diff --git a/build.xml b/build.xml
index 5fa684c95..bd1c0c925 100644
--- a/build.xml
+++ b/build.xml
@@ -175,24 +175,6 @@
           </manifest>
         </jar>
 
-        <jar jarfile="${dist.dir}/MarkAllAlignmentsAsPrimary.jar" whenmanifestonly="skip">
-          <fileset dir="build">
-            <include name="**/*.class" />
-          </fileset>
-          <manifest>
-            <attribute name="Main-Class" value="org.broadinstitute.sting.oneoffprojects.tools.MarkAllAlignmentsAsPrimary" />
-          </manifest>
-        </jar>
-
-        <jar jarfile="${dist.dir}/RepairSeattleBAM.jar" whenmanifestonly="skip">
-          <fileset dir="build">
-            <include name="**/*.class" />
-          </fileset>
-          <manifest>
-            <attribute name="Main-Class" value="org.broadinstitute.sting.oneoffprojects.tools.RepairSeattleBAM" />
-          </manifest>
-        </jar>
-
 	   <jar jarfile="${dist.dir}/VCFTool.jar" whenmanifestonly="skip">
           <fileset dir="build">
             <include name="**/*.class"/>
@@ -238,17 +220,6 @@
             </manifest>
         </jar>
 
-        <jar jarfile="${dist.dir}/MarkAllAlignmentsAsPrimary.jar" update="true" whenmanifestonly="skip">
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}" />
-            </manifest>
-        </jar>
-
-        <jar jarfile="${dist.dir}/RepairSeattleBAM.jar" update="true" whenmanifestonly="skip">
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}" />
-            </manifest>
-        </jar>
     </target>
 
     <target name="core" description="force a build of the Sting core code">
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/tools/MarkAllAlignmentsAsPrimary.java b/java/src/org/broadinstitute/sting/oneoffprojects/tools/MarkAllAlignmentsAsPrimary.java
deleted file mode 100755
index 6e7c37174..000000000
--- a/java/src/org/broadinstitute/sting/oneoffprojects/tools/MarkAllAlignmentsAsPrimary.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package org.broadinstitute.sting.oneoffprojects.tools;
-
-import net.sf.picard.cmdline.CommandLineProgram;
-import net.sf.picard.cmdline.Usage;
-import net.sf.picard.cmdline.Option;
-import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMFileWriter;
-import net.sf.samtools.SAMFileWriterFactory;
-
-import java.io.*;
-
-public class MarkAllAlignmentsAsPrimary extends CommandLineProgram {
-    @Usage(programVersion="1.0") public String USAGE = "Mark all alignments as primary.";
-    @Option(shortName="I", doc="Input file (bam or sam) to extract reads from. If not specified, reads from stdin.",
-            optional=true) public File IN = null;
-    @Option(shortName="O",doc="Output file (bam or sam).",
-            optional=true) public File OUT = null;
-
-    public static void main(final String[] argv) {
-        System.exit(new MarkAllAlignmentsAsPrimary().instanceMain(argv));
-    }
-
-    protected int doWork() {
-        SAMFileReader inReader = new SAMFileReader(IN);
-        SAMFileWriter outWriter = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(inReader.getFileHeader(), true, OUT);
-
-        for (SAMRecord read : inReader ) {
-            read.setNotPrimaryAlignmentFlag(false);
-
-            outWriter.addAlignment(read);
-        }
-
-        inReader.close();
-        outWriter.close();
-
-        return 0;
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/tools/RepairSeattleBAM.java b/java/src/org/broadinstitute/sting/oneoffprojects/tools/RepairSeattleBAM.java
deleted file mode 100755
index f0ee5b534..000000000
--- a/java/src/org/broadinstitute/sting/oneoffprojects/tools/RepairSeattleBAM.java
+++ /dev/null
@@ -1,44 +0,0 @@
-package org.broadinstitute.sting.oneoffprojects.tools;
-
-import net.sf.picard.cmdline.CommandLineProgram;
-import net.sf.picard.cmdline.Usage;
-import net.sf.picard.cmdline.Option;
-import net.sf.samtools.*;
-
-import java.io.*;
-
-public class RepairSeattleBAM extends CommandLineProgram {
-    @Usage(programVersion="1.0") public String USAGE = "Fix read group info";
-    @Option(shortName="I", doc="Input file (bam or sam) to extract reads from. If not specified, reads from stdin.",
-            optional=true) public File IN = null;
-    @Option(shortName="O",doc="Output file (bam or sam).",
-            optional=true) public File OUT = null;
-    @Option(shortName="S",doc="Sample.",
-            optional=true) public String SAMPLE = null;
-
-    public static void main(final String[] argv) {
-        System.exit(new RepairSeattleBAM().instanceMain(argv));
-    }
-
-    protected int doWork() {
-        SAMFileReader inReader = new SAMFileReader(IN);
-
-        for (SAMReadGroupRecord rg : inReader.getFileHeader().getReadGroups()) {
-            rg.setSample(SAMPLE);
-        }
-
-        SAMFileWriter outWriter = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(inReader.getFileHeader(), true, OUT);
-
-        for (SAMRecord read : inReader ) {
-            //read.getReadGroup().setSample(SAMPLE);
-            read.setAttribute("SM", SAMPLE);
-
-            outWriter.addAlignment(read);
-        }
-
-        inReader.close();
-        outWriter.close();
-
-        return 0;
-    }
-}
\ No newline at end of file