BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3400 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/alignment/Alignment.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.alignment;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
 
 /**
  * Represents an alignment of a read to a site in the reference genome.
@@ -203,7 +204,7 @@ public class Alignment {
             read.setCigar(alignment.getCigar());
             if(alignment.isNegativeStrand()) {
                 read.setReadBases(BaseUtils.simpleReverseComplement(read.getReadBases()));
-                read.setBaseQualities(BaseUtils.reverse(read.getBaseQualities()));
+                read.setBaseQualities(Utils.reverse(read.getBaseQualities()));
             }
             read.setAttribute("NM",alignment.getEditDistance());
             read.setAttribute("MD",alignment.getMismatchingPositions());

java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.alignment.bwa;
 
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 import org.broadinstitute.sting.alignment.reference.bwt.BWT;
 import org.broadinstitute.sting.alignment.reference.bwt.BWTWriter;
@@ -173,7 +174,7 @@ public class BWTFiles {
             writeEncodedReferenceSequence(normalizedReferenceSequence,pacFile,bwtFile,saFile);
 
             // Write the encoded files for the reverse version of this reference sequence.
-            byte[] reverseReferenceSequence = BaseUtils.reverse(normalizedReferenceSequence);
+            byte[] reverseReferenceSequence = Utils.reverse(normalizedReferenceSequence);
 
             rpacFile = File.createTempFile("bwt",".rpac");
             rbwtFile = File.createTempFile("bwt",".rbwt");

java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java

@@ -5,6 +5,7 @@ import org.broadinstitute.sting.alignment.bwa.BWAAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
 
 import java.io.File;
 import java.util.*;
@@ -133,7 +134,7 @@ public class BWAJavaAligner extends BWAAligner {
         List<Alignment> successfulMatches = new ArrayList<Alignment>();
 
         Byte[] uncomplementedBases = normalizeBases(read.getReadBases());
-        Byte[] complementedBases = normalizeBases(BaseUtils.reverse(BaseUtils.simpleReverseComplement(read.getReadBases())));
+        Byte[] complementedBases = normalizeBases(Utils.reverse(BaseUtils.simpleReverseComplement(read.getReadBases())));
 
         List<LowerBound> forwardLowerBounds = LowerBound.create(uncomplementedBases,forwardBWT);
         List<LowerBound> reverseLowerBounds = LowerBound.create(complementedBases,reverseBWT);

java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java

@@ -30,6 +30,7 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
 import net.sf.samtools.SAMRecord;
 
@@ -69,7 +70,7 @@ public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
         } else {
             out.println(BaseUtils.simpleReverseComplement(read.getReadString()));
             out.println("+");
-            out.println(BaseUtils.reverse(read.getBaseQualityString()));
+            out.println(Utils.reverse(read.getBaseQualityString()));
         }
 
         if ( sqbw != null ) {

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java

@@ -102,7 +102,7 @@ public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
             // calculate the sum of quality scores for each base
             ReadBackedExtendedEventPileup pileup = context.getExtendedEventPileup();
 
-            List<Pair<String,Integer>> all_events = pileup.getEventStringsWithCounts(BaseUtils.charSeq2byteSeq(ref));
+            List<Pair<String,Integer>> all_events = pileup.getEventStringsWithCounts(Utils.charSeq2byteSeq(ref));
             for ( Pair<String,Integer> p : all_events ) {
                 if ( p.second > bestIndelCount ) {
                     bestIndelCount = p.second;

java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java

@@ -841,8 +841,8 @@ public class MultiSampleCaller extends LocusWalker<MultiSampleCaller.MultiSample
 	char PickAlt(char ref, double[] allele_likelihoods)
 	{
 		Integer[] perm = MathUtils.sortPermutation(allele_likelihoods);
-		if (perm[3] != BaseUtils.simpleBaseToBaseIndex(ref)) { return BaseUtils.baseIndexToSimpleBase(perm[3]); }
+		if (perm[3] != BaseUtils.simpleBaseToBaseIndex(ref)) { return BaseUtils.baseIndexToSimpleBaseAsChar(perm[3]); }
-		else { return BaseUtils.baseIndexToSimpleBase(perm[2]); }
+		else { return BaseUtils.baseIndexToSimpleBaseAsChar(perm[2]); }
 	}
 
 	double Compute_discovery_lod(char ref, ClassicGenotypeLikelihoods[] genotype_likelihoods)

java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java

@@ -359,7 +359,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
     }
 
     public char getSecondaryBase ( SAMRecord read, int offset ) {
-        return BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex( ( (byte[]) read.getAttribute("SQ") )[offset] ) );
+        return BaseUtils.baseIndexToSimpleBaseAsChar(QualityUtils.compressedQualityToBaseIndex( ( (byte[]) read.getAttribute("SQ") )[offset] ) );
     }
 
     public boolean baseIsUsable ( RefMetaDataTracker tracker, ReferenceContext ref, ReadBackedPileup pileup, AlignmentContext context ) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/PairedQualityScoreCountsWalker.java

@@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
 import net.sf.samtools.SAMRecord;
 
@@ -75,7 +76,7 @@ public class PairedQualityScoreCountsWalker extends ReadWalker<Pair<byte[],Boole
     }
 
     private Pair<byte[],Boolean> getCorrectlyOrientedBaseQualities(SAMRecord read) {
-        byte[] quals = read.getReadNegativeStrandFlag() ? BaseUtils.reverse(read.getBaseQualities()) : read.getBaseQualities();
+        byte[] quals = read.getReadNegativeStrandFlag() ? Utils.reverse(read.getBaseQualities()) : read.getBaseQualities();
         return new Pair<byte[], Boolean>(quals, read.getFirstOfPairFlag());
     }
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java

@@ -100,18 +100,18 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateColl
                 if (useNextBestBase || useNextRandomBase || useNonNextBestBase) {
                     byte nextBestBase;
                     if (useNextBestBase) {
-                        nextBestBase = (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(sq[cycle]));
+                        nextBestBase = BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(sq[cycle]));
                     } else if (useNonNextBestBase) {
                         nextBestBase = bases[cycle];
                         Random generator = new Random();
-                        while (nextBestBase == bases[cycle] || nextBestBase == (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(sq[cycle]))) {
+                        while (nextBestBase == bases[cycle] || nextBestBase == BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(sq[cycle]))) {
-                            nextBestBase = (byte) BaseUtils.baseIndexToSimpleBase(generator.nextInt(4));
+                            nextBestBase = BaseUtils.baseIndexToSimpleBase(generator.nextInt(4));
                         }
                     } else {
                         nextBestBase = bases[cycle];
                         Random generator = new Random();
                         while (nextBestBase == bases[cycle]) {
-                            nextBestBase = (byte) BaseUtils.baseIndexToSimpleBase(generator.nextInt(4));
+                            nextBestBase = BaseUtils.baseIndexToSimpleBase(generator.nextInt(4));
                         }
                     }
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java

@@ -131,7 +131,7 @@ public class SnpCallRateByCoverageWalker extends LocusWalker<List<String>, Strin
                                coverage,
                                ((float) coverage)/((float) reads.size()),
                                goodIterations,
-                               BaseUtils.baseIndexToSimpleBase(ref.getBaseIndex()),
+                               (char)BaseUtils.baseIndexToSimpleBase(ref.getBaseIndex()),
                                call == null ? "./." : call.getGenotypeString(),
                                vcCall.getGenotypeString(),
                                call == null ? 0 : call.getType() == vcCall.getType() ? 1 : 0,

java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java

@@ -96,7 +96,7 @@ public class ComputeConfusionMatrix extends LocusWalker<Integer, Integer> {
             }
         }
         
-        String fwAltBase = String.format("%c", BaseUtils.baseIndexToSimpleBase(altBaseIndex));
+        String fwAltBase = String.format("%c", (char)BaseUtils.baseIndexToSimpleBase(altBaseIndex));
         //String rcAltBase = BaseUtils.simpleComplement(fwAltBase);
 
         for (int readIndex = 0; readIndex < context.getReads().size(); readIndex++) {

java/src/org/broadinstitute/sting/playground/tools/BamToFastq.java

@@ -9,6 +9,7 @@ import net.sf.samtools.SAMRecord;
 import java.io.*;
 
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
 
 /**
  * Created by IntelliJ IDEA.
@@ -68,7 +69,7 @@ public class BamToFastq extends CommandLineProgram {
             } else {
                 out.println(BaseUtils.simpleReverseComplement(read.getReadString()));
                 out.println('+');
-                out.println(BaseUtils.reverse(read.getBaseQualityString()));
+                out.println(Utils.reverse(read.getBaseQualityString()));
             }
         }
         inReader.close();

java/src/org/broadinstitute/sting/utils/BaseUtils.java

@@ -8,6 +8,9 @@ import java.util.Random;
  * BaseUtils contains some basic utilities for manipulating nucleotides.
  */
 public class BaseUtils {
+    //
+    // todo -- we need a generalized base abstraction using the Base enum.
+    //
     public final static char[] BASES = { 'A', 'C', 'G', 'T' };
     public final static char[] EXTENDED_BASES = { 'A', 'C', 'G', 'T', 'N', 'D' };
 
@@ -79,7 +82,7 @@ public class BaseUtils {
     private BaseUtils() {}
 
     static public boolean basesAreEqual(byte base1, byte base2) {
-        return simpleBaseToBaseIndex((char)base1) == simpleBaseToBaseIndex((char)base2);
+        return simpleBaseToBaseIndex(base1) == simpleBaseToBaseIndex(base2);
     }
 
 
@@ -89,6 +92,7 @@ public class BaseUtils {
      * @param code
      * @return 0, 1, 2, 3, or -1 if the base can't be understood
      */
+    @Deprecated
     static public char[] iupacToBases(char code) {
         char[] bases = new char[2];
         switch (code) {
@@ -151,6 +155,7 @@ public class BaseUtils {
      * @param base  [AaCcGgTt]
      * @return 0, 1, 2, 3, or -1 if the base can't be understood
      */
+    @Deprecated
     static public int simpleBaseToBaseIndex(char base) {
         switch (base) {
             case '*':               // the wildcard character counts as an A
@@ -170,6 +175,7 @@ public class BaseUtils {
         }
     }
 
+    @Deprecated
     static public int extendedBaseToBaseIndex(char base) {
         switch (base) {
             case 'd':
@@ -185,6 +191,7 @@ public class BaseUtils {
         return simpleBaseToBaseIndex((char)base);
     }
 
+    @Deprecated
     static public boolean isRegularBase(char base) {
         return simpleBaseToBaseIndex(base) != -1;
     }
@@ -193,6 +200,7 @@ public class BaseUtils {
         return isRegularBase((char)base);
     }
 
+    @Deprecated
     static public boolean isNBase(char base) {
         return isNBase((byte)base);
     }
@@ -201,14 +209,13 @@ public class BaseUtils {
         return base == 'N';
     }
 
-
     /**
      * Converts a base index to a simple base
      *
      * @param baseIndex  0, 1, 2, 3
      * @return A, C, G, T, or '.' if the index can't be understood
      */
-    static public char baseIndexToSimpleBase(int baseIndex) {
+    static public byte baseIndexToSimpleBase(int baseIndex) {
         switch (baseIndex) {
             case 0: return 'A';
             case 1: return 'C';
@@ -218,6 +225,11 @@ public class BaseUtils {
         }
     }
 
+    @Deprecated
+    static public char baseIndexToSimpleBaseAsChar(int baseIndex) {
+        return (char)baseIndexToSimpleBase(baseIndex);
+    }
+
     /**
      * Converts a base index to a base index representing its cross-talk partner
      *
@@ -240,8 +252,9 @@ public class BaseUtils {
      * @param base  [AaCcGgTt]
      * @return C, A, T, G, or '.' if the base can't be understood
      */
+    @Deprecated
     static public char crossTalkPartnerBase(char base) {
-        return baseIndexToSimpleBase(crossTalkPartnerIndex(simpleBaseToBaseIndex(base)));
+        return (char)baseIndexToSimpleBase(crossTalkPartnerIndex(simpleBaseToBaseIndex(base)));
     }
 
     /**
@@ -260,7 +273,6 @@ public class BaseUtils {
         }
     }
 
-
     public static byte getSecondBase(final SAMRecord read, int offset) {
         byte base2 = '.'; // todo -- what should the default char really be?
 
@@ -268,7 +280,7 @@ public class BaseUtils {
             byte[] compressedQuals = (byte[]) read.getAttribute("SQ");
 
             if (offset != -1 && compressedQuals != null && compressedQuals.length == read.getReadLength()) {
-                base2 = (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(compressedQuals[offset]));
+                base2 = BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(compressedQuals[offset]));
             }
         }
         else if (read.getAttribute("E2") != null) {
@@ -290,6 +302,7 @@ public class BaseUtils {
      * @param base the base [AaCcGgTt]
      * @return the transition of the base, or the input base if it's not one of the understood ones
      */
+    // todo -- are these right?  Put into recalibator if really color space specific
     static public char transition(char base) {
         switch (base) {
             case 'A':
@@ -310,6 +323,7 @@ public class BaseUtils {
      * @param base the base [AaCcGgTt]
      * @return the transversion of the base, or the input base if it's not one of the understood ones
      */
+    // todo -- are these right?  Put into recalibator if really color space specific
     static public char transversion(char base) {
         switch (base) {
             case 'A':
@@ -330,7 +344,7 @@ public class BaseUtils {
      * @param base the base [AaCcGgTt]
      * @return the complementary base, or the input base if it's not one of the understood ones
      */
-    static public char simpleComplement(char base) {
+    static public byte simpleComplement(byte base) {
         switch (base) {
             case 'A':
             case 'a': return 'T';
@@ -344,6 +358,11 @@ public class BaseUtils {
         }
     }
 
+    @Deprecated
+    static public char simpleComplement(char base) {
+        return (char)simpleComplement((byte)base);
+    }
+
     /**
      * Reverse complement a byte array of bases (that is, chars casted to bytes, *not* base indices in byte form)
      *
@@ -382,6 +401,7 @@ public class BaseUtils {
      * @param bases the char array of bases
      * @return the reverse complement of the char byte array
      */
+    @Deprecated
     static public char[] simpleReverseComplement(char[] bases) {
         char[] rcbases = new char[bases.length];
 
@@ -398,6 +418,7 @@ public class BaseUtils {
      * @param bases  the char array of bases
      * @return the complement of the base char array
      */
+    @Deprecated
     static public char[] simpleComplement(char[] bases) {
         char[] rcbases = new char[bases.length];
 
@@ -429,47 +450,6 @@ public class BaseUtils {
         return new String(simpleComplement(bases.getBytes()));
     }
 
-    /**
-     * Reverse a byte array of bases
-     * 
-     * @param bases  the byte array of bases
-     * @return the reverse of the base byte array
-     */
-    static public byte[] reverse(byte[] bases) {
-        byte[] rcbases = new byte[bases.length];
-
-        for (int i = 0; i < bases.length; i++) {
-            rcbases[i] = bases[bases.length - i - 1];
-        }
-
-        return rcbases;
-    }
-
-    /**
-     * Reverse an int array of bases
-     *
-     * @param bases  the int array of bases
-     * @return the reverse of the base int array
-     */
-    static public int[] reverse(int[] bases) {
-        int[] rcbases = new int[bases.length];
-
-        for (int i = 0; i < bases.length; i++) {
-            rcbases[i] = bases[bases.length - i - 1];
-        }
-
-        return rcbases;
-    }
-
-    /**
-     * Reverse (NOT reverse-complement!!) a string
-     *
-     * @param bases  input string
-     * @return the reversed string
-     */
-    static public String reverse(String bases) {
-        return new String( reverse( bases.getBytes() )) ;
-    }
 
     /**
      * For the most frequent base in the sequence, return the percentage of the read it constitutes.
@@ -498,6 +478,12 @@ public class BaseUtils {
         return ((double) baseCounts[mostFrequentBaseIndex])/((double) sequence.length);
     }
 
+    // --------------------------------------------------------------------------------
+    //
+    // random bases
+    //
+    // --------------------------------------------------------------------------------
+
     /**
      * Return a random base index (A=0, C=1, G=2, T=3).
      *
@@ -529,7 +515,7 @@ public class BaseUtils {
      *
      * @return a random base (A, C, G, T)
      */
-    static public char getRandomBase() {
+    static public byte getRandomBase() {
         return getRandomBase('.');
     }
 
@@ -539,7 +525,7 @@ public class BaseUtils {
      * @param excludeBase the base to exclude
      * @return a random base, excluding the one specified (A, C, G, T)
      */
-    static public char getRandomBase(char excludeBase) {
+    static public byte getRandomBase(char excludeBase) {
         return BaseUtils.baseIndexToSimpleBase(getRandomBaseIndex(BaseUtils.simpleBaseToBaseIndex(excludeBase)));
     }
     
@@ -587,15 +573,6 @@ public class BaseUtils {
     	}
     	return period;
     }
-
-    public static byte[] charSeq2byteSeq(char[] seqIn) {
-        byte[] seqOut = new byte[seqIn.length];
-        for ( int i = 0; i < seqIn.length; i++ ) {
-            seqOut[i] = (byte)seqIn[i];
-        }
-        return seqOut;
-    }
-
 }
 
 /* code snippet for testing sequencePeriod():

java/src/org/broadinstitute/sting/utils/QualityUtils.java

@@ -215,6 +215,6 @@ public class QualityUtils {
      * @return the reverse of the quality array
      */
     static public byte[] reverseQualityArray( byte[] quals ) {
-        return BaseUtils.reverse(quals); // no sense in duplicating functionality
+        return Utils.reverse(quals); // no sense in duplicating functionality
     }
 }

java/src/org/broadinstitute/sting/utils/Utils.java

@@ -420,6 +420,56 @@ public class Utils {
 
         return "{" + join(", ", pairs) + "}";
     }
+
+    /**
+     * Reverse a byte array of bases
+     *
+     * @param bases  the byte array of bases
+     * @return the reverse of the base byte array
+     */
+    static public byte[] reverse(byte[] bases) {
+        byte[] rcbases = new byte[bases.length];
+
+        for (int i = 0; i < bases.length; i++) {
+            rcbases[i] = bases[bases.length - i - 1];
+        }
+
+        return rcbases;
+    }
+
+    /**
+     * Reverse an int array of bases
+     *
+     * @param bases  the int array of bases
+     * @return the reverse of the base int array
+     */
+    static public int[] reverse(int[] bases) {
+        int[] rcbases = new int[bases.length];
+
+        for (int i = 0; i < bases.length; i++) {
+            rcbases[i] = bases[bases.length - i - 1];
+        }
+
+        return rcbases;
+    }
+
+    /**
+     * Reverse (NOT reverse-complement!!) a string
+     *
+     * @param bases  input string
+     * @return the reversed string
+     */
+    static public String reverse(String bases) {
+        return new String( reverse( bases.getBytes() )) ;
+    }
+
+    public static byte[] charSeq2byteSeq(char[] seqIn) {
+        byte[] seqOut = new byte[seqIn.length];
+        for ( int i = 0; i < seqIn.length; i++ ) {
+            seqOut[i] = (byte)seqIn[i];
+        }
+        return seqOut;
+    }    
 }
 
 

java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java

@@ -74,7 +74,7 @@ public class DupUtils {
     }
 
     private static Pair<Byte, Byte> baseProbs2BaseAndQual(double[] probs, int maxQScore) {
-        char bestBase = 0;
+        byte bestBase = 0;
         double bestProb = Double.NEGATIVE_INFINITY;
         double sumProbs = 0;
 
@@ -101,13 +101,13 @@ public class DupUtils {
 //            System.out.printf("encoded    Q %2d%n", qual);
 //        }
 
-        return new Pair<Byte, Byte>((byte)bestBase, qual);
+        return new Pair<Byte, Byte>(bestBase, qual);
     }
 
     private static void print4BaseQuals(String header, double[] probs) {
         System.out.printf("%s log10(P(b)) is ", header);
         for ( int i = 0; i < 4; i++ ) {
-            System.out.printf("%c=%+.8f ", BaseUtils.baseIndexToSimpleBase(i), probs[i]);
+            System.out.printf("%c=%+.8f ", (char)BaseUtils.baseIndexToSimpleBase(i), probs[i]);
         }
         System.out.printf("%n");
     }

java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java

@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
 
 
 public class AlignmentUtils {
@@ -348,7 +349,7 @@ public class AlignmentUtils {
     public static byte [] getQualsInCycleOrder(SAMRecord read) {
         if ( isReadUnmapped(read) || ! read.getReadNegativeStrandFlag() ) return read.getBaseQualities();
 
-        return BaseUtils.reverse(read.getBaseQualities());
+        return Utils.reverse(read.getBaseQualities());
     }
 
     /** Takes the alignment of the read sequence <code>readSeq</code> to the reference sequence <code>refSeq</code>