From c2858c898841de081aa9bc6c4fade7bc89e1636f Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 8 Jun 2010 21:39:39 +0000
Subject: [PATCH] Minor performance enhancement.  Checkpoint commit before
 major performance overhaul.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3504 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/iterators/DownsamplingLocusIteratorByState.java  | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java b/java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
index 11167860e..ec32ef32b 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
@@ -406,9 +406,10 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
                 ArrayList<PileupElement> pile = new ArrayList<PileupElement>(readStates.size());
 
                 // todo -- performance problem -- should be lazy, really
+                GenomeLoc location = getLocation();
                 for ( SAMRecordState state : readStates ) {
                     if ( state.getCurrentCigarOperator() != CigarOperator.D && state.getCurrentCigarOperator() != CigarOperator.N ) {
-                        if ( filterRead(state.getRead(), getLocation().getStart(), filters ) ) {
+                        if ( filterRead(state.getRead(), location.getStart(), filters ) ) {
                             discarded_bases++;
                             //printStatus("Adaptor bases", discarded_adaptor_bases);
                             continue;
@@ -429,10 +430,9 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
                     }
                 }
 
-                GenomeLoc loc = getLocation();
                 updateReadStates(); // critical - must be called after we get the current state offsets and location
                 // if we got reads with non-D/N over the current position, we are done
-                if ( pile.size() != 0 ) nextAlignmentContext = new AlignmentContext(loc, new ReadBackedPileup(loc, pile, size, nDeletions, nMQ0Reads));
+                if ( pile.size() != 0 ) nextAlignmentContext = new AlignmentContext(location, new ReadBackedPileup(location, pile, size, nDeletions, nMQ0Reads));
             }
         }
     }
@@ -751,7 +751,7 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
             List<SAMRecordState> readStatesBySample = new LinkedList<SAMRecordState>();
             int readCount = 0;
             for(SAMRecord read: reads) {
-                if(readCount < maxReads) {
+                if(readCount <=  maxReads) {
                     SAMRecordState state = new SAMRecordState(read, readInfo.generateExtendedEvents());
                     state.stepForwardOnGenome();
                     readStatesBySample.add(state);