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Merging the best parts of Mark's fix for the O(n^2) algorithm and my 

concurrently-written fix for the same.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5520 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-03-26 13:32:23 +00:00
parent d8fbda17ab
commit 28ae53d796
1 changed files with 44 additions and 13 deletions
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55
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -309,7 +309,7 @@ public class LocusIteratorByState extends LocusIterator {
public void printState() { public void printState() {
for(Sample sample: samples) { for(Sample sample: samples) {
Iterator<SAMRecordState> iterator = readStates.iteratorForSample(sample); Iterator<SAMRecordState> iterator = readStates.iterator(sample);
while(iterator.hasNext()) { while(iterator.hasNext()) {
SAMRecordState state = iterator.next(); SAMRecordState state = iterator.next();
logger.debug(String.format("printState():")); logger.debug(String.format("printState():"));
@ -367,9 +367,9 @@ public class LocusIteratorByState extends LocusIterator {
boolean hasBeenSampled = false; boolean hasBeenSampled = false;
for(Sample sample: samples) { for(Sample sample: samples) {
ReadStateManager.PerSampleReadStateManager psrsm = readStates.readStatesBySample.get(sample); Iterator<SAMRecordState> iterator = readStates.iterator(sample);
ArrayList<ExtendedEventPileupElement> indelPile = new ArrayList<ExtendedEventPileupElement>(psrsm.size()); List<ExtendedEventPileupElement> indelPile = new ArrayList<ExtendedEventPileupElement>(readStates.size(sample));
hasBeenSampled |= loc.getStart() <= psrsm.getDownsamplingExtent(); hasBeenSampled |= loc.getStart() <= readStates.getDownsamplingExtent(sample);
size = 0; size = 0;
nDeletions = 0; nDeletions = 0;
@ -377,7 +377,8 @@ public class LocusIteratorByState extends LocusIterator {
nMQ0Reads = 0; nMQ0Reads = 0;
int maxDeletionLength = 0; int maxDeletionLength = 0;
for ( SAMRecordState state : psrsm ) { while(iterator.hasNext()) {
SAMRecordState state = iterator.next();
if ( state.hadIndel() ) { if ( state.hadIndel() ) {
size++; size++;
if ( state.getEventBases() == null ) { if ( state.getEventBases() == null ) {
@ -432,16 +433,17 @@ public class LocusIteratorByState extends LocusIterator {
Map<Sample,ReadBackedPileupImpl> fullPileup = new HashMap<Sample,ReadBackedPileupImpl>(); Map<Sample,ReadBackedPileupImpl> fullPileup = new HashMap<Sample,ReadBackedPileupImpl>();
boolean hasBeenSampled = false; boolean hasBeenSampled = false;
for ( Sample sample: samples ) { for(Sample sample: samples) {
ReadStateManager.PerSampleReadStateManager psrsm = readStates.readStatesBySample.get(sample); Iterator<SAMRecordState> iterator = readStates.iterator(sample);
ArrayList<PileupElement> pile = new ArrayList<PileupElement>(psrsm.size()); List<PileupElement> pile = new ArrayList<PileupElement>(readStates.size(sample));
hasBeenSampled |= location.getStart() <= psrsm.getDownsamplingExtent(); hasBeenSampled |= location.getStart() <= readStates.getDownsamplingExtent(sample);
size = 0; size = 0;
nDeletions = 0; nDeletions = 0;
nMQ0Reads = 0; nMQ0Reads = 0;
for ( SAMRecordState state : psrsm ) { while(iterator.hasNext()) {
SAMRecordState state = iterator.next();
if ( state.getCurrentCigarOperator() != CigarOperator.D && state.getCurrentCigarOperator() != CigarOperator.N ) { if ( state.getCurrentCigarOperator() != CigarOperator.D && state.getCurrentCigarOperator() != CigarOperator.N ) {
if ( filterRead(state.getRead(), location.getStart(), filters ) ) { if ( filterRead(state.getRead(), location.getStart(), filters ) ) {
//discarded_bases++; //discarded_bases++;
@ -496,7 +498,7 @@ public class LocusIteratorByState extends LocusIterator {
private void updateReadStates() { private void updateReadStates() {
for(Sample sample: samples) { for(Sample sample: samples) {
Iterator<SAMRecordState> it = readStates.iteratorForSample(sample); Iterator<SAMRecordState> it = readStates.iterator(sample);
while ( it.hasNext() ) { while ( it.hasNext() ) {
SAMRecordState state = it.next(); SAMRecordState state = it.next();
CigarOperator op = state.stepForwardOnGenome(); CigarOperator op = state.stepForwardOnGenome();
@ -548,7 +550,13 @@ public class LocusIteratorByState extends LocusIterator {
samplePartitioner = new SamplePartitioner(readSelectors); samplePartitioner = new SamplePartitioner(readSelectors);
} }
public Iterator<SAMRecordState> iteratorForSample(final Sample sample) { /**
* Returns a iterator over all the reads associated with the given sample. Note that remove() is implemented
* for this iterator; if present, total read states will be decremented.
* @param sample The sample.
* @return Iterator over the reads associated with that sample.
*/
public Iterator<SAMRecordState> iterator(final Sample sample) {
return new Iterator<SAMRecordState>() { return new Iterator<SAMRecordState>() {
private Iterator<SAMRecordState> wrappedIterator = readStatesBySample.get(sample).iterator(); private Iterator<SAMRecordState> wrappedIterator = readStatesBySample.get(sample).iterator();
@ -571,10 +579,33 @@ public class LocusIteratorByState extends LocusIterator {
return totalReadStates == 0; return totalReadStates == 0;
} }
/**
* Retrieves the total number of reads in the manager across all samples.
* @return Total number of reads over all samples.
*/
public int size() { public int size() {
return totalReadStates; return totalReadStates;
} }
/**
* Retrieves the total number of reads in the manager in the given sample.
* @param sample The sample.
* @return Total number of reads in the given sample.
*/
public int size(final Sample sample) {
return readStatesBySample.get(sample).size();
}
/**
* The extent of downsampling; basically, the furthest base out which has 'fallen
* victim' to the downsampler.
* @param sample Sample, downsampled independently.
* @return Integer stop of the furthest undownsampled region.
*/
public int getDownsamplingExtent(final Sample sample) {
return readStatesBySample.get(sample).getDownsamplingExtent();
}
public SAMRecordState getFirst() { public SAMRecordState getFirst() {
for(Sample sample: samples) { for(Sample sample: samples) {
PerSampleReadStateManager reads = readStatesBySample.get(sample); PerSampleReadStateManager reads = readStatesBySample.get(sample);