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(1) changes in catVariants (work still under development) (2) changes to CV to throw an error when GenotypeMergeType is PRIORITIZE but no priority (rod_priority_list) is not given. Reported by TechnicalVault on the forum on Nov 14 2012

This commit is contained in:
Ami Levy-Moonshine 2012-12-09 23:40:03 -05:00
parent 5d78a61f7a
commit 3a420d163e
2 changed files with 5 additions and 42 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -228,7 +228,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
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");
if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE ){
if ( PRIORITY_STRING != null || genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE ){
priority = new ArrayList<String>(Arrays.asList(PRIORITY_STRING.split(",")));
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);

45
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -451,7 +451,7 @@ public class VariantContextUtils {
if ( unsortedVCs == null || unsortedVCs.size() == 0 )
return null;
if ( annotateOrigin && priorityListOfVCs == null && genotypeMergeOptions == GenotypeMergeType.PRIORITIZE)
if ( annotateOrigin && priorityListOfVCs == null )
throw new IllegalArgumentException("Cannot merge calls and annotate their origins without a complete priority list of VariantContexts");
if ( genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE )
@ -597,7 +597,7 @@ public class VariantContextUtils {
if ( annotateOrigin ) { // we care about where the call came from
String setValue;
if ( nFiltered == 0 && variantSources.size() == preFilteredVCs.size() ) // nothing was unfiltered
if ( nFiltered == 0 && variantSources.size() == priorityListOfVCs.size() ) // nothing was unfiltered
setValue = MERGE_INTERSECTION;
else if ( nFiltered == VCs.size() ) // everything was filtered out
setValue = MERGE_FILTER_IN_ALL;
@ -840,11 +840,8 @@ public class VariantContextUtils {
if ( mergeOption == GenotypeMergeType.PRIORITIZE && priorityListOfVCs == null )
throw new IllegalArgumentException("Cannot merge calls by priority with a null priority list");
if ( mergeOption != GenotypeMergeType.PRIORITIZE ){
if (priorityListOfVCs != null )
logger.info("Priority string was provided but is not used since GenotypeMergeType is not PRIORITIZE");
if ( priorityListOfVCs == null || mergeOption == GenotypeMergeType.UNSORTED )
return new ArrayList<VariantContext>(unsortedVCs);
}
else {
ArrayList<VariantContext> sorted = new ArrayList<VariantContext>(unsortedVCs);
Collections.sort(sorted, new CompareByPriority(priorityListOfVCs));
@ -982,40 +979,6 @@ public class VariantContextUtils {
private static final List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
public static final double SUM_GL_THRESH_NOCALL = -0.1; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
/**
* Split variant context into its biallelic components if there are more than 2 alleles
*
* For VC has A/B/C alleles, returns A/B and A/C contexts.
* Genotypes are all no-calls now (it's not possible to fix them easily)
* Alleles are right trimmed to satisfy VCF conventions
*
* If vc is biallelic or non-variant it is just returned
*
* Chromosome counts are updated (but they are by definition 0)
*
* @param vc a potentially multi-allelic variant context
* @return a list of bi-allelic (or monomorphic) variant context
*/
public static List<VariantContext> splitVariantContextToBiallelics(final VariantContext vc) {
if ( ! vc.isVariant() || vc.isBiallelic() )
// non variant or biallelics already satisfy the contract
return Collections.singletonList(vc);
else {
final List<VariantContext> biallelics = new LinkedList<VariantContext>();
for ( final Allele alt : vc.getAlternateAlleles() ) {
VariantContextBuilder builder = new VariantContextBuilder(vc);
final List<Allele> alleles = Arrays.asList(vc.getReference(), alt);
builder.alleles(alleles);
builder.genotypes(VariantContextUtils.subsetDiploidAlleles(vc, alleles, false));
calculateChromosomeCounts(builder, true);
biallelics.add(reverseTrimAlleles(builder.make()));
}
return biallelics;
}
}
/**
* subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately)
*
@ -1270,7 +1233,7 @@ public class VariantContextUtils {
* @param testString String to test
* @return Number of repetitions (0 if testString is not a concatenation of n repeatUnit's
*/
public static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) {
protected static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) {
int numRepeats = 0;
for (int start = 0; start < testString.length; start += repeatUnit.length) {
int end = start + repeatUnit.length;