zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

fixing merge conflict.

This commit is contained in:
Ryan Poplin 2011-11-08 14:55:05 -05:00
parent 94dc447a70 b0e6afec48
commit e973ca2010
1 changed files with 9 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

16
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
View File

@ -528,10 +528,10 @@ public class PairHMMIndelErrorModel {
} }
else { else {
byte[] readBases = Arrays.copyOfRange(unclippedReadBases,numStartClippedBases, final byte[] readBases = Arrays.copyOfRange(unclippedReadBases,numStartClippedBases,
unclippedReadBases.length-numEndClippedBases); unclippedReadBases.length-numEndClippedBases);
byte[] readQuals = Arrays.copyOfRange(unclippedReadQuals,numStartClippedBases, final byte[] readQuals = Arrays.copyOfRange(unclippedReadQuals,numStartClippedBases,
unclippedReadBases.length-numEndClippedBases); unclippedReadBases.length-numEndClippedBases);
int j=0; int j=0;
@ -540,6 +540,7 @@ public class PairHMMIndelErrorModel {
double[][] matchMetricArray = null, XMetricArray = null, YMetricArray = null; double[][] matchMetricArray = null, XMetricArray = null, YMetricArray = null;
byte[] previousHaplotypeSeen = null; byte[] previousHaplotypeSeen = null;
double[] previousGOP = null; double[] previousGOP = null;
double[] previousGCP = null;
int startIdx; int startIdx;
for (Allele a: haplotypeMap.keySet()) { for (Allele a: haplotypeMap.keySet()) {
@ -555,7 +556,7 @@ public class PairHMMIndelErrorModel {
long indStart = start - haplotype.getStartPosition(); long indStart = start - haplotype.getStartPosition();
long indStop = stop - haplotype.getStartPosition(); long indStop = stop - haplotype.getStartPosition();
byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(), final byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
(int)indStart, (int)indStop); (int)indStart, (int)indStop);
double readLikelihood; double readLikelihood;
@ -572,13 +573,14 @@ public class PairHMMIndelErrorModel {
if (previousHaplotypeSeen == null) if (previousHaplotypeSeen == null)
startIdx = 0; startIdx = 0;
else { else {
int s1 = computeFirstDifferingPosition(haplotypeBases, previousHaplotypeSeen); final int s1 = computeFirstDifferingPosition(haplotypeBases, previousHaplotypeSeen);
int s2 = computeFirstDifferingPosition(currentContextGOP, previousGOP); final int s2 = computeFirstDifferingPosition(currentContextGOP, previousGOP);
startIdx = Math.min(s1,s2); final int s3 = computeFirstDifferingPosition(currentContextGCP, previousGCP);
startIdx = Math.min(Math.min(s1, s2), s3);
} }
previousHaplotypeSeen = haplotypeBases.clone(); previousHaplotypeSeen = haplotypeBases.clone();
previousGOP = currentContextGOP.clone(); previousGOP = currentContextGOP.clone();
previousGCP = currentContextGCP.clone();
readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals, readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals,