Move MSG - plus now obsolete classes which it depends on -- to oneoffprojects (with permission from Jared).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2224 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -1,11 +1,11 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.oneoffprojects.multisamplecaller;
+
+import org.broadinstitute.sting.utils.*;
 
 import net.sf.samtools.*;
 
 import java.util.List;
 import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Random;
 
 /**
  * Created by IntelliJ IDEA.
@@ -14,7 +14,6 @@ import java.util.Random;
  * Time: 8:54:05 AM
  * To change this template use File | Settings | File Templates.
  */
-@Deprecated
 abstract public class BasicPileup {
     public static final char DELETION_CHAR = 'D';
 

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

@@ -1,12 +1,9 @@
-package org.broadinstitute.sting.playground.utils;
+package org.broadinstitute.sting.oneoffprojects.multisamplecaller;
 
-import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.QualityUtils;
 
 import static java.lang.Math.log10;
 import static java.lang.Math.pow;
-import java.util.HashMap;
 import java.lang.Cloneable;
 
 public class ClassicGenotypeLikelihoods implements Cloneable {

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

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.playground.utils;
+package org.broadinstitute.sting.oneoffprojects.multisamplecaller;
 
 import java.lang.*;
 import java.util.*;

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

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.playground.utils;
+package org.broadinstitute.sting.oneoffprojects.multisamplecaller;
 
 import java.util.HashMap;
 

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

@@ -1,5 +1,5 @@
 
-package org.broadinstitute.sting.playground.gatk.walkers;
+package org.broadinstitute.sting.oneoffprojects.multisamplecaller;
 
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMReadGroupRecord;
@@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.playground.utils.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
@@ -20,7 +19,7 @@ import java.io.*;
 // Beta iterative multi-sample caller
 // j.maguire 6-11-2009
 
-public class MultiSampleCaller2 extends LocusWalker<MultiSampleCaller2.MultiSampleCallResult,String>
+public class MultiSampleCaller extends LocusWalker<MultiSampleCaller.MultiSampleCallResult,String>
 {
     @Argument(required=false, shortName="fractional_counts", doc="should we use fractional counts?") public boolean FRACTIONAL_COUNTS = false;
     @Argument(required=false, shortName="max_iterations", doc="Maximum number of iterations for EM") public int MAX_ITERATIONS = 10;

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

@@ -184,10 +184,62 @@ public class DupUtils {
         return l;
     }
 
+    // TODO -- get rid of all this crappy, obsolete pileup code
+
+    @Deprecated
+    private static ArrayList<Byte> getBasesAsArrayList( List<SAMRecord> reads, List<Integer> offsets ) {
+        ArrayList<Byte> bases = new ArrayList<Byte>(reads.size());
+        for (byte value : getBasesAsArray(reads, offsets))
+            bases.add(value);
+        return bases;
+     }
+
+    @Deprecated
+    private static ArrayList<Byte> getQualsAsArrayList( List<SAMRecord> reads, List<Integer> offsets ) {
+        ArrayList<Byte> quals = new ArrayList<Byte>(reads.size());
+        for (byte value : getQualsAsArray(reads, offsets))
+            quals.add(value);
+        return quals;
+    }
+
+    @Deprecated
+    public static byte[] getBasesAsArray( List<SAMRecord> reads, List<Integer> offsets ) {
+        byte array[] = new byte[reads.size()];
+        int index = 0;
+        for ( int i = 0; i < reads.size(); i++ ) {
+            SAMRecord read = reads.get(i);
+            int offset = offsets.get(i);
+            if ( offset == -1 ) {
+               array[index++] = ((byte)'D');
+            } else {
+                array[index++] = read.getReadBases()[offset];
+            }
+        }
+        return array;
+     }
+
+    @Deprecated
+    private static byte[] getQualsAsArray( List<SAMRecord> reads, List<Integer> offsets ) {
+        byte array[] = new byte[reads.size()];
+        int index = 0;
+        for ( int i = 0; i < reads.size(); i++ ) {
+            SAMRecord read = reads.get(i);
+            int offset = offsets.get(i);
+
+            // skip deletion sites
+            if ( offset == -1 ) {
+                array[index++] = ((byte)0);
+            } else {
+                array[index++] = read.getBaseQualities()[offset];
+            }
+        }
+        return array;
+    }
+
     private static Pair<Byte, Byte> combineBaseProbs(List<SAMRecord> duplicates, int readOffset, int maxQScore) {
         List<Integer> offsets = constantOffset(duplicates, readOffset);
-        ArrayList<Byte> bases = BasicPileup.getBasesAsArrayList(duplicates, offsets);
+        ArrayList<Byte> bases = getBasesAsArrayList(duplicates, offsets);
-        ArrayList<Byte> quals = BasicPileup.getQualsAsArrayList(duplicates, offsets);
+        ArrayList<Byte> quals = getQualsAsArrayList(duplicates, offsets);
         final boolean debug = false;
 
         // calculate base probs