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

More optimizations for HaplotypeScore: pulling final constants out of loops 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4530 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-20 17:40:57 +00:00
parent 20fac43521
commit 4f77581087
1 changed files with 21 additions and 13 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

34
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
View File

@ -173,23 +173,25 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
double[] baseQualities = new double[contextSize]; double[] baseQualities = new double[contextSize];
Arrays.fill(baseQualities,0.0); Arrays.fill(baseQualities,0.0);
final byte[] readBases = read.getReadBases();
final byte[] readQuals = read.getBaseQualities();
for (int i = 0; i < contextSize; i++ ) { for (int i = 0; i < contextSize; i++ ) {
int baseOffset = i + baseOffsetStart; int baseOffset = i + baseOffsetStart;
if ( baseOffset < 0 ) if ( baseOffset < 0 )
continue; continue;
if ( baseOffset >= read.getReadLength() ) if ( baseOffset >= readBases.length )
break; break;
haplotypeBases[i] = read.getReadBases()[baseOffset]; haplotypeBases[i] = readBases[baseOffset];
baseQualities[i] = (double)read.getBaseQualities()[baseOffset]; baseQualities[i] = (double)readQuals[baseOffset];
} }
return new Haplotype(haplotypeBases, baseQualities); return new Haplotype(haplotypeBases, baseQualities);
} }
private Haplotype getConsensusHaplotype(Haplotype haplotypeA, Haplotype haplotypeB) { private Haplotype getConsensusHaplotype(Haplotype haplotypeA, Haplotype haplotypeB) {
byte[] a = haplotypeA.getBasesAsBytes(); final byte[] a = haplotypeA.getBasesAsBytes();
byte[] b = haplotypeB.getBasesAsBytes(); final byte[] b = haplotypeB.getBasesAsBytes();
if (a.length != b.length) if (a.length != b.length)
throw new ReviewedStingException("Haplotypes a and b must be of same length"); throw new ReviewedStingException("Haplotypes a and b must be of same length");
@ -201,6 +203,9 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
byte[] consensusChars = new byte[length]; byte[] consensusChars = new byte[length];
double[] consensusQuals = new double[length]; double[] consensusQuals = new double[length];
final double[] qualsA = haplotypeA.getQuals();
final double[] qualsB = haplotypeB.getQuals();
for (int i=0; i < length; i++) { for (int i=0; i < length; i++) {
chA = a[i]; chA = a[i];
chB = b[i]; chB = b[i];
@ -214,14 +219,14 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
} }
else if ((chA == wc)) { else if ((chA == wc)) {
consensusChars[i] = chB; consensusChars[i] = chB;
consensusQuals[i] = haplotypeB.getQuals()[i]; consensusQuals[i] = qualsB[i];
} }
else if ((chB == wc)){ else if ((chB == wc)){
consensusChars[i] = chA; consensusChars[i] = chA;
consensusQuals[i] = haplotypeA.getQuals()[i]; consensusQuals[i] = qualsA[i];
} else { } else {
consensusChars[i] = chA; consensusChars[i] = chA;
consensusQuals[i] = haplotypeA.getQuals()[i]+haplotypeB.getQuals()[i]; consensusQuals[i] = qualsA[i]+qualsB[i];
} }
} }
@ -275,18 +280,21 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
// actually be a miscall in a matching direction, which would happen at a e / 3 rate. If b != c, then // actually be a miscall in a matching direction, which would happen at a e / 3 rate. If b != c, then
// the chance that it is actually a mismatch is 1 - e, since any of the other 3 options would be a mismatch. // the chance that it is actually a mismatch is 1 - e, since any of the other 3 options would be a mismatch.
// so the probability-weighted mismatch rate is sum_i ( matched ? e_i / 3 : 1 - e_i ) for i = 1 ... n // so the probability-weighted mismatch rate is sum_i ( matched ? e_i / 3 : 1 - e_i ) for i = 1 ... n
final byte[] haplotypeBases = haplotype.getBasesAsBytes();
final byte[] readBases = read.getReadBases();
final byte[] readQuals = read.getBaseQualities();
for ( int i = 0; i < contextSize; i++ ) { for ( int i = 0; i < contextSize; i++ ) {
int baseOffset = i + baseOffsetStart; int baseOffset = i + baseOffsetStart;
if ( baseOffset < 0 ) if ( baseOffset < 0 )
continue; continue;
if ( baseOffset >= read.getReadLength() ) if ( baseOffset >= readBases.length )
break; break;
byte haplotypeBase = haplotype.getBasesAsBytes()[i]; byte haplotypeBase = haplotypeBases[i];
byte readBase = read.getReadBases()[baseOffset]; byte readBase = readBases[baseOffset];
boolean matched = BaseUtils.basesAreEqual(readBase, haplotypeBase ); boolean matched = BaseUtils.basesAreEqual(readBase, haplotypeBase );
double e = QualityUtils.qualToErrorProb(read.getBaseQualities()[baseOffset]); double e = QualityUtils.qualToErrorProb(readQuals[baseOffset]);
expected += e; expected += e;
mismatches += matched ? e : 1 - e / 3; mismatches += matched ? e : 1 - e / 3;
@ -294,7 +302,7 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
// the mismatching of poorly determined regions of the consensus // the mismatching of poorly determined regions of the consensus
if ( DEBUG ) System.out.printf("Read %s: scoring %c vs. %c => e = %f Q%d esum %f vs. msum %f%n", if ( DEBUG ) System.out.printf("Read %s: scoring %c vs. %c => e = %f Q%d esum %f vs. msum %f%n",
read.getReadName(), (char)haplotypeBase, (char)readBase, e, read.getBaseQualities()[baseOffset], expected, mismatches); read.getReadName(), (char)haplotypeBase, (char)readBase, e, readQuals[baseOffset], expected, mismatches);
} }
return mismatches - expected; return mismatches - expected;