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Pre-allocate 10 alt alleles worth of PLs in the cache for efficiency. This effectively means that we never need to re-allocate the cache in the future because we can't ever really handle that many alt alleles.

This commit is contained in:
Eric Banks 2012-03-23 13:51:00 -04:00
parent ff26f2bf68
commit d3f2bc4361
1 changed files with 5 additions and 1 deletions
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6
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
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@ -222,7 +222,10 @@ public class GenotypeLikelihoods {
/* /*
* a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles * a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles
*/ */
private static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = new GenotypeLikelihoodsAllelePair[]{ new GenotypeLikelihoodsAllelePair(0, 0) }; private static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex;
static {
calculatePLcache(65); // start with data for 10 alternate alleles
}
private static void calculatePLcache(final int minIndex) { private static void calculatePLcache(final int minIndex) {
// how many alternate alleles do we need to calculate for? // how many alternate alleles do we need to calculate for?
@ -266,6 +269,7 @@ public class GenotypeLikelihoods {
*/ */
public static GenotypeLikelihoodsAllelePair getAllelePair(final int PLindex) { public static GenotypeLikelihoodsAllelePair getAllelePair(final int PLindex) {
// make sure that we've cached enough data // make sure that we've cached enough data
// TODO -- this is not thread-safe!
if ( PLindex >= PLIndexToAlleleIndex.length ) if ( PLindex >= PLIndexToAlleleIndex.length )
calculatePLcache(PLindex); calculatePLcache(PLindex);