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Fix chartl's issue -- reduceInit() is sometimes called unnecessarily at the 

end of a traversal.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2889 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-02-25 21:02:18 +00:00
parent 3d92e5a737
commit 3289826892
1 changed files with 17 additions and 3 deletions
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20
java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
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@ -123,6 +123,12 @@ public abstract class Accumulator {
* and aggregates those results into a single list.
*/
private static class IntervalAccumulator extends Accumulator {
/**
* True if a new interval is being started. This flag is used to
* ensure that reduceInit() is not called unnecessarily.
*/
private boolean startingNewInterval = true;
/**
* An iterator through all intervals in the series.
*/
@ -138,19 +144,27 @@ public abstract class Accumulator {
*/
private final List<Pair<GenomeLoc,Object>> intervalAccumulator = new ArrayList<Pair<GenomeLoc,Object>>();
/**
* Holds the next value to be passed in as the reduce result.
*/
private Object nextReduceInit = null;
protected IntervalAccumulator(Walker walker, GenomeLocSortedSet intervals) {
super(walker);
this.intervalIterator = intervals.iterator();
if(intervalIterator.hasNext()) currentInterval = intervalIterator.next();
nextReduceInit = walker.reduceInit();
}
/**
* Interval accumulator always feeds reduceInit into every new traversal.
*/
public Object getReduceInit() { return nextReduceInit; }
public Object getReduceInit() {
if(startingNewInterval) {
startingNewInterval = false;
nextReduceInit = walker.reduceInit();
}
return nextReduceInit;
}
/**
* Create a holder for interval results if none exists. Add the result to the holder.
@ -164,7 +178,7 @@ public abstract class Accumulator {
if(currentInterval != null && currentInterval.getContig().equals(location.getContig()) && currentInterval.getStop() == location.getStop()) {
intervalAccumulator.add(new Pair<GenomeLoc,Object>(currentInterval,result));
nextReduceInit = walker.reduceInit();
startingNewInterval = true;
}
else
nextReduceInit = result;