zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

(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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -228,7 +228,7 @@ 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 ( PRIORITY_STRING != null || genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE ){
priority = new ArrayList<String>(Arrays.asList(PRIORITY_STRING.split(","))); priority = new ArrayList<String>(Arrays.asList(PRIORITY_STRING.split(",")));
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);

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 ) if ( unsortedVCs == null || unsortedVCs.size() == 0 )
return null; 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"); throw new IllegalArgumentException("Cannot merge calls and annotate their origins without a complete priority list of VariantContexts");
if ( genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE ) if ( genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE )
@ -597,7 +597,7 @@ public class VariantContextUtils {
if ( annotateOrigin ) { // we care about where the call came from if ( annotateOrigin ) { // we care about where the call came from
String setValue; 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; setValue = MERGE_INTERSECTION;
else if ( nFiltered == VCs.size() ) // everything was filtered out else if ( nFiltered == VCs.size() ) // everything was filtered out
setValue = MERGE_FILTER_IN_ALL; setValue = MERGE_FILTER_IN_ALL;
@ -840,11 +840,8 @@ 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 ( mergeOption != GenotypeMergeType.PRIORITIZE ){ if ( priorityListOfVCs == null || mergeOption == GenotypeMergeType.UNSORTED )
if (priorityListOfVCs != null )
logger.info("Priority string was provided but is not used since GenotypeMergeType is not PRIORITIZE");
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));
@ -982,40 +979,6 @@ public class VariantContextUtils {
private static final List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL); 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. 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) * 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 * @param testString String to test
* @return Number of repetitions (0 if testString is not a concatenation of n repeatUnit's * @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; int numRepeats = 0;
for (int start = 0; start < testString.length; start += repeatUnit.length) { for (int start = 0; start < testString.length; start += repeatUnit.length) {
int end = start + repeatUnit.length; int end = start + repeatUnit.length;