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Ryan noticed that I accidentally killed a public interface method for getting tag information. 

Reinstated.  Proper unit test to follow.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5434 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-03-14 15:51:19 +00:00
parent 3e3ec85807
commit 5406e779d2
1 changed files with 10 additions and 0 deletions
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10
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -34,6 +34,7 @@ import org.broadinstitute.sting.commandline.ArgumentSource;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.CommandLineUtils; import org.broadinstitute.sting.commandline.CommandLineUtils;
import org.broadinstitute.sting.commandline.ParsingEngine; import org.broadinstitute.sting.commandline.ParsingEngine;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
@ -653,6 +654,15 @@ public class GenomeAnalysisEngine {
outputs.add(stub); outputs.add(stub);
} }
/**
* Returns the tag associated with a given command-line argument.
* @param key Object for which to inspect the tag.
* @return Tags object associated with the given key, or an empty Tag structure if none are present.
*/
public Tags getTags(Object key) {
return parsingEngine.getTags(key);
}
protected void initializeDataSources() { protected void initializeDataSources() {
logger.info("Strictness is " + argCollection.strictnessLevel); logger.info("Strictness is " + argCollection.strictnessLevel);