diff --git a/public/java/src/org/broadinstitute/sting/utils/gcf/GCF.java b/public/java/src/org/broadinstitute/sting/utils/gcf/GCF.java
deleted file mode 100644
index b4ad81c02..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/gcf/GCF.java
+++ /dev/null
@@ -1,253 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.gcf;
-
-import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.*;
-
-import java.io.*;
-import java.util.*;
-
-/**
- * GATK binary VCF record
- *
- * @author Your Name
- * @since Date created
- */
-public class GCF {
-    private final static int RECORD_TERMINATOR = 123456789;
-    private int chromOffset;
-    private int start, stop;
-    private String id;
-    private List<Allele> alleleMap;
-    private int alleleOffsets[];
-    private float qual;
-    private byte refPad;
-    private String info;
-    private int filterOffset;
-
-    private List<GCFGenotype> genotypes = Collections.emptyList();
-
-    public GCF(final GCFHeaderBuilder GCFHeaderBuilder, final VariantContext vc, boolean skipGenotypes) {
-        chromOffset = GCFHeaderBuilder.encodeString(vc.getChr());
-        start = vc.getStart();
-        stop = vc.getEnd();
-        refPad = vc.hasReferenceBaseForIndel() ? vc.getReferenceBaseForIndel() : 0;
-        id = vc.getID();
-
-        // encode alleles
-        alleleMap = new ArrayList<Allele>(vc.getNAlleles());
-        alleleOffsets = new int[vc.getNAlleles()];
-        alleleMap.add(vc.getReference());
-        alleleOffsets[0] = GCFHeaderBuilder.encodeAllele(vc.getReference());
-        for ( int i = 0; i < vc.getAlternateAlleles().size(); i++ ) {
-            alleleMap.add(vc.getAlternateAllele(i));
-            alleleOffsets[i+1] = GCFHeaderBuilder.encodeAllele(vc.getAlternateAllele(i));
-        }
-
-        qual = (float)vc.getLog10PError(); //qualToByte(vc.getPhredScaledQual());
-        info = infoFieldString(vc, GCFHeaderBuilder);
-        filterOffset = GCFHeaderBuilder.encodeString(StandardVCFWriter.getFilterString(vc));
-
-        if ( ! skipGenotypes ) {
-            genotypes = encodeGenotypes(GCFHeaderBuilder, vc);
-        }
-    }
-
-    public GCF(DataInputStream inputStream, boolean skipGenotypes) throws IOException, EOFException {
-        chromOffset = inputStream.readInt();
-
-        // have we reached the footer?
-        if ( chromOffset == GCFHeader.FOOTER_START_MARKER )
-            throw new EOFException();
-
-        start = inputStream.readInt();
-        stop = inputStream.readInt();
-        id = inputStream.readUTF();
-        refPad = inputStream.readByte();
-        alleleOffsets = readIntArray(inputStream);
-        qual = inputStream.readFloat();
-        info = inputStream.readUTF();
-        filterOffset = inputStream.readInt();
-
-        int nGenotypes = inputStream.readInt();
-        int sizeOfGenotypes = inputStream.readInt();
-        if ( skipGenotypes ) {
-            genotypes = Collections.emptyList();
-            inputStream.skipBytes(sizeOfGenotypes);
-        } else {
-            genotypes = new ArrayList<GCFGenotype>(nGenotypes);
-            for ( int i = 0; i < nGenotypes; i++ )
-                genotypes.add(new GCFGenotype(this, inputStream));
-        }
-
-        int recordDone = inputStream.readInt();
-        if ( recordDone != RECORD_TERMINATOR )
-            throw new UserException.MalformedFile("Record not terminated by RECORD_TERMINATOR key");
-    }
-
-    public int write(DataOutputStream outputStream) throws IOException {
-        int startSize = outputStream.size();
-        outputStream.writeInt(chromOffset);
-        outputStream.writeInt(start);
-        outputStream.writeInt(stop);
-        outputStream.writeUTF(id);
-        outputStream.writeByte(refPad);
-        writeIntArray(alleleOffsets, outputStream, true);
-        outputStream.writeFloat(qual);
-        outputStream.writeUTF(info);
-        outputStream.writeInt(filterOffset);
-
-        int nGenotypes = genotypes.size();
-        int expectedSizeOfGenotypes = nGenotypes == 0 ? 0 : genotypes.get(0).sizeInBytes() * nGenotypes;
-        outputStream.writeInt(nGenotypes);
-        outputStream.writeInt(expectedSizeOfGenotypes);
-        int obsSizeOfGenotypes = 0;
-        for ( GCFGenotype g : genotypes )
-            obsSizeOfGenotypes += g.write(outputStream);
-        if ( obsSizeOfGenotypes != expectedSizeOfGenotypes )
-            throw new RuntimeException("Expect and observed genotype sizes disagree! expect = " + expectedSizeOfGenotypes + " obs =" + obsSizeOfGenotypes);
-
-        outputStream.writeInt(RECORD_TERMINATOR);
-        return outputStream.size() - startSize;
-    }
-
-    public VariantContext decode(final String source, final GCFHeader header) {
-        final String contig = header.getString(chromOffset);
-        alleleMap = header.getAlleles(alleleOffsets);
-
-        VariantContextBuilder builder = new VariantContextBuilder(source, contig, start, stop, alleleMap);
-        builder.genotypes(decodeGenotypes(header));
-        builder.log10PError(qual);
-        builder.filters(header.getFilters(filterOffset));
-        builder.attribute("INFO", info);
-        builder.referenceBaseForIndel(refPad == 0 ? null : refPad);
-        return builder.make();
-    }
-
-    private GenotypesContext decodeGenotypes(final GCFHeader header) {
-        if ( genotypes.isEmpty() )
-            return VariantContext.NO_GENOTYPES;
-        else {
-            GenotypesContext map = GenotypesContext.create(genotypes.size());
-
-            for ( int i = 0; i < genotypes.size(); i++ ) {
-                final String sampleName = header.getSample(i);
-                final Genotype g = genotypes.get(i).decode(sampleName, header, this, alleleMap);
-                map.add(g);
-            }
-
-            return map;
-        }
-    }
-
-    private List<GCFGenotype> encodeGenotypes(final GCFHeaderBuilder GCFHeaderBuilder, final VariantContext vc) {
-        int nGenotypes = vc.getNSamples();
-        if ( nGenotypes > 0 ) {
-            List<GCFGenotype> genotypes = new ArrayList<GCFGenotype>(nGenotypes);
-            for ( int i = 0; i < nGenotypes; i++ ) genotypes.add(null);
-
-            for ( Genotype g : vc.getGenotypes() ) {
-                int i = GCFHeaderBuilder.encodeSample(g.getSampleName());
-                genotypes.set(i, new GCFGenotype(GCFHeaderBuilder, alleleMap, g));
-            }
-
-            return genotypes;
-        } else {
-            return Collections.emptyList();
-        }
-    }
-
-    public int getNAlleles() { return alleleOffsets.length; }
-
-
-    private final String infoFieldString(VariantContext vc, final GCFHeaderBuilder GCFHeaderBuilder) {
-        StringBuilder s = new StringBuilder();
-
-        boolean first = true;
-        for ( Map.Entry<String, Object> field : vc.getAttributes().entrySet() ) {
-            String key = field.getKey();
-            int stringIndex = GCFHeaderBuilder.encodeString(key);
-            String outputValue = StandardVCFWriter.formatVCFField(field.getValue());
-            if ( outputValue != null ) {
-                if ( ! first ) s.append(";");
-                s.append(stringIndex).append("=").append(outputValue);
-                first = false;
-            }
-        }
-
-        return s.toString();
-    }
-
-    protected final static int BUFFER_SIZE = 1048576; // 2**20
-
-    public static DataInputStream createDataInputStream(final InputStream stream) {
-        return new DataInputStream(new BufferedInputStream(stream, BUFFER_SIZE));
-    }
-
-    public static FileInputStream createFileInputStream(final File file) throws FileNotFoundException {
-        return new FileInputStream(file);
-    }
-
-    protected final static int[] readIntArray(final DataInputStream inputStream) throws IOException {
-        return readIntArray(inputStream, inputStream.readInt());
-    }
-
-    protected final static int[] readIntArray(final DataInputStream inputStream, int size) throws IOException {
-        int[] array = new int[size];
-        for ( int i = 0; i < array.length; i++ )
-            array[i] = inputStream.readInt();
-        return array;
-    }
-
-    protected final static void writeIntArray(int[] array, final DataOutputStream outputStream, boolean writeSize) throws IOException {
-        if ( writeSize ) outputStream.writeInt(array.length);
-        for ( int i : array )
-            outputStream.writeInt(i);
-    }
-
-    protected final static byte[] readByteArray(final DataInputStream inputStream) throws IOException {
-        return readByteArray(inputStream, inputStream.readInt());
-    }
-
-    protected final static byte[] readByteArray(final DataInputStream inputStream, int size) throws IOException {
-        byte[] array = new byte[size];
-        for ( int i = 0; i < array.length; i++ )
-            array[i] = inputStream.readByte();
-        return array;
-    }
-
-    protected final static void writeByteArray(byte[] array, final DataOutputStream outputStream, boolean writeSize) throws IOException {
-        if ( writeSize ) outputStream.writeInt(array.length);
-        for ( byte i : array )
-            outputStream.writeByte(i);
-    }
-
-    protected final static byte qualToByte(double phredScaledQual) {
-        return (byte)Math.round(Math.min(phredScaledQual, 255));
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/gcf/GCFGenotype.java b/public/java/src/org/broadinstitute/sting/utils/gcf/GCFGenotype.java
deleted file mode 100644
index f8fdd9291..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/gcf/GCFGenotype.java
+++ /dev/null
@@ -1,147 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.gcf;
-
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-
-import java.io.DataInputStream;
-import java.io.DataOutputStream;
-import java.io.IOException;
-import java.util.*;
-
-/**
- * GATK binary VCF record
- *
- * @author Your Name
- * @since Date created
- */
-public class GCFGenotype {
-    private byte gq;
-    private int gt;
-    private int dp;
-    private int ad[];
-    private byte[] pl;
-
-    // todo -- what to do about phasing?  Perhaps we shouldn't support it
-    // todo -- is the FL field generic or just a flag?  Should we even support per sample filtering?
-
-    public GCFGenotype(final GCFHeaderBuilder GCFHeaderBuilder, final List<Allele> allAlleles, Genotype genotype) {
-        gq = GCF.qualToByte(genotype.getPhredScaledQual());
-        gt = encodeAlleles(genotype.getAlleles(), allAlleles);
-
-        dp = genotype.getAttributeAsInt("DP", 0);
-
-        int nAlleles = allAlleles.size();
-        ad = new int[nAlleles];
-
-        int npls = nAllelesToNPls(nAlleles);
-        pl = new byte[npls];
-    }
-
-    private int nAllelesToNPls( int nAlleles ) {
-        return nAlleles*(nAlleles+1) / 2;
-    }
-
-    public GCFGenotype(GCF GCF, DataInputStream inputStream) throws IOException {
-        int gqInt = inputStream.readUnsignedByte();
-        gq = (byte)gqInt;
-        gt = inputStream.readInt();
-        dp = inputStream.readInt();
-        ad = GCF.readIntArray(inputStream, GCF.getNAlleles());
-        pl = GCF.readByteArray(inputStream, nAllelesToNPls(GCF.getNAlleles()));
-    }
-
-    // 2 alleles => 1 + 8 + 8 + 3 => 20
-    protected int sizeInBytes() {
-        return 1 // gq
-                + 4 * 2 // gt + dp
-                + 4 * ad.length // ad
-                + 1 * pl.length; // pl
-    }
-
-    public Genotype decode(final String sampleName, final GCFHeader header, GCF GCF, List<Allele> alleleIndex) {
-        final List<Allele> alleles = decodeAlleles(gt, alleleIndex);
-        final double log10PError = gq / -10.0;
-        final Set<String> filters = Collections.emptySet();
-        final Map<String, Object> attributes = new HashMap<String, Object>();
-        attributes.put("DP", dp);
-        attributes.put("AD", ad);
-        attributes.put("PL", pl);
-
-        return new Genotype(sampleName, alleles, log10PError, filters, attributes, false);
-    }
-
-    private static int encodeAlleles(List<Allele> gtList, List<Allele> allAlleles) {
-        final int nAlleles = gtList.size();
-        if ( nAlleles  > 4 )
-            throw new IllegalArgumentException("encodeAlleles doesn't support more than 4 alt alleles, but I saw " + gtList);
-
-        int gtInt = 0;
-        for ( int i = 0; i < nAlleles ; i++ ) {
-            final int bitOffset = i * 8;
-            final int allelei = getAlleleIndex(gtList.get(i), allAlleles);
-            final int gti = (allelei + 1) << bitOffset;
-            gtInt = gtInt | gti;
-        }
-
-        return gtInt;
-    }
-
-    private static int getAlleleIndex(Allele q, List<Allele> allAlleles) {
-        if ( q.isNoCall() )
-            return 254;
-        for ( int i = 0; i < allAlleles.size(); i++ )
-            if ( q.equals(allAlleles.get(i)) )
-                return i;
-        throw new IllegalStateException("getAlleleIndex passed allele not in map! allele " + q + " allAlleles " + allAlleles);
-    }
-
-    private static List<Allele> decodeAlleles(int gtInt, List<Allele> alleleIndex) {
-        List<Allele> alleles = new ArrayList<Allele>(4);
-
-        for ( int i = 0; i < 32; i += 8 ) {
-            final int gi = (gtInt & (0x000000FF << i)) >> i;
-            if ( gi != 0 ) {
-                final int allelei = gi - 1;
-                alleles.add( allelei == 254 ? Allele.NO_CALL : alleleIndex.get(allelei) );
-            } else {
-                break;
-            }
-        }
-
-        return alleles;
-    }
-
-    public int write(DataOutputStream outputStream) throws IOException {
-        int startSize = outputStream.size();
-        outputStream.writeByte(gq);
-        outputStream.writeInt(gt);
-        outputStream.writeInt(dp);
-        GCF.writeIntArray(ad, outputStream, false);
-        GCF.writeByteArray(pl, outputStream, false);
-        return outputStream.size() - startSize;
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeader.java b/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeader.java
deleted file mode 100644
index 6d96eda56..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeader.java
+++ /dev/null
@@ -1,205 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.gcf;
-
-import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-
-import java.io.*;
-import java.util.*;
-
-/**
- * [Short one sentence description of this walker]
- * <p/>
- * <p>
- * [Functionality of this walker]
- * </p>
- * <p/>
- * <h2>Input</h2>
- * <p>
- * [Input description]
- * </p>
- * <p/>
- * <h2>Output</h2>
- * <p>
- * [Output description]
- * </p>
- * <p/>
- * <h2>Examples</h2>
- * <pre>
- *    java
- *      -jar GenomeAnalysisTK.jar
- *      -T $WalkerName
- *  </pre>
- *
- * @author Your Name
- * @since Date created
- */
-public class GCFHeader {
-    final protected static Logger logger = Logger.getLogger(GCFHeader.class);
-
-    public final static int GCF_VERSION = 1;
-    public final static byte[] GCF_FILE_START_MARKER = "GCF\1".getBytes();
-    public final static int FOOTER_START_MARKER = -1;
-    public final static long HEADER_FORWARD_REFERENCE_OFFSET = GCF_FILE_START_MARKER.length + 4; // for the version
-
-    final int version;
-    long footerPosition;
-    final List<Allele> alleles;
-    final List<String> strings;
-    final List<String> samples;
-    final List<Set<String>> filters;
-
-    public GCFHeader(final Map<Allele, Integer> allelesIn, final Map<String, Integer> stringIn, final Map<String, Integer> samplesIn) {
-        version = GCF_VERSION;
-        footerPosition = 0;
-        this.alleles = linearize(allelesIn);
-        this.strings = linearize(stringIn);
-        this.samples = linearize(samplesIn);
-        this.filters = null; // not used with this constructor
-    }
-
-    public GCFHeader(FileInputStream fileInputStream) throws IOException {
-        DataInputStream inputStream = new DataInputStream(fileInputStream);
-        byte[] headerTest = new byte[GCF_FILE_START_MARKER.length];
-        inputStream.read(headerTest);
-        if ( ! Arrays.equals(headerTest, GCF_FILE_START_MARKER) ) {
-            throw new UserException("Could not read GVCF file.  GCF_FILE_START_MARKER missing.  Saw " + new String(headerTest));
-        } else {
-            version = inputStream.readInt();
-            logger.info("Read GCF version " + version);
-            footerPosition = inputStream.readLong();
-            logger.info("Read footer position of " + footerPosition);
-            long lastPos = fileInputStream.getChannel().position();
-            logger.info("  Last position is " + lastPos);
-
-            // seek to the footer
-            fileInputStream.getChannel().position(footerPosition);
-            if ( inputStream.readInt() != FOOTER_START_MARKER )
-                throw new UserException.MalformedFile("Malformed GCF file: couldn't find the footer marker");
-            alleles = stringsToAlleles(readStrings(inputStream));
-            strings = readStrings(inputStream);
-            samples = readStrings(inputStream);
-            logger.info(String.format("Allele map of %d elements", alleles.size()));
-            logger.info(String.format("String map of %d elements", strings.size()));
-            logger.info(String.format("Sample map of %d elements", samples.size()));
-            filters = initializeFilterCache();
-            fileInputStream.getChannel().position(lastPos);
-        }
-    }
-
-    public static int writeHeader(final DataOutputStream outputStream) throws IOException {
-        int startBytes = outputStream.size();
-        outputStream.write(GCF_FILE_START_MARKER);
-        outputStream.writeInt(GCF_VERSION);
-        outputStream.writeLong(0);
-        return outputStream.size() - startBytes;
-    }
-
-    public int writeFooter(final DataOutputStream outputStream) throws IOException {
-        int startBytes = outputStream.size();
-        outputStream.writeInt(FOOTER_START_MARKER); // has to be the same as chrom encoding
-        write(outputStream, allelesToStrings(alleles));
-        write(outputStream, strings);
-        write(outputStream, samples);
-        return outputStream.size() - startBytes;
-    }
-
-    private void write(DataOutputStream outputStream, List<String> l) throws IOException {
-        outputStream.writeInt(l.size());
-        for ( String elt : l ) outputStream.writeUTF(elt);
-    }
-
-    private List<String> allelesToStrings(List<Allele> alleles) {
-        List<String> strings = new ArrayList<String>(alleles.size());
-        for ( Allele allele : alleles ) strings.add(allele.toString());
-        return strings;
-    }
-
-    private List<Set<String>> initializeFilterCache() {
-        // required to allow offset -> set lookup
-        List<Set<String>> l = new ArrayList<Set<String>>(strings.size());
-        for ( int i = 0; i < strings.size(); i++ ) l.add(null);
-        return l;
-    }
-
-    private static List<Allele> stringsToAlleles(final List<String> strings) {
-        final List<Allele> alleles = new ArrayList<Allele>(strings.size());
-        for ( String string : strings ) {
-            boolean isRef = string.endsWith("*");
-            if ( isRef ) string = string.substring(0, string.length() - 1);
-            alleles.add(Allele.create(string, isRef));
-        }
-        return alleles;
-    }
-
-    private static List<String> readStrings(final DataInputStream inputStream) throws IOException {
-        final int nStrings = inputStream.readInt();
-
-        final List<String> strings = new ArrayList<String>(nStrings);
-        for ( int i = 0; i < nStrings; i++ ) {
-            strings.add(inputStream.readUTF());
-        }
-
-        return strings;
-    }
-
-    private static <T> List<T> linearize(final Map<T, Integer> map) {
-        final ArrayList<T> l = new ArrayList<T>(map.size());
-        for ( int i = 0; i < map.size(); i++ ) l.add(null);
-        for ( final Map.Entry<T, Integer> elt : map.entrySet() )
-            l.set(elt.getValue(), elt.getKey());
-        return l;
-    }
-
-    public String getSample(final int offset) { return samples.get(offset); }
-    public String getString(final int offset) { return strings.get(offset); }
-    public Allele getAllele(final int offset) { return alleles.get(offset); }
-    public List<Allele> getAlleles(final int[] offsets) {
-        final List<Allele> alleles = new ArrayList<Allele>(offsets.length);
-        for ( int i : offsets ) alleles.add(getAllele(i));
-        return alleles;
-    }
-
-    public Set<String> getFilters(final int offset) {
-        Set<String> cached = filters.get(offset);
-
-        if ( cached != null )
-            return cached;
-        else {
-            final String filterString = getString(offset);
-            if ( filterString.equals(VCFConstants.UNFILTERED) )
-                return null; // UNFILTERED records are represented by null
-            else {
-                Set<String> set = VCFCodec.parseFilters(null, -1, filterString);
-                filters.set(offset, set); // remember the result
-                return set;
-            }
-        }
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeaderBuilder.java b/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeaderBuilder.java
deleted file mode 100644
index 40e01ec72..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeaderBuilder.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.gcf;
-
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * [Short one sentence description of this walker]
- * <p/>
- * <p>
- * [Functionality of this walker]
- * </p>
- * <p/>
- * <h2>Input</h2>
- * <p>
- * [Input description]
- * </p>
- * <p/>
- * <h2>Output</h2>
- * <p>
- * [Output description]
- * </p>
- * <p/>
- * <h2>Examples</h2>
- * <pre>
- *    java
- *      -jar GenomeAnalysisTK.jar
- *      -T $WalkerName
- *  </pre>
- *
- * @author Your Name
- * @since Date created
- */
-public class GCFHeaderBuilder {
-    Map<Allele, Integer> alleles = new HashMap<Allele, Integer>();
-    Map<String, Integer> strings = new HashMap<String, Integer>();
-    Map<String, Integer> samples = new HashMap<String, Integer>();
-
-    public GCFHeader createHeader() {
-        return new GCFHeader(alleles, strings, samples);
-    }
-
-    public int encodeString(final String chr)    { return encode(strings, chr); }
-    public int encodeAllele(final Allele allele) { return encode(alleles, allele); }
-    public int encodeSample(final String sampleName) { return encode(samples, sampleName); }
-
-    private <T> int encode(Map<T, Integer> map, T key) {
-        Integer v = map.get(key);
-        if ( v == null ) {
-            v = map.size();
-            map.put(key, v);
-        }
-        return v;
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/gcf/GCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/gcf/GCFWriter.java
deleted file mode 100644
index 18fae18c4..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/gcf/GCFWriter.java
+++ /dev/null
@@ -1,123 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.gcf;
-
-import net.sf.samtools.SAMSequenceDictionary;
-import org.broadinstitute.sting.utils.codecs.vcf.IndexingVCFWriter;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-
-import java.io.*;
-
-/**
- * GCFWriter implementing the VCFWriter interface
- * @author Your Name
- * @since Date created
- */
-public class GCFWriter extends IndexingVCFWriter {
-    final boolean skipGenotypes;
-    final FileOutputStream fileOutputStream;
-    final DataOutputStream dataOutputStream;
-    final GCFHeaderBuilder gcfHeaderBuilder;
-    int nbytes = 0;
-    VCFHeader header = null;
-    File location;
-
-    // --------------------------------------------------------------------------------
-    //
-    // Constructors
-    //
-    // --------------------------------------------------------------------------------
-
-    public GCFWriter(final File location, final SAMSequenceDictionary refDict, boolean enableOnTheFlyIndexing, boolean doNotWriteGenotypes) {
-        super(writerName(location, null), location, null, refDict, enableOnTheFlyIndexing);
-        this.location = location;
-        this.skipGenotypes = doNotWriteGenotypes;
-
-        // write the output
-        try {
-            fileOutputStream = new FileOutputStream(location);
-            dataOutputStream = createDataOutputStream(fileOutputStream);
-            gcfHeaderBuilder = new GCFHeaderBuilder();
-        } catch ( FileNotFoundException e ) {
-            throw new UserException.CouldNotCreateOutputFile(location, e);
-        }
-    }
-
-    // --------------------------------------------------------------------------------
-    //
-    // VCFWriter interface functions
-    //
-    // --------------------------------------------------------------------------------
-
-    @Override
-    public void writeHeader(VCFHeader header) {
-        this.header = header;
-        try {
-            nbytes += GCFHeader.writeHeader(dataOutputStream);
-        } catch ( IOException e ) {
-            throw new UserException.CouldNotCreateOutputFile(getStreamName(), "Couldn't write header", e);
-        }
-    }
-
-    @Override
-    public void add(VariantContext vc) {
-        super.add(vc);
-        GCF gcf = new GCF(gcfHeaderBuilder, vc, skipGenotypes);
-        try {
-            nbytes += gcf.write(dataOutputStream);
-        } catch ( IOException e ) {
-            throw new UserException.CouldNotCreateOutputFile(getStreamName(), "Failed to add gcf record " + gcf + " to stream " + getStreamName(), e);
-        }
-    }
-
-    @Override
-    public void close() {
-        // todo -- write out VCF header lines
-        GCFHeader gcfHeader = gcfHeaderBuilder.createHeader();
-        try {
-            long headerPosition = nbytes;
-            nbytes += gcfHeader.writeFooter(dataOutputStream);
-            dataOutputStream.close();
-            //System.out.println("Writing forward reference to " + headerPosition);
-
-            RandomAccessFile raFile = new RandomAccessFile(location, "rw");
-            raFile.seek(GCFHeader.HEADER_FORWARD_REFERENCE_OFFSET);
-            raFile.writeLong(headerPosition);
-            raFile.close();
-        } catch ( IOException e ) {
-            throw new ReviewedStingException("Failed to close GCFWriter " + getStreamName(), e);
-        }
-
-        super.close();
-    }
-
-    private static final DataOutputStream createDataOutputStream(final OutputStream stream) {
-        return new DataOutputStream(new BufferedOutputStream(stream, GCF.BUFFER_SIZE));
-    }
-
-}