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Fixing bugs in downsampler introduced when I added Ryan's dup eliminator. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3407 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-05-21 02:53:12 +00:00
parent a10fca0d5c
commit 388dd8d64d
1 changed files with 21 additions and 25 deletions
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46
java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
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@ -538,17 +538,22 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
public Iterator<SAMRecordState> iterator() { public Iterator<SAMRecordState> iterator() {
return new Iterator<SAMRecordState>() { return new Iterator<SAMRecordState>() {
private final Iterator<Map<String,List<SAMRecordState>>> alignmentStartIterator; private Iterator<Map<String,List<SAMRecordState>>> alignmentStartIterator;
private Map<String,List<SAMRecordState>> currentAlignmentStart;
private Iterator<List<SAMRecordState>> sampleIterator; private Iterator<List<SAMRecordState>> sampleIterator;
private List<SAMRecordState> currentSample;
private Iterator<SAMRecordState> readStateIterator; private Iterator<SAMRecordState> readStateIterator;
private SAMRecordState nextReadState; private SAMRecordState nextReadState;
private int readsInHanger = countReadsInHanger(); private int readsInHanger = countReadsInHanger();
{ {
pruneEmptyElementsInHanger();
alignmentStartIterator = readStatesByAlignmentStart.iterator(); alignmentStartIterator = readStatesByAlignmentStart.iterator();
sampleIterator = alignmentStartIterator.hasNext() ? alignmentStartIterator.next().values().iterator() : null; currentAlignmentStart = alignmentStartIterator.hasNext() ? alignmentStartIterator.next() : null;
readStateIterator = (sampleIterator!=null && sampleIterator.hasNext()) ? sampleIterator.next().iterator() : null; sampleIterator = currentAlignmentStart!=null ? currentAlignmentStart.values().iterator() : null;
currentSample = sampleIterator!=null && sampleIterator.hasNext() ? sampleIterator.next() : null;
readStateIterator = currentSample!=null ? currentSample.iterator() : null;
} }
public boolean hasNext() { public boolean hasNext() {
@ -570,6 +575,8 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
if(readStateIterator == null) if(readStateIterator == null)
throw new StingException("Attempted to remove read, but no previous read was found."); throw new StingException("Attempted to remove read, but no previous read was found.");
readStateIterator.remove(); readStateIterator.remove();
if(currentSample.isEmpty()) sampleIterator.remove();
if(currentAlignmentStart.isEmpty()) alignmentStartIterator.remove();
} }
private void advance() { private void advance() {
@ -577,12 +584,15 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
if(readStateIterator!=null && readStateIterator.hasNext()) if(readStateIterator!=null && readStateIterator.hasNext())
nextReadState = readStateIterator.next(); nextReadState = readStateIterator.next();
else if(sampleIterator!=null && sampleIterator.hasNext()) { else if(sampleIterator!=null && sampleIterator.hasNext()) {
readStateIterator = sampleIterator.next().iterator(); currentSample = sampleIterator.next();
readStateIterator = currentSample.iterator();
nextReadState = readStateIterator.hasNext() ? readStateIterator.next() : null; nextReadState = readStateIterator.hasNext() ? readStateIterator.next() : null;
} }
else if(alignmentStartIterator!=null && alignmentStartIterator.hasNext()) { else if(alignmentStartIterator!=null && alignmentStartIterator.hasNext()) {
sampleIterator = alignmentStartIterator.next().values().iterator(); currentAlignmentStart = alignmentStartIterator.next();
readStateIterator = sampleIterator.hasNext() ? sampleIterator.next().iterator() : null; sampleIterator = currentAlignmentStart != null ? currentAlignmentStart.values().iterator() : null;
currentSample = (sampleIterator!=null && sampleIterator.hasNext()) ? sampleIterator.next() : null;
readStateIterator = currentSample!=null ? currentSample.iterator() : null;
nextReadState = (readStateIterator!=null && readStateIterator.hasNext()) ? readStateIterator.next() : null; nextReadState = (readStateIterator!=null && readStateIterator.hasNext()) ? readStateIterator.next() : null;
} }
@ -592,7 +602,6 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
} }
public boolean isEmpty() { public boolean isEmpty() {
pruneEmptyElementsInHanger();
return readStatesByAlignmentStart.isEmpty(); return readStatesByAlignmentStart.isEmpty();
} }
@ -610,7 +619,6 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
} }
public boolean hasNext() { public boolean hasNext() {
pruneEmptyElementsInHanger();
return !readStatesByAlignmentStart.isEmpty() || iterator.hasNext(); return !readStatesByAlignmentStart.isEmpty() || iterator.hasNext();
} }
@ -669,9 +677,9 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
addReadsToHanger(culledReadStatesBySample,sampleName,newReads,targetCoverage-readsInHanger); addReadsToHanger(culledReadStatesBySample,sampleName,newReads,targetCoverage-readsInHanger);
} }
readStatesByAlignmentStart.add(culledReadStatesBySample);
} }
if(!culledReadStatesBySample.isEmpty())
readStatesByAlignmentStart.add(culledReadStatesBySample);
} }
private ReservoirDownsampler<SAMRecord> getDownsampler(String sampleName) { private ReservoirDownsampler<SAMRecord> getDownsampler(String sampleName) {
@ -700,6 +708,8 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
} }
private void addReadsToHanger(final Map<String,List<SAMRecordState>> newHanger, final String sampleName, final Collection<SAMRecord> reads, final int maxReads) { private void addReadsToHanger(final Map<String,List<SAMRecordState>> newHanger, final String sampleName, final Collection<SAMRecord> reads, final int maxReads) {
if(reads.isEmpty())
return;
List<SAMRecordState> hangerEntry = new LinkedList<SAMRecordState>(); List<SAMRecordState> hangerEntry = new LinkedList<SAMRecordState>();
int readCount = 0; int readCount = 0;
for(SAMRecord read: reads) { for(SAMRecord read: reads) {
@ -714,20 +724,6 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
} }
newHanger.put(sampleName,hangerEntry); newHanger.put(sampleName,hangerEntry);
} }
private void pruneEmptyElementsInHanger() {
Iterator<Map<String,List<SAMRecordState>>> hangerIterator = readStatesByAlignmentStart.iterator();
while(hangerIterator.hasNext()) {
Map<String,List<SAMRecordState>> hangerEntry = hangerIterator.next();
Iterator<List<SAMRecordState>> entryBySampleIterator = hangerEntry.values().iterator();
while(entryBySampleIterator.hasNext()) {
if(entryBySampleIterator.next().size() == 0)
entryBySampleIterator.remove();
}
if(hangerEntry.size() == 0)
hangerIterator.remove();
}
}
} }
} }