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Merge pull request #1050 from broadinstitute/vrr_true_false_list_removal 

Removes a very inefficient way to iterate in ReferenceConfidenceModel…
This commit is contained in:
Valentin Ruano Rubio 2015-07-16 14:03:21 -04:00
parent 45a1d82305 7f74303f2b
commit b296576505
1 changed files with 6 additions and 14 deletions
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20
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java
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@ -491,20 +491,12 @@ public class ReferenceConfidenceModel {
// consider each indel size up to max in term, checking if an indel that deletes either the ref bases (deletion
// or read bases (insertion) would fit as well as the origin baseline sum of mismatching quality scores
for ( int indelSize = 1; indelSize <= maxIndelSize; indelSize++ ) {
for ( final boolean checkInsertion : Arrays.asList(true, false) ) {
final int readI, refI;
if ( checkInsertion ) {
readI = readStart + indelSize;
refI = refStart;
} else {
readI = readStart;
refI = refStart + indelSize;
}
final int score = sumMismatchingQualities(readBases, readQuals, readI, refBases, refI, baselineMMSum);
if ( score <= baselineMMSum )
return false;
}
// check insertions:
if (sumMismatchingQualities(readBases, readQuals, readStart + indelSize, refBases, refStart, baselineMMSum) <= baselineMMSum)
return false;
// check deletions:
if (sumMismatchingQualities(readBases, readQuals, readStart, refBases, refStart + indelSize, baselineMMSum) <= baselineMMSum)
return false;
}
return true;