortName = "cds", required = false)
public File cdsFile; public File cdsFile = null;
GATKReport simpleReport; GATKReport simpleReport;
GenomeLocSortedSet target; GenomeLocSortedSet target;
@ -133,7 +134,8 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
target = new GenomeLocSortedSet(parser); target = new GenomeLocSortedSet(parser);
cds = new GenomeLocSortedSet(parser); cds = new GenomeLocSortedSet(parser);
parseFile(targetsFile, target, parser); parseFile(targetsFile, target, parser);
parseFile(cdsFile, cds, parser); if (cdsFile != null)
parseFile(cdsFile, cds, parser);
} }
public Metrics reduceInit() { public Metrics reduceInit() {