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change the way CombineVariants check the priority arguments in order to throw error when the genotypeMergeOption argument is set to PRIORITIZE but PRIORITY_STRING is not provided

This commit is contained in:
Ami Levy-Moonshine 2012-11-21 10:47:35 -05:00
parent d07f3d4a5a
commit 4714ccc284
2 changed files with 14 additions and 12 deletions
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15
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -134,7 +134,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
protected VariantContextWriter vcfWriter = null; protected VariantContextWriter vcfWriter = null;
@Argument(shortName="genotypeMergeOptions", doc="Determines how we should merge genotype records for samples shared across the ROD files", required=false) @Argument(shortName="genotypeMergeOptions", doc="Determines how we should merge genotype records for samples shared across the ROD files", required=false)
public VariantContextUtils.GenotypeMergeType genotypeMergeOption = VariantContextUtils.GenotypeMergeType.PRIORITIZE; public VariantContextUtils.GenotypeMergeType genotypeMergeOption = null;
@Argument(shortName="filteredRecordsMergeType", doc="Determines how we should handle records seen at the same site in the VCF, but with different FILTER fields", required=false) @Argument(shortName="filteredRecordsMergeType", doc="Determines how we should handle records seen at the same site in the VCF, but with different FILTER fields", required=false)
public VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED; public VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED;
@ -200,13 +200,13 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
} else } else
logger.warn("VCF output file not an instance of VCFWriterStub; cannot enable sites only output option"); logger.warn("VCF output file not an instance of VCFWriterStub; cannot enable sites only output option");
if ( PRIORITY_STRING == null ) { validateAnnotateUnionArguments();
if ( PRIORITY_STRING == null && genotypeMergeOption == null) {
genotypeMergeOption = VariantContextUtils.GenotypeMergeType.UNSORTED; genotypeMergeOption = VariantContextUtils.GenotypeMergeType.UNSORTED;
//PRIORITY_STRING = Utils.join(",", vcfRods.keySet()); Deleted by Ami (7/10/12) //PRIORITY_STRING = Utils.join(",", vcfRods.keySet()); Deleted by Ami (7/10/12)
logger.info("Priority string not provided, using arbitrary genotyping order: " + PRIORITY_STRING); logger.info("Priority string not provided, using arbitrary genotyping order: "+priority);
} }
validateAnnotateUnionArguments();
samples = sitesOnlyVCF ? Collections.<String>emptySet() : SampleUtils.getSampleList(vcfRods, genotypeMergeOption); samples = sitesOnlyVCF ? Collections.<String>emptySet() : SampleUtils.getSampleList(vcfRods, genotypeMergeOption);
if ( SET_KEY.toLowerCase().equals("null") ) if ( SET_KEY.toLowerCase().equals("null") )
@ -228,11 +228,8 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE && PRIORITY_STRING == null ) if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE && PRIORITY_STRING == null )
throw new UserException.MissingArgument("rod_priority_list", "Priority string must be provided if you want to prioritize genotypes"); throw new UserException.MissingArgument("rod_priority_list", "Priority string must be provided if you want to prioritize genotypes");
if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE ) if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE ){
priority = new ArrayList<String>(Arrays.asList(PRIORITY_STRING.split(","))); priority = new ArrayList<String>(Arrays.asList(PRIORITY_STRING.split(",")));
else
priority = new ArrayList<String>(rodNames);
if ( rodNames.size() != priority.size() ) if ( rodNames.size() != priority.size() )
throw new UserException.BadArgumentValue("rod_priority_list", "The priority list must contain exactly one rod binding per ROD provided to the GATK: rodNames=" + rodNames + " priority=" + priority); throw new UserException.BadArgumentValue("rod_priority_list", "The priority list must contain exactly one rod binding per ROD provided to the GATK: rodNames=" + rodNames + " priority=" + priority);
@ -240,6 +237,8 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
throw new UserException.BadArgumentValue("rod_priority_list", "Not all priority elements provided as input RODs: " + PRIORITY_STRING); throw new UserException.BadArgumentValue("rod_priority_list", "Not all priority elements provided as input RODs: " + PRIORITY_STRING);
} }
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null ) // RodWalkers can make funky map calls if ( tracker == null ) // RodWalkers can make funky map calls
return 0; return 0;

5
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
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@ -840,8 +840,11 @@ public class VariantContextUtils {
if ( mergeOption == GenotypeMergeType.PRIORITIZE && priorityListOfVCs == null ) if ( mergeOption == GenotypeMergeType.PRIORITIZE && priorityListOfVCs == null )
throw new IllegalArgumentException("Cannot merge calls by priority with a null priority list"); throw new IllegalArgumentException("Cannot merge calls by priority with a null priority list");
if ( priorityListOfVCs == null || mergeOption == GenotypeMergeType.UNSORTED ) if ( mergeOption == GenotypeMergeType.UNSORTED ){
if (priorityListOfVCs != null )
logger.info("Priority string was provided but is not used since GenotypeMergeType is UNSORTED");
return new ArrayList<VariantContext>(unsortedVCs); return new ArrayList<VariantContext>(unsortedVCs);
}
else { else {
ArrayList<VariantContext> sorted = new ArrayList<VariantContext>(unsortedVCs); ArrayList<VariantContext> sorted = new ArrayList<VariantContext>(unsortedVCs);
Collections.sort(sorted, new CompareByPriority(priorityListOfVCs)); Collections.sort(sorted, new CompareByPriority(priorityListOfVCs));