Renamed FragmentPileup to FragmentUtils

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java

@@ -27,10 +27,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import net.sf.samtools.SAMUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.FragmentUtils;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.pileup.FragmentPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -259,12 +259,12 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
         int n = 0;
 
         // for each fragment, add to the likelihoods
-        FragmentPileup fpile = new FragmentPileup(pileup);
+        FragmentUtils fpile = new FragmentUtils(pileup);
 
         for ( PileupElement p : fpile.getOneReadPileup() )
             n += add(p, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual);
 
-        for ( FragmentPileup.TwoReadPileupElement twoRead : fpile.getTwoReadPileup() )
+        for ( FragmentUtils.TwoReadPileupElement twoRead : fpile.getTwoReadPileup() )
             n += add(twoRead, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual);
 
         return n;
@@ -286,7 +286,7 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
         }
     }
 
-    public int add(FragmentPileup.TwoReadPileupElement twoRead, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) {
+    public int add(FragmentUtils.TwoReadPileupElement twoRead, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) {
         final byte observedBase1 = twoRead.getFirst().getBase();
         final byte qualityScore1 = qualToUse(twoRead.getFirst(), ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual);
         final byte observedBase2 = twoRead.getSecond().getBase();

public/java/src/org/broadinstitute/sting/utils/FragmentUtils.java

@@ -1,6 +1,8 @@
-package org.broadinstitute.sting.utils.pileup;
+package org.broadinstitute.sting.utils;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
@@ -23,7 +25,7 @@ import java.util.*;
  * Date: 3/26/11
  * Time: 10:09 PM
  */
-public class FragmentPileup {
+public class FragmentUtils {
     Collection<PileupElement> oneReadPile = null;
     Collection<TwoReadPileupElement> twoReadPile = null;
 
@@ -36,12 +38,12 @@ public class FragmentPileup {
      * Create a new Fragment-based pileup from the standard read-based pileup
      * @param pileup
      */
-    public FragmentPileup(ReadBackedPileup pileup) {
+    public FragmentUtils(ReadBackedPileup pileup) {
         skipNonOverlapping(pileup);
     }
 
     /** For performance testing only */
-    protected FragmentPileup(ReadBackedPileup pileup, FragmentMatchingAlgorithm algorithm) {
+    protected FragmentUtils(ReadBackedPileup pileup, FragmentMatchingAlgorithm algorithm) {
         switch ( algorithm ) {
             case ORIGINAL: oldSlowCalculation(pileup); break;
             case skipNonOverlapping: skipNonOverlapping(pileup); break;

public/java/test/org/broadinstitute/sting/utils/pileup/FragmentPileupBenchmark.java

@@ -28,7 +28,7 @@ import com.google.caliper.Param;
 import com.google.caliper.SimpleBenchmark;
 import com.google.caliper.runner.CaliperMain;
 import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.FragmentUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
@@ -62,20 +62,20 @@ public class FragmentPileupBenchmark extends SimpleBenchmark {
         }
     }
 
-    private void run(int rep, FragmentPileup.FragmentMatchingAlgorithm algorithm) {
+    private void run(int rep, FragmentUtils.FragmentMatchingAlgorithm algorithm) {
         int nFrags = 0;
         for ( int i = 0; i < rep; i++ ) {
             for ( ReadBackedPileup rbp : pileups )
-                nFrags += new FragmentPileup(rbp, algorithm).getTwoReadPileup().size();
+                nFrags += new FragmentUtils(rbp, algorithm).getTwoReadPileup().size();
         }
     }
 
     public void timeOriginal(int rep) {
-        run(rep, FragmentPileup.FragmentMatchingAlgorithm.ORIGINAL);
+        run(rep, FragmentUtils.FragmentMatchingAlgorithm.ORIGINAL);
     }
 
     public void timeSkipNonOverlapping(int rep) {
-        run(rep, FragmentPileup.FragmentMatchingAlgorithm.skipNonOverlapping);
+        run(rep, FragmentUtils.FragmentMatchingAlgorithm.skipNonOverlapping);
     }
 
     public static void main(String[] args) {

public/java/test/org/broadinstitute/sting/utils/pileup/FragmentPileupUnitTest.java

@@ -25,10 +25,9 @@
 package org.broadinstitute.sting.utils.pileup;
 
 import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.FragmentUtils;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeTest;
@@ -113,7 +112,7 @@ public class FragmentPileupUnitTest extends BaseTest {
     public void testMe(FragmentPileupTest test) {
         for ( TestState testState : test.states ) {
             ReadBackedPileup rbp = testState.pileup;
-            FragmentPileup fp = new FragmentPileup(rbp);
+            FragmentUtils fp = new FragmentUtils(rbp);
             Assert.assertEquals(fp.getTwoReadPileup().size(), testState.shouldBeFragment ? 1 : 0);
             Assert.assertEquals(fp.getOneReadPileup().size(), testState.shouldBeFragment ? 0 : 1);
         }