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restore the right version of VariantContextUtils.java in my unstable dir

This commit is contained in:
Ami Levy-Moonshine 2012-12-10 10:28:56 -05:00
parent 46edab6d6a
commit 573ace4403
1 changed files with 35 additions and 1 deletions
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36
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
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@ -979,6 +979,40 @@ 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)
*
@ -1233,7 +1267,7 @@ public class VariantContextUtils {
* @param testString String to test
* @return Number of repetitions (0 if testString is not a concatenation of n repeatUnit's
*/
protected static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) {
public 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;