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fix to guarantee emission in sorted order 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1122 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-30 13:48:41 +00:00
parent 03f8177a53
commit 8aa3b65e7f
1 changed files with 24 additions and 4 deletions
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28
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -51,6 +51,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// we need to sort the reads ourselves because SAM headers get messed up and claim to be "unsorted" sometimes // we need to sort the reads ourselves because SAM headers get messed up and claim to be "unsorted" sometimes
private TreeSet<ComparableSAMRecord> readsToWrite = null; private TreeSet<ComparableSAMRecord> readsToWrite = null;
private TreeSet<ComparableSAMRecord> nextSetOfReadsToWrite = null;
public void initialize() { public void initialize() {
@ -119,9 +120,23 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
//testCleanWithInsertion(); //testCleanWithInsertion();
if ( writer != null ) { if ( writer != null ) {
Iterator<ComparableSAMRecord> iter = readsToWrite.iterator(); // Although we can guarantee that reads will be emitted in order WITHIN an interval
while ( iter.hasNext() ) // (since we sort them ourselves), we can't guarantee it BETWEEN intervals. So,
writer.addAlignment(iter.next().getRecord()); // we need to keep track of the PREVIOUS interval's reads: if they don't overlap
// with those from this interval then we can emit them; otherwise, we merge them.
if ( nextSetOfReadsToWrite != null ) {
if ( readsToWrite.size() > 0 && nextSetOfReadsToWrite.size() > 0 &&
readsToWrite.first().getRecord().getAlignmentStart() < nextSetOfReadsToWrite.last().getRecord().getAlignmentStart() ) {
nextSetOfReadsToWrite.addAll(readsToWrite);
} else {
Iterator<ComparableSAMRecord> iter = nextSetOfReadsToWrite.iterator();
while ( iter.hasNext() )
writer.addAlignment(iter.next().getRecord());
nextSetOfReadsToWrite = new TreeSet<ComparableSAMRecord>(readsToWrite);
}
} else {
nextSetOfReadsToWrite = new TreeSet<ComparableSAMRecord>(readsToWrite);
}
readsToWrite.clear(); readsToWrite.clear();
} }
return 1; return 1;
@ -136,7 +151,11 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
} }
public void onTraversalDone(Integer result) { public void onTraversalDone(Integer result) {
out.println("Saw " + result + " intervals"); if ( nextSetOfReadsToWrite != null ) {
Iterator<ComparableSAMRecord> iter = nextSetOfReadsToWrite.iterator();
while ( iter.hasNext() )
writer.addAlignment(iter.next().getRecord());
}
if ( writer != null ) { if ( writer != null ) {
writer.close(); writer.close();
} }
@ -161,6 +180,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
logger.error("Failed to close "+OUT_SNPS+" gracefully. Data may be corrupt."); logger.error("Failed to close "+OUT_SNPS+" gracefully. Data may be corrupt.");
} }
} }
out.println("Saw " + result + " intervals");
} }