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

Cleaner, more efficient way of determining the last dependent set in the queue.

This commit is contained in:
Eric Banks 2012-01-25 16:21:10 -05:00
parent ef335a5812
commit add6918f32
1 changed files with 26 additions and 30 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

56
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
View File

@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.*;
import java.io.PrintStream;
@ -166,7 +166,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
final int numChr = 2*numSamples;
// queue of AC conformations to process
final Queue<ExactACset> ACqueue = new LinkedList<ExactACset>();
final LinkedList<ExactACset> ACqueue = new LinkedList<ExactACset>();
// mapping of ExactACset indexes to the objects
final HashMap<ExactACcounts, ExactACset> indexesToACset = new HashMap<ExactACcounts, ExactACset>(numChr+1);
@ -210,7 +210,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
final double maxLog10L,
final int numChr,
final boolean preserveData,
final Queue<ExactACset> ACqueue,
final LinkedList<ExactACset> ACqueue,
final HashMap<ExactACcounts, ExactACset> indexesToACset,
final double[][] log10AlleleFrequencyPriors,
final AlleleFrequencyCalculationResult result,
@ -250,7 +250,6 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
if ( ACwiggle == 0 ) // all alternate alleles already sum to 2N so we cannot possibly go to higher frequencies
return log10LofK;
ExactACset lastSet = null; // keep track of the last set placed in the queue so that we can tell it to clean us up when done processing
final int numAltAlleles = set.ACcounts.getCounts().length;
// genotype likelihoods are a linear vector that can be thought of as a row-wise upper triangular matrix of log10Likelihoods.
@ -261,7 +260,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
for ( int allele = 0; allele < numAltAlleles; allele++ ) {
final int[] ACcountsClone = set.ACcounts.getCounts().clone();
ACcountsClone[allele]++;
lastSet = updateACset(ACcountsClone, numChr, set, ++PLindex, ACqueue, indexesToACset);
updateACset(ACcountsClone, numChr, set, ++PLindex, ACqueue, indexesToACset);
}
// add conformations for the k+2 case if it makes sense; note that the 2 new alleles may be the same or different
@ -284,20 +283,17 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
// IMPORTANT: we must first add the cases where the 2 new alleles are different so that the queue maintains its ordering
for ( DependentSet dependent : differentAlleles )
lastSet = updateACset(dependent.ACcounts, numChr, set, dependent.PLindex, ACqueue, indexesToACset);
updateACset(dependent.ACcounts, numChr, set, dependent.PLindex, ACqueue, indexesToACset);
for ( DependentSet dependent : sameAlleles )
lastSet = updateACset(dependent.ACcounts, numChr, set, dependent.PLindex, ACqueue, indexesToACset);
updateACset(dependent.ACcounts, numChr, set, dependent.PLindex, ACqueue, indexesToACset);
}
// if the last dependent set was not at the back of the queue (i.e. not just added), then we need to iterate
// over all the dependent sets to find the last one in the queue (otherwise it will be cleaned up too early)
if ( !preserveData && lastSet == null ) {
//if ( DEBUG )
// System.out.printf(" *** iterating over dependent sets for set=%s%n", set.ACcounts);
lastSet = determineLastDependentSetInQueue(set.ACcounts, ACqueue);
// determine which is the last dependent set in the queue (not necessarily the last one added above) so we can know when it is safe to clean up this column
if ( !preserveData ) {
final ExactACset lastSet = determineLastDependentSetInQueue(set.ACcounts, ACqueue);
if ( lastSet != null )
lastSet.dependentACsetsToDelete.add(set.ACcounts);
}
if ( lastSet != null )
lastSet.dependentACsetsToDelete.add(set.ACcounts);
return log10LofK;
}
@ -305,19 +301,17 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
// adds the ExactACset represented by the ACcounts to the ACqueue if not already there (creating it if needed) and
// also adds it as a dependency to the given callingSetIndex.
// returns the ExactACset if that set was not already in the queue and null otherwise.
private static ExactACset updateACset(final int[] ACcounts,
final int numChr,
final ExactACset callingSet,
final int PLsetIndex,
final Queue<ExactACset> ACqueue,
final HashMap<ExactACcounts, ExactACset> indexesToACset) {
private static void updateACset(final int[] ACcounts,
final int numChr,
final ExactACset callingSet,
final int PLsetIndex,
final Queue<ExactACset> ACqueue,
final HashMap<ExactACcounts, ExactACset> indexesToACset) {
final ExactACcounts index = new ExactACcounts(ACcounts);
boolean wasInQueue = true;
if ( !indexesToACset.containsKey(index) ) {
ExactACset set = new ExactACset(numChr/2 +1, index);
indexesToACset.put(index, set);
ACqueue.add(set);
wasInQueue = false;
}
// add the given dependency to the set
@ -325,16 +319,18 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
// System.out.println(" *** adding dependency from " + index + " to " + callingSet.ACcounts);
final ExactACset set = indexesToACset.get(index);
set.ACsetIndexToPLIndex.put(callingSet.ACcounts, PLsetIndex);
return wasInQueue ? null : set;
}
private static ExactACset determineLastDependentSetInQueue(final ExactACcounts callingSetIndex, final Queue<ExactACset> ACqueue) {
ExactACset set = null;
for ( ExactACset queued : ACqueue ) {
if ( queued.dependentACsetsToDelete.contains(callingSetIndex) )
set = queued;
private static ExactACset determineLastDependentSetInQueue(final ExactACcounts callingSetIndex, final LinkedList<ExactACset> ACqueue) {
Iterator<ExactACset> reverseIterator = ACqueue.descendingIterator();
while ( reverseIterator.hasNext() ) {
final ExactACset queued = reverseIterator.next();
if ( queued.ACsetIndexToPLIndex.containsKey(callingSetIndex) )
return queued;
}
return set;
// shouldn't get here
throw new ReviewedStingException("Error: no sets in the queue currently hold " + callingSetIndex + " as a dependent!");
}
private static void computeLofK(final ExactACset set,