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Optimizations across the board, with help from Guillermo, Matt, and JProfiler. Too tired to give details now. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4535 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-20 20:47:41 +00:00
parent f76865abbc
commit 91049269c2
3 changed files with 24 additions and 20 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -44,6 +44,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
private final static boolean DEBUG = false;
private final static int MIN_CONTEXT_WING_SIZE = 10;
private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 20;
private final static char REGEXP_WILDCARD = '.';
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
@ -124,7 +125,7 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
*/
}
if (!foundHaplotypeMatch) {
if (!foundHaplotypeMatch && haplotypeList.size() < MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER) {
haplotypeList.add(elem);
}
}
@ -293,7 +294,7 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
byte haplotypeBase = haplotypeBases[i];
byte readBase = readBases[baseOffset];
boolean matched = BaseUtils.basesAreEqual(readBase, haplotypeBase );
boolean matched = readBase == haplotypeBase;
double e = QualityUtils.qualToErrorProb(readQuals[baseOffset]);
expected += e;
mismatches += matched ? e : 1 - e / 3;

17
java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
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@ -23,7 +23,13 @@ public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotatio
if ( stratifiedContexts.size() == 0 )
return null;
ArrayList<Integer> qualities = new ArrayList<Integer>();
int totalSize = 0;
for ( StratifiedAlignmentContext context : stratifiedContexts.values() )
totalSize += context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size();
int[] qualities = new int[totalSize];
int index = 0;
for ( Map.Entry<String, StratifiedAlignmentContext> sample : stratifiedContexts.entrySet() ) {
AlignmentContext context = sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
ReadBackedPileup pileup = null;
@ -34,14 +40,11 @@ public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotatio
if (pileup != null) {
for (PileupElement p : pileup )
qualities.add(p.getRead().getMappingQuality());
qualities[index++] = p.getRead().getMappingQuality();
}
}
int[] quals = new int[qualities.size()];
int index = 0;
for ( Integer i : qualities )
quals[index++] = i;
double rms = MathUtils.rms(quals);
double rms = MathUtils.rms(qualities);
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.2f", rms));
return map;

22
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -318,12 +318,6 @@ public class UnifiedGenotyperEngine {
ReadBackedPileup pileup = rawContext.getBasePileup();
// filter the reads
filterPileup(pileup, badBaseFilter);
// filter the context based on bad mates and mismatch rate
//pileup = pileup.getFilteredPileup(badReadPileupFilter);
// don't call when there is no coverage
if ( pileup.size() == 0 && !UAC.ALL_BASES_MODE )
return null;
@ -335,6 +329,9 @@ public class UnifiedGenotyperEngine {
// stratify the AlignmentContext and cut by sample
stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(pileup, UAC.ASSUME_SINGLE_SAMPLE);
// filter the reads
filterPileup(stratifiedContexts, badBaseFilter);
}
return stratifiedContexts;
@ -405,11 +402,14 @@ public class UnifiedGenotyperEngine {
verboseWriter.println();
}
private void filterPileup(ReadBackedPileup pileup, BadBaseFilter badBaseFilter) {
for ( PileupElement p : pileup ) {
final SAMRecord read = p.getRead();
if ( read instanceof GATKSAMRecord )
((GATKSAMRecord)read).setGoodBases(badBaseFilter, true);
private void filterPileup(Map<String, StratifiedAlignmentContext> stratifiedContexts, BadBaseFilter badBaseFilter) {
for ( StratifiedAlignmentContext context : stratifiedContexts.values() ) {
ReadBackedPileup pileup = context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
for ( PileupElement p : pileup ) {
final SAMRecord read = p.getRead();
if ( read instanceof GATKSAMRecord )
((GATKSAMRecord)read).setGoodBases(badBaseFilter, true);
}
}
}