diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java index b62d7a334..ab2a5bb2a 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java +++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java @@ -56,8 +56,8 @@ import org.broadinstitute.sting.utils.QualityUtils; * Date: 10/16/12 */ public final class LoglessPairHMM extends PairHMM { - protected static final double SCALE_FACTOR_LOG10 = 300.0; - protected static final double INITIAL_CONDITION = Math.pow(10, SCALE_FACTOR_LOG10); + protected static final double INITIAL_CONDITION = Math.pow(2, 1020); + protected static final double INITIAL_CONDITION_LOG10 = Math.log10(INITIAL_CONDITION); private static final int matchToMatch = 0; private static final int indelToMatch = 1; @@ -118,7 +118,7 @@ public final class LoglessPairHMM extends PairHMM { for (int j = 1; j < paddedHaplotypeLength; j++) { finalSumProbabilities += matchMatrix[endI][j] + insertionMatrix[endI][j]; } - return Math.log10(finalSumProbabilities) - SCALE_FACTOR_LOG10; + return Math.log10(finalSumProbabilities) - INITIAL_CONDITION_LOG10; } /**