diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
index 1976ab819..baf1f2e90 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
@@ -193,7 +193,7 @@ public class LocusIteratorByState extends LocusIterator {
             logger.debug(String.format("printState():"));
             SAMRecord read = state.getRead();
             int offset = state.getReadOffset();
-            logger.debug(String.format("  read: %s(%d)=%s, cigar=%s", read.getReadName(), offset, read.getReadString().charAt(offset), read.getCigarString()));
+            logger.debug(String.format("  read: %s(%d)=%s, cigar=%s", read.getReadName(), offset, (char)read.getReadBases()[offset], read.getCigarString()));
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
index 78b447e01..338f63a51 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
@@ -163,7 +163,7 @@ public class FisherStrand extends StandardVariantAnnotation {
 	    if ( offset == -1 )
 		continue;
 
-            int readAllele = BaseUtils.simpleBaseToBaseIndex(read.getReadString().charAt(offset));
+            int readAllele = BaseUtils.simpleBaseToBaseIndex((char)read.getReadBases()[offset]);
             boolean isFW = !read.getReadNegativeStrandFlag();
 
             if (readAllele == allele1 || readAllele == allele2) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
index afa009054..30b7b49cb 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
@@ -281,7 +281,7 @@ public class GenotypeLikelihoods implements Cloneable {
                 continue;
 
             SAMRecord read = pileup.getReads().get(i);
-            char base = read.getReadString().charAt(offset);
+            char base = (char)read.getReadBases()[offset];
             byte qual = read.getBaseQualities()[offset];
             if ( ! ignoreBadBases || ! badBase(base) ) {
                 n += add(base, qual, read, offset);
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
index dbe8a16f8..9acda1079 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
@@ -126,7 +126,7 @@ public class CalculateBaseLikelihoodsWalker extends LocusWalker<Integer, Pair<Lo
             for (int i = 0; i < reads.size(); i++) {
                 read = reads.get(i);
                 offset = offsets.get(i);
-                base = read.getReadString().charAt(offset);
+                base = (char)read.getReadBases()[offset];
                 qual = read.getBaseQualities()[offset];
                 //mapquality = read.getMappingQuality();
                 if (!ReadsToDiscard.contains(read.getReadName()) && BaseUtils.simpleBaseToBaseIndex(base) != -1) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
index a4f065957..7af5cd32d 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
@@ -341,7 +341,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
             for (int i = 0; i < reads.size(); i++) {
                 read = reads.get(i);
                 offset = offsets.get(i);
-                base = read.getReadString().charAt(offset);
+                base = (char)read.getReadBases()[offset];
                 qual = read.getBaseQualities()[offset];
                 mapquality = read.getMappingQuality();
                 if (mapquality >= 5 && BaseUtils.simpleBaseToBaseIndex(base) != -1) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java
index c158d547f..1c25a952a 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java
@@ -138,7 +138,7 @@ public class PopPriorWalker extends LocusWalker<Integer, Integer> {
             }
 
             int offset = offsets.get(i);
-            char base = read.getReadString().charAt(offset);
+            char base = (char)read.getReadBases()[offset];
             byte qual = read.getBaseQualities()[offset];
 
             if (qual == 0) { continue; }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintCoverageWalker.java
index 93510206d..ebbdb5653 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintCoverageWalker.java
@@ -44,7 +44,7 @@ public class PrintCoverageWalker extends LocusWalker<Integer, Integer> {
             }
 
             int offset = context.getOffsets().get(i);
-            char base = read.getReadString().charAt(offset);
+            char base = (char)read.getReadBases()[offset];
             if (base == 'a' || base == 'A') { aCount++; }
             if (base == 'c' || base == 'C') { cCount++; }
             if (base == 'g' || base == 'G') { gCount++; }
diff --git a/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
index aeff9a789..18c28679c 100644
--- a/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
@@ -41,7 +41,7 @@ public class AlignmentUtils {
                 case M:
                     for ( int l = 0 ; l < ce.getLength() ; l++, i_ref++, i_read++ ) {
                         char refChr = (char)ref[i_ref];
-                        char readChr = r.getReadString().charAt(i_read);
+                        char readChr = (char)r.getReadBases()[i_read];
                         if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 ||
                              BaseUtils.simpleBaseToBaseIndex(refChr)  == -1 )
                             continue; // do not count Ns/Xs/etc ?
@@ -77,8 +77,8 @@ public class AlignmentUtils {
             switch( ce.getOperator() ) {
                 case M:
                     for ( int l = 0 ; l < ce.getLength() ; l++, i_ref++, i_read++ ) {
-                        char refChr = (char)ref[i_ref];
-                        char readChr = r.getReadString().charAt(i_read);
+                        char refChr = ref[i_ref];
+                        char readChr = (char)r.getReadBases()[i_read];
                         if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 ||
                              BaseUtils.simpleBaseToBaseIndex(refChr)  == -1 )
                             continue; // do not count Ns/Xs/etc ?