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Merge pull request #625 from broadinstitute/intel_updateCell_inlined 

(Optional) Inlined the code from updateCell
This commit is contained in:
MauricioCarneiro 2014-05-07 10:11:09 -04:00
parent bd33c3334e fb8578ec8e
commit f03a12263a
1 changed files with 6 additions and 1 deletions
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7
protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
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@ -101,7 +101,12 @@ public class LoglessPairHMM extends N2MemoryPairHMM {
for (int i = 1; i < paddedReadLength; i++) {
// +1 here is because hapStartIndex is 0-based, but our matrices are 1 based
for (int j = hapStartIndex+1; j < paddedHaplotypeLength; j++) {
updateCell(i, j, prior[i][j], transition[i]);
//Inlined the code from updateCell - helps JIT to detect hotspots and produce good native code
matchMatrix[i][j] = prior[i][j] * ( matchMatrix[i - 1][j - 1] * transition[i][matchToMatch] +
insertionMatrix[i - 1][j - 1] * transition[i][indelToMatch] +
deletionMatrix[i - 1][j - 1] * transition[i][indelToMatch] );
insertionMatrix[i][j] = matchMatrix[i - 1][j] * transition[i][matchToInsertion] + insertionMatrix[i - 1][j] * transition[i][insertionToInsertion];
deletionMatrix[i][j] = matchMatrix[i][j - 1] * transition[i][matchToDeletion] + deletionMatrix[i][j - 1] * transition[i][deletionToDeletion];
}
}