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Simple performance optimization -- cache the number of reads in the locus hanger. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3417 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-05-21 19:26:16 +00:00
parent 355396109b
commit b10950c691
1 changed files with 23 additions and 18 deletions
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41
java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
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@ -515,6 +515,7 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
private final int targetCoverage; private final int targetCoverage;
private final Deque<Map<String,List<SAMRecordState>>> readStatesByAlignmentStart; private final Deque<Map<String,List<SAMRecordState>>> readStatesByAlignmentStart;
private int totalReadStatesInHanger = 0;
/** /**
* Store a random number generator with a consistent seed for consistent downsampling from run to run. * Store a random number generator with a consistent seed for consistent downsampling from run to run.
@ -546,7 +547,7 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
private Iterator<SAMRecordState> readStateIterator; private Iterator<SAMRecordState> readStateIterator;
private SAMRecordState nextReadState; private SAMRecordState nextReadState;
private int readsInHanger = countReadsInHanger(); private int readsInHanger = totalReadStatesInHanger;
{ {
alignmentStartIterator = readStatesByAlignmentStart.iterator(); alignmentStartIterator = readStatesByAlignmentStart.iterator();
@ -577,6 +578,7 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
readStateIterator.remove(); readStateIterator.remove();
if(currentSample.isEmpty()) sampleIterator.remove(); if(currentSample.isEmpty()) sampleIterator.remove();
if(currentAlignmentStart.isEmpty()) alignmentStartIterator.remove(); if(currentAlignmentStart.isEmpty()) alignmentStartIterator.remove();
totalReadStatesInHanger--;
} }
private void advance() { private void advance() {
@ -643,6 +645,7 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
} }
Map<String,List<SAMRecordState>> culledReadStatesBySample = new HashMap<String,List<SAMRecordState>>(); Map<String,List<SAMRecordState>> culledReadStatesBySample = new HashMap<String,List<SAMRecordState>>();
int readStatesInHangerEntry = 0;
for(Map.Entry<String,ReservoirDownsampler<SAMRecord>> entry: downsamplersBySampleName.entrySet()) { for(Map.Entry<String,ReservoirDownsampler<SAMRecord>> entry: downsamplersBySampleName.entrySet()) {
String sampleName = entry.getKey(); String sampleName = entry.getKey();
@ -653,7 +656,7 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
int readsInHanger = countReadsInHanger(sampleName); int readsInHanger = countReadsInHanger(sampleName);
if(readsInHanger+newReads.size()<=targetCoverage || downsamplingMethod.type==DownsampleType.EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR) if(readsInHanger+newReads.size()<=targetCoverage || downsamplingMethod.type==DownsampleType.EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR)
addReadsToHanger(culledReadStatesBySample,sampleName,newReads,newReads.size()); readStatesInHangerEntry += addReadsToHanger(culledReadStatesBySample,sampleName,newReads,newReads.size());
else { else {
Iterator<Map<String,List<SAMRecordState>>> backIterator = readStatesByAlignmentStart.descendingIterator(); Iterator<Map<String,List<SAMRecordState>>> backIterator = readStatesByAlignmentStart.descendingIterator();
boolean readPruned = true; boolean readPruned = true;
@ -675,11 +678,13 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
firstHangerForSample.clear(); firstHangerForSample.clear();
} }
addReadsToHanger(culledReadStatesBySample,sampleName,newReads,targetCoverage-readsInHanger); readStatesInHangerEntry += addReadsToHanger(culledReadStatesBySample,sampleName,newReads,targetCoverage-readsInHanger);
} }
} }
if(!culledReadStatesBySample.isEmpty()) if(!culledReadStatesBySample.isEmpty()) {
readStatesByAlignmentStart.add(culledReadStatesBySample); readStatesByAlignmentStart.add(culledReadStatesBySample);
totalReadStatesInHanger += readStatesInHangerEntry;
}
} }
private ReservoirDownsampler<SAMRecord> getDownsampler(String sampleName) { private ReservoirDownsampler<SAMRecord> getDownsampler(String sampleName) {
@ -689,15 +694,6 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
return downsamplersBySampleName.get(sampleName); return downsamplersBySampleName.get(sampleName);
} }
private int countReadsInHanger() {
int count = 0;
for(Map<String,List<SAMRecordState>> hangerEntry: readStatesByAlignmentStart) {
for(List<SAMRecordState> reads: hangerEntry.values())
count += reads.size();
}
return count;
}
private int countReadsInHanger(final String sampleName) { private int countReadsInHanger(final String sampleName) {
int count = 0; int count = 0;
for(Map<String,List<SAMRecordState>> hangerEntry: readStatesByAlignmentStart) { for(Map<String,List<SAMRecordState>> hangerEntry: readStatesByAlignmentStart) {
@ -707,22 +703,31 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
return count; return count;
} }
private void addReadsToHanger(final Map<String,List<SAMRecordState>> newHanger, final String sampleName, final Collection<SAMRecord> reads, final int maxReads) { /**
* Add reads with the given sample name to the given hanger entry.
* @param newHangerEntry The hanger entry to add.
* @param sampleName Sample name of the given reads. Should match the entry in each read's read group.
* @param reads Reads to add. Selected reads will be pulled from this source.
* @param maxReads Maximum number of reads to add.
* @return Total number of reads added.
*/
private int addReadsToHanger(final Map<String,List<SAMRecordState>> newHangerEntry, final String sampleName, final Collection<SAMRecord> reads, final int maxReads) {
if(reads.isEmpty()) if(reads.isEmpty())
return; return 0;
List<SAMRecordState> hangerEntry = new LinkedList<SAMRecordState>(); List<SAMRecordState> readStatesBySample = new LinkedList<SAMRecordState>();
int readCount = 0; int readCount = 0;
for(SAMRecord read: reads) { for(SAMRecord read: reads) {
if(readCount >= maxReads) if(readCount >= maxReads)
break; break;
SAMRecordState state = new SAMRecordState(read, readInfo.generateExtendedEvents()); SAMRecordState state = new SAMRecordState(read, readInfo.generateExtendedEvents());
state.stepForwardOnGenome(); state.stepForwardOnGenome();
hangerEntry.add(state); readStatesBySample.add(state);
// TODO: What if we downsample the extended events away? // TODO: What if we downsample the extended events away?
if (state.hadIndel()) hasExtendedEvents = true; if (state.hadIndel()) hasExtendedEvents = true;
readCount++; readCount++;
} }
newHanger.put(sampleName,hangerEntry); newHangerEntry.put(sampleName,readStatesBySample);
return readCount;
} }
} }
} }