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

Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Christopher Hartl 2012-02-01 10:32:11 -05:00
parent faba3dd530 e8528bc526
commit 25d943f706
10 changed files with 27 additions and 22 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
View File

@ -11,6 +11,7 @@ import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
import java.util.Collection;
@ -101,7 +102,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
while (isShardTraversePending() || isTreeReducePending()) {
// Check for errors during execution.
if(hasTraversalErrorOccurred())
throw new ReviewedStingException("An error has occurred during the traversal.",getTraversalError());
throw getTraversalError();
// Too many files sitting around taking up space? Merge them.
if (isMergeLimitExceeded())
@ -344,10 +345,15 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
return error != null;
}
private synchronized Throwable getTraversalError() {
private synchronized StingException getTraversalError() {
if(!hasTraversalErrorOccurred())
throw new ReviewedStingException("User has attempted to retrieve a traversal error when none exists");
return error;
// If the error is already a StingException, pass it along as is. Otherwise, wrap it.
if(error instanceof StingException)
return (StingException)error;
else
return new ReviewedStingException("An error occurred during the traversal.",error);
}
/**

5
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
View File

@ -82,7 +82,6 @@ public class LocusIteratorByState extends LocusIterator {
CigarElement curElement = null;
int nCigarElements = 0;
int cigarElementCounter = -1; // how far are we into a single cigarElement
// The logical model for generating extended events is as follows: the "record state" implements the traversal
@ -468,7 +467,7 @@ public class LocusIteratorByState extends LocusIterator {
if (op == CigarOperator.D) {
if (readInfo.includeReadsWithDeletionAtLoci()) { // only add deletions to the pileup if we are authorized to do so
pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.I, false));
pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
size++;
nDeletions++;
if (read.getMappingQuality() == 0)
@ -477,7 +476,7 @@ public class LocusIteratorByState extends LocusIterator {
}
else {
if (!filterBaseInRead(read, location.getStart())) {
pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.I, op == CigarOperator.S));
pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
size++;
if (read.getMappingQuality() == 0)
nMQ0Reads++;

6
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
View File

@ -216,7 +216,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
// band-pass filter the list of isActive probabilities and turn into active regions
private ArrayList<ActiveRegion> integrateActiveList( final ArrayList<Double> activeList, final GenomeLoc firstIsActiveStart, final int activeRegionExtension ) {
final double ACTIVE_PROB_THRESHOLD = 0.2;
final double ACTIVE_PROB_THRESHOLD = 0.2; // BUGBUG: needs to be set-able by the walker author
final ArrayList<ActiveRegion> returnList = new ArrayList<ActiveRegion>();
if( activeList.size() == 0 ) {
return returnList;
@ -227,8 +227,8 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
} else {
final Double[] activeProbArray = activeList.toArray(new Double[activeList.size()]);
final double[] filteredProbArray = new double[activeProbArray.length];
final int FILTER_SIZE = 10;
final int MAX_ACTIVE_REGION = 200;
final int FILTER_SIZE = 50; // BUGBUG: needs to be set-able by the walker author
final int MAX_ACTIVE_REGION = 425; // BUGBUG: needs to be set-able by the walker author
for( int iii = 0; iii < activeProbArray.length; iii++ ) {
double maxVal = 0;
for( int jjj = Math.max(0, iii-FILTER_SIZE); jjj < Math.min(activeList.size(), iii+FILTER_SIZE); jjj++ ) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -335,7 +335,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
if (ref.getWindow().getStop() < loc.getStop() + HAPLOTYPE_SIZE)
return null;
if (!(priors instanceof DiploidIndelGenotypePriors))
throw new StingException("Only diploid-based Indel priors are supported in the DINDEL GL model");
throw new StingException("Only diploid-based Indel priors are supported in the INDEL GL model");
if (alleleList.isEmpty())
return null;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
View File

@ -212,7 +212,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
public class BAQedPileupElement extends PileupElement {
public BAQedPileupElement( final PileupElement PE ) {
super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeInsertion(), PE.isSoftClipped());
super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeInsertion(), PE.isNextToSoftClip());
}
@Override

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
View File

@ -15,7 +15,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
* @Author chartl
* @Date May 26, 2010
*/
@Analysis(name = "Indel length histograms", description = "Shows the distrbution of insertion/deletion event lengths (negative for deletion, positive for insertion)")
@Analysis(name = "Indel length histograms", description = "Shows the distribution of insertion/deletion event lengths (negative for deletion, positive for insertion)")
public class IndelLengthHistogram extends VariantEvaluator {
private static final int SIZE_LIMIT = 100;
@DataPoint(description="Histogram of indel lengths")

2
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
View File

@ -204,7 +204,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
protected abstract AbstractReadBackedPileup<RBP, PE> createNewPileup(GenomeLoc loc, PileupElementTracker<PE> pileupElementTracker);
protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped);
protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip);
// --------------------------------------------------------
//

12
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
View File

@ -24,7 +24,7 @@ public class PileupElement implements Comparable<PileupElement> {
protected final int offset;
protected final boolean isDeletion;
protected final boolean isBeforeInsertion;
protected final boolean isSoftClipped;
protected final boolean isNextToSoftClip;
/**
@ -34,13 +34,13 @@ public class PileupElement implements Comparable<PileupElement> {
* @param offset the position in the read for this base. All deletions must be left aligned! (-1 is only allowed for reads starting with insertions)
* @param isDeletion whether or not this base is a deletion
* @param isBeforeInsertion whether or not this base is before an insertion
* @param isSoftClipped whether or not this base was softclipped
* @param isNextToSoftClip whether or not this base is next to a soft clipped base
*/
@Requires({
"read != null",
"offset >= -1",
"offset <= read.getReadLength()"})
public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeInsertion, final boolean isSoftClipped) {
public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeInsertion, final boolean isNextToSoftClip) {
if (offset < 0 && isDeletion)
throw new ReviewedStingException("Pileup Element cannot create a deletion with a negative offset");
@ -48,7 +48,7 @@ public class PileupElement implements Comparable<PileupElement> {
this.offset = offset;
this.isDeletion = isDeletion;
this.isBeforeInsertion = isBeforeInsertion;
this.isSoftClipped = isSoftClipped;
this.isNextToSoftClip = isNextToSoftClip;
}
public boolean isDeletion() {
@ -59,8 +59,8 @@ public class PileupElement implements Comparable<PileupElement> {
return isBeforeInsertion;
}
public boolean isSoftClipped() {
return isSoftClipped;
public boolean isNextToSoftClip() {
return isNextToSoftClip;
}
public boolean isInsertionAtBeginningOfRead() {

2
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
View File

@ -96,7 +96,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
}
@Override
protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped) {
protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
throw new UnsupportedOperationException("Not enough information provided to create a new pileup element");
}

4
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
View File

@ -71,7 +71,7 @@ public class ReadBackedPileupImpl extends AbstractReadBackedPileup<ReadBackedPil
}
@Override
protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped) {
return new PileupElement(read, offset, isDeletion, isBeforeInsertion, isSoftClipped);
protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
return new PileupElement(read, offset, isDeletion, isBeforeInsertion, isNextToSoftClip);
}
}