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Forgot to consider the optimized case in hasAllele

This commit is contained in:
Eric Banks 2012-04-24 11:32:28 -04:00
parent 91bad244d5
commit d6277b70d8
1 changed files with 7 additions and 6 deletions
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13
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -593,25 +593,26 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @return True if this context contains Allele allele, or false otherwise
*/
public boolean hasAllele(final Allele allele) {
return hasAllele(allele, false, getAlleles());
return hasAllele(allele, false, true);
}
public boolean hasAllele(final Allele allele, final boolean ignoreRefState) {
return hasAllele(allele, ignoreRefState, getAlleles());
return hasAllele(allele, ignoreRefState, true);
}
public boolean hasAlternateAllele(final Allele allele) {
return hasAllele(allele, false, getAlternateAlleles());
return hasAllele(allele, false, false);
}
public boolean hasAlternateAllele(final Allele allele, final boolean ignoreRefState) {
return hasAllele(allele, ignoreRefState, getAlternateAlleles());
return hasAllele(allele, ignoreRefState, false);
}
private boolean hasAllele(final Allele allele, final boolean ignoreRefState, final List<Allele> allelesToConsider) {
if ( allele == REF || allele == ALT ) // optimization for cached cases
private boolean hasAllele(final Allele allele, final boolean ignoreRefState, final boolean considerRefAllele) {
if ( (considerRefAllele && allele == REF) || allele == ALT ) // optimization for cached cases
return true;
final List<Allele> allelesToConsider = considerRefAllele ? getAlleles() : getAlternateAlleles();
for ( Allele a : allelesToConsider ) {
if ( a.equals(allele, ignoreRefState) )
return true;