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fix for parallelism bug 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3451 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-05-27 22:16:14 +00:00
parent cded9ec985
commit e1b0aefb29
2 changed files with 1 additions and 5 deletions
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2
java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -59,7 +59,7 @@ public class ShardTraverser implements Callable {
long startTime = System.currentTimeMillis(); long startTime = System.currentTimeMillis();
Object accumulator = walker.reduceInit(); Object accumulator = walker.reduceInit();
WindowMaker windowMaker = new WindowMaker(microScheduler.getReadIterator(shard),shard.getGenomeLocs()); WindowMaker windowMaker = new WindowMaker(microScheduler.getReadIterator(shard),shard.getGenomeLocs(),walker.getMandatoryReadFilters());
ShardDataProvider dataProvider = null; ShardDataProvider dataProvider = null;
try { try {
for(WindowMaker.WindowMakerIterator iterator: windowMaker) { for(WindowMaker.WindowMakerIterator iterator: windowMaker) {

4
java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
View File

@ -55,10 +55,6 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
*/ */
private boolean shardGenerated = false; private boolean shardGenerated = false;
public WindowMaker(StingSAMIterator iterator, List<GenomeLoc> intervals) {
this(iterator, intervals, new ArrayList<SamRecordFilter>());
}
/** /**
* Create a new window maker with the given iterator as a data source, covering * Create a new window maker with the given iterator as a data source, covering
* the given intervals. * the given intervals.