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CombineVariants no longer requires rod_priority_string 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4800 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-12-07 15:39:43 +00:00
parent bc885b7bd0
commit 70980b659a
1 changed files with 8 additions and 2 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
@ -81,9 +82,14 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
private List<String> priority = null; private List<String> priority = null;
public void initialize() { public void initialize() {
validateAnnotateUnionArguments();
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), null); Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), null);
if ( PRIORITY_STRING == null ) {
PRIORITY_STRING = Utils.join(",", vcfRods.keySet());
logger.info("Priority string not provided, using arbitrary genotyping order: " + PRIORITY_STRING);
}
validateAnnotateUnionArguments();
Set<String> samples = SampleUtils.getSampleList(vcfRods, genotypeMergeOption); Set<String> samples = SampleUtils.getSampleList(vcfRods, genotypeMergeOption);
if ( SET_KEY.toLowerCase().equals("null") ) if ( SET_KEY.toLowerCase().equals("null") )