diff --git a/java/src/org/broadinstitute/sting/playground/fourbasecaller/RepairBadlyCombinedSamFile.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/RepairBadlyCombinedSamFile.java
deleted file mode 100644
index f70c8cc46..000000000
--- a/java/src/org/broadinstitute/sting/playground/fourbasecaller/RepairBadlyCombinedSamFile.java
+++ /dev/null
@@ -1,94 +0,0 @@
-package org.broadinstitute.sting.playground.fourbasecaller;
-
-import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
-import org.broadinstitute.sting.utils.QualityUtils;
-
-import java.io.File;
-import java.util.Random;
-
-import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMFileWriter;
-import net.sf.samtools.SAMFileWriterFactory;
-
-public class RepairBadlyCombinedSamFile extends CommandLineProgram {
-    public static RepairBadlyCombinedSamFile Instance = null;
-
-    public File ASAM;
-    public File OSAM;
-    private Random rg;
-
-    public static void main(String[] argv) {
-        Instance = new RepairBadlyCombinedSamFile();
-        start(Instance, argv);
-    }
-
-    protected void setupArgs() {
-        m_parser.addRequiredArg("aligned_sam",   "A", "Second input SAM file", "ASAM");
-        m_parser.addRequiredArg("sam_out",       "O", "Output SAM file",       "OSAM");
-    }
-
-    protected int execute() {
-        rg = new Random();
-        
-        SAMFileReader asamr = new SAMFileReader(ASAM);
-        asamr.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
-
-        SAMFileWriter osamw = new SAMFileWriterFactory().makeSAMOrBAMWriter(asamr.getFileHeader(), false, OSAM);
-
-        for (SAMRecord samRecord : asamr) {
-            byte[] bases = samRecord.getReadBases();
-            byte[] newbases = new byte[bases.length];
-
-            if (samRecord.getReadNegativeStrandFlag()) {
-                byte[] quals = samRecord.getBaseQualities();
-                byte[] sq    = (byte[]) samRecord.getAttribute("SQ");
-
-                byte[] newquals = new byte[bases.length];
-                byte[] newsq    = new byte[bases.length];
-
-                for (int i = 0; i < bases.length; i++) {
-                    byte newbase;
-                    switch (bases[bases.length - i - 1]) {
-                        case 'A': newbase = 'T'; break;
-                        case 'C': newbase = 'G'; break;
-                        case 'G': newbase = 'C'; break;
-                        case 'T': newbase = 'A'; break;
-                        default: newbase = getRandomBase(); // hack.  This is so downstream applications don't barf on an ambiguous base 'matching' the reference
-                    }
-                    newbases[i] = newbase;
-                    newquals[i] = quals[bases.length - i - 1];
-                    newsq[i]    = QualityUtils.complementCompressedQuality(newquals[bases.length - i - 1]);
-                }
-
-                samRecord.setReadBases(newbases);
-                samRecord.setBaseQualities(newquals);
-                samRecord.setAttribute("SQ", newsq);
-            } else {
-                for (int i = 0; i < bases.length; i++) {
-                    newbases[i] = (bases[i] == 'A' || bases[i] == 'C' || bases[i] == 'G' || bases[i] == 'T') ? bases[i] : getRandomBase();
-                }
-
-                samRecord.setReadBases(newbases);
-            }
-            
-            osamw.addAlignment(samRecord);
-        }
-
-        osamw.close();
-
-        return 0;
-    }
-
-    private byte getRandomBase() {
-        int baseIndex = rg.nextInt(4);
-
-        switch (baseIndex) {
-            case 0: return 'A';
-            case 1: return 'C';
-            case 2: return 'G';
-            case 3: return 'T';
-            default: return '.'; // unreachable
-        }
-    }
-}