From c3a933ce84a963b46b70f73888b0918984fcdb49 Mon Sep 17 00:00:00 2001
From: Michael McCowan <mccowan@broadinstitute.org>
Date: Mon, 19 Aug 2013 12:42:28 -0400
Subject: [PATCH] Adaptations to accomodate Tribble API changes, comprising
 mostly of the following. * Refactoring implementations of
 readHeader(LineReader) -> readActualHeader(LineIterator), including nullary
 implementations where applicable. * Galvanizing fo generic types. * Test
 fixups, mostly to pass around LineIterators instead of LineReaders. * New rev
 of tribble, which incorporates a fix that addresses a problem with
 TribbleIndexedFeatureReader reading a header twice in some instances. * New
 rev of sam, to make AbstractIterator visible (was moved from picard -> sam in
 Tribble API refactor).

---
 .../HaplotypeCallerIntegrationTest.java       |   8 +--
 .../variantutils/CombineVariantsUnitTest.java |  15 +++--
 .../ConcordanceMetricsUnitTest.java           |  60 ++++++++----------
 .../storage/VariantContextWriterStorage.java  |  16 ++---
 .../utils/codecs/beagle/BeagleCodec.java      |  13 ++--
 .../utils/codecs/hapmap/RawHapMapCodec.java   |  20 +++---
 .../utils/codecs/refseq/RefSeqCodec.java      |  10 ++-
 .../codecs/sampileup/SAMPileupCodec.java      |   8 ++-
 .../utils/codecs/samread/SAMReadCodec.java    |   8 ++-
 .../sting/utils/codecs/table/TableCodec.java  |  43 ++++++-------
 .../sting/utils/variant/GATKVCFUtils.java     |  57 +++++++----------
 .../org/broadinstitute/sting/BaseTest.java    |   6 +-
 .../gatk/EngineFeaturesIntegrationTest.java   |   9 ++-
 .../gatk/refdata/utils/TestFeatureReader.java |   2 +-
 .../BandPassActivityProfileUnitTest.java      |   8 ++-
 .../utils/codecs/hapmap/HapMapUnitTest.java   |  39 ++++++------
 .../variant/VariantContextBenchmark.java      |   4 +-
 .../sting/queue/util/VCF_BAM_utilities.scala  |   6 +-
 settings/repository/net.sf/sam-1.96.1515.xml  |   3 -
 .../{sam-1.96.1515.jar => sam-1.96.1525.jar}  | Bin 623321 -> 636980 bytes
 settings/repository/net.sf/sam-1.96.1525.xml  |   3 +
 ...le-1.96.1525.jar => tribble-1.96.1526.jar} | Bin 301966 -> 302059 bytes
 ...le-1.96.1525.xml => tribble-1.96.1526.xml} |   2 +-
 23 files changed, 173 insertions(+), 167 deletions(-)
 delete mode 100644 settings/repository/net.sf/sam-1.96.1515.xml
 rename settings/repository/net.sf/{sam-1.96.1515.jar => sam-1.96.1525.jar} (94%)
 mode change 100644 => 100755
 create mode 100644 settings/repository/net.sf/sam-1.96.1525.xml
 rename settings/repository/org.broad/{tribble-1.96.1525.jar => tribble-1.96.1526.jar} (93%)
 rename settings/repository/org.broad/{tribble-1.96.1525.xml => tribble-1.96.1526.xml} (76%)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index e3f7bd706..e216a8af2 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -47,7 +47,7 @@
 package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
 import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broad.tribble.readers.AsciiLineReader;
+import org.broad.tribble.readers.LineIterator;
 import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -190,9 +190,9 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         // confirm that the call is the correct one
         final VCFCodec codec = new VCFCodec();
         final FileInputStream s = new FileInputStream(outputVCF);
-        final AsciiLineReader lineReader = new AsciiLineReader(new PositionalBufferedStream(s));
-        codec.readHeader(lineReader);
-        final String line = lineReader.readLine();
+        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
+        codec.readHeader(lineIterator);
+        final String line = lineIterator.next();
         Assert.assertFalse(line == null);
         final VariantContext vc = codec.decode(line);
         Assert.assertTrue(vc.isBiallelic());
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java
index 6d38940bc..f369ad210 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java
@@ -46,16 +46,20 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.variant.vcf.*;
+import org.broadinstitute.variant.vcf.VCFCodec;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.broadinstitute.variant.vcf.VCFUtils;
 import org.testng.Assert;
-
 import org.testng.annotations.Test;
 
 import java.io.StringBufferInputStream;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
 
 /**
  * test out pieces of the combine variants code
@@ -154,7 +158,8 @@ public class CombineVariantsUnitTest {
 
     private VCFHeader createHeader(String headerStr) {
         VCFCodec codec = new VCFCodec();
-        VCFHeader head = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(headerStr))));
+        VCFHeader head = null;
+        head = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(headerStr))));
         return head;
     }
 
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
index bd9ff4f80..50c896450 100755
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
@@ -46,25 +46,20 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
+import net.sf.picard.reference.ReferenceSequenceFile;
+import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.variant.variantcontext.Allele;
-import org.broadinstitute.variant.variantcontext.Genotype;
-import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
-import org.broadinstitute.variant.variantcontext.GenotypeType;
-import org.broadinstitute.variant.variantcontext.VariantContext;
-import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.*;
 import org.broadinstitute.variant.vcf.VCFCodec;
 import org.broadinstitute.variant.vcf.VCFHeader;
-import org.testng.annotations.Test;
-import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.readers.PositionalBufferedStream;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -72,7 +67,6 @@ import java.io.StringBufferInputStream;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import net.sf.picard.reference.ReferenceSequenceFile;
 
 public class ConcordanceMetricsUnitTest extends BaseTest {
 
@@ -139,8 +133,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VariantContext eval = data.getFirst();
         VariantContext truth = data.getSecond();
         VCFCodec codec = new VCFCodec();
-        VCFHeader evalHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        VCFHeader compHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
         metrics.update(eval,truth);
         Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
@@ -189,8 +183,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VariantContext eval = data.getFirst();
         VariantContext truth = data.getSecond();
         VCFCodec codec = new VCFCodec();
-        VCFHeader evalHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        VCFHeader compHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
         metrics.update(eval,truth);
         Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
@@ -209,8 +203,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         eval = data.getSecond();
         truth = data.getFirst();
         codec = new VCFCodec();
-        evalHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        compHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         metrics = new ConcordanceMetrics(evalHeader,compHeader);
         metrics.update(eval,truth);
         Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
@@ -264,8 +258,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VariantContext eval = data.getFirst();
         VariantContext truth = data.getSecond();
         VCFCodec codec = new VCFCodec();
-        VCFHeader evalHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        VCFHeader compHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
         metrics.update(eval,truth);
         Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample1").getnMismatchingAlt(),1);
@@ -317,8 +311,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VariantContext eval = data.getFirst();
         VariantContext truth = data.getSecond();
         VCFCodec codec = new VCFCodec();
-        VCFHeader evalHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        VCFHeader compHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
         metrics.update(eval,truth);
         Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),0);
@@ -366,8 +360,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VariantContext eval = data.getFirst();
         VariantContext truth = data.getSecond();
         VCFCodec codec = new VCFCodec();
-        VCFHeader evalHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        VCFHeader compHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
         metrics.update(eval,truth);
         Assert.assertTrue(eval.getGenotype("test1_sample2").getType().equals(GenotypeType.UNAVAILABLE));
@@ -520,8 +514,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         List<Pair<VariantContext,VariantContext>> data = getData6();
 
         VCFCodec codec = new VCFCodec();
-        VCFHeader evalHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
-        VCFHeader compHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
+        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
+        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
         ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
 
         for ( Pair<VariantContext,VariantContext> contextPair : data ) {
@@ -554,8 +548,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
         VariantContext eval = data.getFirst();
         VariantContext truth = data.getSecond();
         VCFCodec codec = new VCFCodec();
-        VCFHeader evalHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
-        VCFHeader compHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
+        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
         ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
         int[][] table = metrics.getOverallGenotypeConcordance().getTable();
         // set up the table
@@ -588,9 +582,9 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
     @Test(enabled=true)
     public void testRobustness() {
         VCFCodec codec = new VCFCodec();
-        VCFHeader evalHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_1))));
-        VCFHeader disjointCompHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_2))));
-        VCFHeader overlapCompHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_3))));
+        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_1))));
+        VCFHeader disjointCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_2))));
+        VCFHeader overlapCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_3))));
         ConcordanceMetrics disjointMetrics = new ConcordanceMetrics(evalHeader,disjointCompHeader);
         ConcordanceMetrics overlapMetrics = new ConcordanceMetrics(evalHeader,overlapCompHeader);
 
@@ -720,8 +714,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testSites() {
         VCFCodec codec = new VCFCodec();
-        VCFHeader evalHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
-        VCFHeader compHeader = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
+        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
+        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
         ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader);
 
         List<Pair<VariantContext,VariantContext>> data = getData7();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
index 80841bae7..e1dc36f5c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
@@ -28,17 +28,18 @@ package org.broadinstitute.sting.gatk.io.storage;
 import net.sf.samtools.util.BlockCompressedOutputStream;
 import org.apache.log4j.Logger;
 import org.broad.tribble.AbstractFeatureReader;
+import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
 import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
-import org.broadinstitute.variant.bcf2.BCF2Utils;
-import org.broadinstitute.variant.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.variant.bcf2.BCF2Utils;
 import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.broadinstitute.variant.variantcontext.writer.Options;
 import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.vcf.VCFHeader;
 
 import java.io.*;
 import java.util.Arrays;
@@ -205,12 +206,11 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
             if ( fd == null )
                 throw new UserException.LocalParallelizationProblem(file);
 
-            final FeatureCodec<VariantContext> codec = fd.getCodec();
-            final AbstractFeatureReader<VariantContext> source =
-                    AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), codec, false);
-            
-            for ( final VariantContext vc : source.iterator() ) {
-                target.writer.add(vc);
+            final FeatureCodec codec = fd.getCodec();
+            final AbstractFeatureReader<Feature, ?> source = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), codec, false);
+
+            for ( final Feature vc : source.iterator() ) {
+                target.writer.add((VariantContext) vc);
             }
 
             source.close();
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
index 6ab3c9a16..4a6becf6f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
@@ -51,9 +51,8 @@ package org.broadinstitute.sting.utils.codecs.beagle;
 
 
 import org.broad.tribble.AsciiFeatureCodec;
-import org.broad.tribble.Feature;
 import org.broad.tribble.exception.CodecLineParsingException;
-import org.broad.tribble.readers.LineReader;
+import org.broad.tribble.readers.LineIterator;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -131,8 +130,8 @@ public class BeagleCodec extends AsciiFeatureCodec<BeagleFeature> implements Ref
         this.genomeLocParser =  genomeLocParser;
     }
 
-    public Object readHeader(LineReader reader)
-    {
+    @Override
+    public Object readActualHeader(LineIterator reader) {
         int[] lineCounter = new int[1];
         try {
             header = readHeader(reader, lineCounter);
@@ -181,14 +180,14 @@ public class BeagleCodec extends AsciiFeatureCodec<BeagleFeature> implements Ref
         return header;
     }
 
-    private static String[] readHeader(final LineReader source, int[] lineCounter) throws IOException {
+    private static String[] readHeader(final LineIterator source, int[] lineCounter) throws IOException {
 
         String[] header = null;
         int numLines = 0;
 
         //find the 1st line that's non-empty and not a comment
-        String line;
-        while( (line = source.readLine()) != null ) {
+        while(source.hasNext()) {
+            final String line = source.next();
             numLines++;
             if ( line.trim().isEmpty() ) {
                 continue;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
index 38ff35c3f..b2b31b572 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
@@ -28,9 +28,7 @@ package org.broadinstitute.sting.utils.codecs.hapmap;
 import org.broad.tribble.AsciiFeatureCodec;
 import org.broad.tribble.FeatureCodecHeader;
 import org.broad.tribble.annotation.Strand;
-import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.readers.LineReader;
-import org.broad.tribble.readers.PositionalBufferedStream;
+import org.broad.tribble.readers.LineIterator;
 
 import java.io.IOException;
 import java.util.Arrays;
@@ -112,18 +110,16 @@ public class RawHapMapCodec extends AsciiFeatureCodec<RawHapMapFeature> {
                 headerLine);
     }
 
-    public Object readHeader(LineReader reader) {
-        try {
-            headerLine = reader.readLine();
-        } catch (IOException e) {
-            throw new IllegalArgumentException("Unable to read a line from the line reader");
-        }
+    @Override
+    public Object readActualHeader(final LineIterator lineIterator) {
+        this.headerLine = lineIterator.next();
         return headerLine;
     }
 
     @Override
-    public FeatureCodecHeader readHeader(final PositionalBufferedStream stream) throws IOException {
-        final AsciiLineReader br = new AsciiLineReader(stream);
-        return new FeatureCodecHeader(readHeader(br), br.getPosition());
+    public FeatureCodecHeader readHeader(final LineIterator lineIterator) throws IOException {
+        final String header = (String) readActualHeader(lineIterator);
+        // TODO: This approach may cause issues with files formatted with \r\n-style line-endings.
+        return new FeatureCodecHeader(header, header.length() + 1);
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
index 82ee76a81..3c2329b8f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
@@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils.codecs.refseq;
 import org.broad.tribble.AsciiFeatureCodec;
 import org.broad.tribble.Feature;
 import org.broad.tribble.TribbleException;
+import org.broad.tribble.readers.LineIterator;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -93,7 +94,8 @@ public class RefSeqCodec extends AsciiFeatureCodec<RefSeqFeature> implements Ref
     }
 
     @Override
-    public Feature decodeLoc(String line) {
+    public Feature decodeLoc(final LineIterator lineIterator) {
+        final String line = lineIterator.next();
         if (line.startsWith("#")) return null;
         String fields[] = line.split("\t");
         if (fields.length < 3) throw new TribbleException("RefSeq (decodeLoc) : Unable to parse line -> " + line + ", we expected at least 3 columns, we saw " + fields.length);
@@ -160,4 +162,10 @@ public class RefSeqCodec extends AsciiFeatureCodec<RefSeqFeature> implements Ref
         feature.setExon_frames(exon_frames);
         return feature;
     }
+
+    @Override
+    public Object readActualHeader(LineIterator lineIterator) {
+        // No header for this format
+        return null;
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java
index 37e44bf8c..34705c4c9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java
@@ -26,8 +26,8 @@
 package org.broadinstitute.sting.utils.codecs.sampileup;
 
 import org.broad.tribble.AsciiFeatureCodec;
-import org.broad.tribble.Feature;
 import org.broad.tribble.exception.CodecLineParsingException;
+import org.broad.tribble.readers.LineIterator;
 import org.broad.tribble.util.ParsingUtils;
 
 import java.util.ArrayList;
@@ -163,6 +163,12 @@ public class SAMPileupCodec extends AsciiFeatureCodec<SAMPileupFeature> {
         return feature;
     }
 
+    @Override
+    public Object readActualHeader(LineIterator lineIterator) {
+        // No header for this format
+        return null;
+    }
+
     private void parseIndels(String genotype,SAMPileupFeature feature) {
         String [] obs = genotype.split("/"); // get observations, now need to tinker with them a bit
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java
index 69127b289..cfc5d2c2d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java
@@ -29,8 +29,8 @@ import net.sf.samtools.Cigar;
 import net.sf.samtools.TextCigarCodec;
 import net.sf.samtools.util.StringUtil;
 import org.broad.tribble.AsciiFeatureCodec;
-import org.broad.tribble.Feature;
 import org.broad.tribble.exception.CodecLineParsingException;
+import org.broad.tribble.readers.LineIterator;
 import org.broad.tribble.util.ParsingUtils;
 
 /**
@@ -114,4 +114,10 @@ public class SAMReadCodec extends AsciiFeatureCodec<SAMReadFeature> {
                                   bases,
                                   qualities);
     }
+
+    @Override
+    public Object readActualHeader(LineIterator lineIterator) {
+        // No header for this format
+        return null;
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
index 9e66056f2..f69001d9d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
@@ -26,14 +26,14 @@
 package org.broadinstitute.sting.utils.codecs.table;
 
 import org.broad.tribble.AsciiFeatureCodec;
-import org.broad.tribble.readers.LineReader;
+import org.broad.tribble.readers.LineIterator;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 
 /**
  * Reads tab deliminated tabular text files
@@ -97,30 +97,29 @@ public class TableCodec extends AsciiFeatureCodec<TableFeature> implements Refer
         String[] split = line.split(delimiterRegex);
         if (split.length < 1)
             throw new IllegalArgumentException("TableCodec line = " + line + " doesn't appear to be a valid table format");
-        return new TableFeature(genomeLocParser.parseGenomeLoc(split[0]),Arrays.asList(split),header);
+        return new TableFeature(genomeLocParser.parseGenomeLoc(split[0]),Arrays.asList(split), header);
     }
 
     @Override
-    public Object readHeader(LineReader reader) {
-        String line = "";
-        try {
-            boolean isFirst = true;
-            while ((line = reader.readLine()) != null) {
-                if ( isFirst && ! line.startsWith(headerDelimiter) && ! line.startsWith(commentDelimiter)) {
-                    throw new UserException.MalformedFile("TableCodec file does not have a header");
-                }
-		isFirst &= line.startsWith(commentDelimiter);
-                if (line.startsWith(headerDelimiter)) {
-                    if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines.  The second is = " + line);
-                    String spl[] = line.split(delimiterRegex);
-                    for (String s : spl) header.add(s);
-                    return header;
-                } else if (!line.startsWith(commentDelimiter)) {
-                    break;
-                }
+    public Object readActualHeader(final LineIterator reader) {
+        boolean isFirst = true;
+        while (reader.hasNext()) {
+            final String line = reader.peek(); // Peek to avoid reading non-header data
+            if ( isFirst && ! line.startsWith(headerDelimiter) && ! line.startsWith(commentDelimiter)) {
+                throw new UserException.MalformedFile("TableCodec file does not have a header");
+            }
+            isFirst &= line.startsWith(commentDelimiter);
+            if (line.startsWith(headerDelimiter)) {
+                reader.next(); // "Commit" the peek
+                if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines.  The second is = " + line);
+                final String spl[] = line.split(delimiterRegex);
+                Collections.addAll(header, spl);
+                return header;
+            } else if (line.startsWith(commentDelimiter)) {
+                reader.next(); // "Commit" the peek
+            } else {
+                break;
             }
-        } catch (IOException e) {
-            throw new UserException.MalformedFile("unable to parse header from TableCodec file",e);
         }
         return header;
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
index 09db585a6..49200911b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
@@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils.variant;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.FeatureCodecHeader;
+import org.broad.tribble.readers.LineIterator;
 import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
@@ -177,31 +178,26 @@ public class GATKVCFUtils {
     /**
      * Utility class to read all of the VC records from a file
      *
-     * @param source
+     * @param file
      * @param codec
      * @return
      * @throws IOException
      */
-    public final static Pair<VCFHeader, VCIterable> readAllVCs( final File source, final FeatureCodec<VariantContext> codec ) throws IOException {
+    public final static <SOURCE> Pair<VCFHeader, VCIterable<SOURCE>> readAllVCs( final File file, final FeatureCodec<VariantContext, SOURCE> codec) throws IOException {
         // read in the features
-        PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source));
-        FeatureCodecHeader header = codec.readHeader(pbs);
-        pbs.close();
-
-        pbs = new PositionalBufferedStream(new FileInputStream(source));
-        pbs.skip(header.getHeaderEnd());
-
+        SOURCE source = codec.makeSourceFromStream(new FileInputStream(file));
+        FeatureCodecHeader header = codec.readHeader(source);
         final VCFHeader vcfHeader = (VCFHeader)header.getHeaderValue();
-        return new Pair<VCFHeader, VCIterable>(vcfHeader, new VCIterable(pbs, codec, vcfHeader));
+        return new Pair<>(vcfHeader, new VCIterable<>(source, codec, vcfHeader));
     }
 
-    public static class VCIterable implements Iterable<VariantContext>, Iterator<VariantContext> {
-        final PositionalBufferedStream pbs;
-        final FeatureCodec<VariantContext> codec;
+    public static class VCIterable<SOURCE> implements Iterable<VariantContext>, Iterator<VariantContext> {
+        final SOURCE source;
+        final FeatureCodec<VariantContext, SOURCE> codec;
         final VCFHeader header;
 
-        private VCIterable(final PositionalBufferedStream pbs, final FeatureCodec<VariantContext> codec, final VCFHeader header) {
-            this.pbs = pbs;
+        private VCIterable(final SOURCE source, final FeatureCodec<VariantContext, SOURCE> codec, final VCFHeader header) {
+            this.source = source;
             this.codec = codec;
             this.header = header;
         }
@@ -213,17 +209,13 @@ public class GATKVCFUtils {
 
         @Override
         public boolean hasNext() {
-            try {
-                return ! pbs.isDone();
-            } catch ( IOException e ) {
-                throw new RuntimeException(e);
-            }
+            return ! codec.isDone(source);
         }
 
         @Override
         public VariantContext next() {
             try {
-                final VariantContext vc = codec.decode(pbs);
+                final VariantContext vc = codec.decode(source);
                 return vc == null ? null : vc.fullyDecode(header, false);
             } catch ( IOException e ) {
                 throw new RuntimeException(e);
@@ -249,20 +241,19 @@ public class GATKVCFUtils {
         final List<VariantContext> vcs = new ArrayList<VariantContext>();
         final VCFCodec codec = new VCFCodec();
         PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source));
-        FeatureCodecHeader header = codec.readHeader(pbs);
-        pbs.close();
+        final LineIterator vcfSource = codec.makeSourceFromStream(pbs);
+        try {
+            final VCFHeader vcfHeader = (VCFHeader) codec.readActualHeader(vcfSource);
 
-        pbs = new PositionalBufferedStream(new FileInputStream(source));
-        pbs.skip(header.getHeaderEnd());
+            while (vcfSource.hasNext()) {
+                final VariantContext vc = codec.decode(vcfSource);
+                if ( vc != null )
+                    vcs.add(vc);
+            }
 
-        final VCFHeader vcfHeader = (VCFHeader)header.getHeaderValue();
-
-        while ( ! pbs.isDone() ) {
-            final VariantContext vc = codec.decode(pbs);
-            if ( vc != null )
-                vcs.add(vc);
+            return new Pair<VCFHeader, List<VariantContext>>(vcfHeader, vcs);
+        } finally {
+            codec.close(vcfSource);
         }
-
-        return new Pair<VCFHeader, List<VariantContext>>(vcfHeader, vcs);
     }
 }
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java
index 5efe2dfc3..9d23062c0 100644
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -30,6 +30,8 @@ import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.apache.log4j.PatternLayout;
 import org.apache.log4j.spi.LoggingEvent;
+import org.broad.tribble.readers.LineIterator;
+import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.commandline.CommandLineUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.crypt.CryptUtils;
@@ -450,8 +452,8 @@ public abstract class BaseTest {
     }
 
     public static void assertVCFandBCFFilesAreTheSame(final File vcfFile, final File bcfFile) throws IOException {
-        final Pair<VCFHeader, GATKVCFUtils.VCIterable> vcfData = GATKVCFUtils.readAllVCs(vcfFile, new VCFCodec());
-        final Pair<VCFHeader, GATKVCFUtils.VCIterable> bcfData = GATKVCFUtils.readAllVCs(bcfFile, new BCF2Codec());
+        final Pair<VCFHeader, GATKVCFUtils.VCIterable<LineIterator>> vcfData = GATKVCFUtils.readAllVCs(vcfFile, new VCFCodec());
+        final Pair<VCFHeader, GATKVCFUtils.VCIterable<PositionalBufferedStream>> bcfData = GATKVCFUtils.readAllVCs(bcfFile, new BCF2Codec());
         assertVCFHeadersAreEqual(bcfData.getFirst(), vcfData.getFirst());
         assertVariantContextStreamsAreEqual(bcfData.getSecond(), vcfData.getSecond());
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
index c65d62149..f1839e6ac 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
@@ -28,11 +28,9 @@ package org.broadinstitute.sting.gatk;
 import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
-import org.broad.tribble.readers.AsciiLineReader;
 import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -48,7 +46,6 @@ import org.broadinstitute.variant.vcf.VCFCodec;
 import org.broadinstitute.variant.vcf.VCFHeader;
 import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.testng.Assert;
-import org.testng.TestException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -218,7 +215,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
                 1, Arrays.asList(""));
         spec.disableShadowBCF();
         final File vcf = executeTest("testGATKVersionInVCF", spec).first.get(0);
-        final VCFHeader header = (VCFHeader)new VCFCodec().readHeader(new AsciiLineReader(new FileInputStream(vcf)));
+        final VCFCodec codec = new VCFCodec();
+        final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(vcf)));
         final VCFHeaderLine versionLine = header.getMetaDataLine(GATKVCFUtils.GATK_COMMAND_LINE_KEY);
         Assert.assertNotNull(versionLine);
         Assert.assertTrue(versionLine.toString().contains("SelectVariants"));
@@ -232,7 +230,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
                 1, Arrays.asList(""));
         spec.disableShadowBCF();
         final File vcf = executeTest("testMultipleGATKVersionsInVCF", spec).first.get(0);
-        final VCFHeader header = (VCFHeader)new VCFCodec().readHeader(new AsciiLineReader(new FileInputStream(vcf)));
+        final VCFCodec codec = new VCFCodec();
+        final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(vcf)));
 
         boolean foundHC = false;
         boolean foundSV = false;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java
index adcc21291..988355813 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java
@@ -34,7 +34,7 @@ import java.io.IOException;
 /**
  * Feature reader with additional test utilities. The iterators can be checked to see if they are closed.
  */
-public class TestFeatureReader extends TribbleIndexedFeatureReader<Feature> {
+public class TestFeatureReader extends TribbleIndexedFeatureReader<Feature, Object> {
     public TestFeatureReader(String featurePath, FeatureCodec codec) throws IOException {
         super(featurePath, codec, true);
     }
diff --git a/public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java
index 2470364c4..fb238ef54 100644
--- a/public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java
@@ -31,6 +31,7 @@ package org.broadinstitute.sting.utils.activeregion;
 
 import net.sf.picard.reference.ReferenceSequenceFile;
 import org.apache.commons.lang.ArrayUtils;
+import org.broad.tribble.readers.LineIterator;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -48,7 +49,10 @@ import org.testng.annotations.Test;
 
 import java.io.File;
 import java.io.FileNotFoundException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
 
 
 public class BandPassActivityProfileUnitTest extends BaseTest {
@@ -261,7 +265,7 @@ public class BandPassActivityProfileUnitTest extends BaseTest {
 
         final File file = new File(path);
         final VCFCodec codec = new VCFCodec();
-        final Pair<VCFHeader, GATKVCFUtils.VCIterable> reader = GATKVCFUtils.readAllVCs(file, codec);
+        final Pair<VCFHeader, GATKVCFUtils.VCIterable<LineIterator>> reader = GATKVCFUtils.readAllVCs(file, codec);
 
         final List<ActiveRegion> incRegions = new ArrayList<ActiveRegion>();
         final BandPassActivityProfile incProfile = new BandPassActivityProfile(genomeLocParser, null);
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
index 5cd13b818..1ac79dcf3 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
@@ -26,7 +26,9 @@
 package org.broadinstitute.sting.utils.codecs.hapmap;
 
 import org.broad.tribble.annotation.Strand;
-import org.broad.tribble.readers.AsciiLineReader;
+import org.broad.tribble.readers.LineIterator;
+import org.broad.tribble.readers.LineIteratorImpl;
+import org.broad.tribble.readers.LineReaderUtil;
 import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.BaseTest;
 import org.testng.Assert;
@@ -53,15 +55,13 @@ public class HapMapUnitTest extends BaseTest {
     @Test
     public void testReadHeader() {
         RawHapMapCodec codec = new RawHapMapCodec();
-        AsciiLineReader reader = getReader();
+        final LineIterator reader = getLineIterator();
         try {
-            String header = reader.readLine();
-            reader.close();
-            Assert.assertTrue(header.equals(codec.readHeader(getReader())));
-        } catch (IOException e) {
-            Assert.fail("Unable to read from file " + hapMapFile);
+            String header = reader.next();
+            Assert.assertTrue(header.equals(codec.readActualHeader(getLineIterator())));
+        } finally {
+            codec.close(reader);
         }
-        reader.close();
     }
 
     @Test
@@ -114,22 +114,20 @@ public class HapMapUnitTest extends BaseTest {
     public void testReadCorrectNumberOfRecords() {
         // setup the record for reading our 500 line file (499 records, 1 header line)
         RawHapMapCodec codec = new RawHapMapCodec();
-        AsciiLineReader reader = getReader();
+        final LineIterator reader = getLineIterator();
 
-        String line;
         int count = 0;
         try {
             codec.readHeader(reader);
-            line = reader.readLine();
-            while (line != null) {
-                codec.decode(line);
-                line = reader.readLine();
+            while (reader.hasNext()) {
+                codec.decode(reader.next());
                 ++count;
             }
         } catch (IOException e) {
             Assert.fail("IOException " + e.getMessage());
+        } finally {
+            codec.close(reader);
         }
-        reader.close();
         Assert.assertEquals(count,499);
     }
 
@@ -137,25 +135,26 @@ public class HapMapUnitTest extends BaseTest {
     public void testGetSampleNames() {
         // setup the record for reading our 500 line file (499 records, 1 header line)
         RawHapMapCodec codec = new RawHapMapCodec();
-        AsciiLineReader reader = getReader();
+        final LineIterator reader = getLineIterator();
 
         String line;
         try {
             codec.readHeader(reader);
-            line = reader.readLine();
+            line = reader.next();
             RawHapMapFeature feature = (RawHapMapFeature) codec.decode(line);
             Assert.assertEquals(feature.getSampleIDs().length,87);
 
         } catch (IOException e) {
             Assert.fail("IOException " + e.getMessage());
+        } finally {
+            codec.close(reader);
         }
-        reader.close();
     }
 
 
-    public AsciiLineReader getReader() {
+    public LineIterator getLineIterator() {
         try {
-            return new AsciiLineReader(new PositionalBufferedStream(new FileInputStream(hapMapFile)));
+            return new LineIteratorImpl(LineReaderUtil.fromBufferedStream(new PositionalBufferedStream(new FileInputStream(hapMapFile))));
         } catch (FileNotFoundException e) {
             Assert.fail("Unable to open hapmap file : " + hapMapFile);
         }
diff --git a/public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java b/public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java
index 51a47d86d..381b282e0 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java
@@ -105,7 +105,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
         public void run(T vc);
     }
 
-    private <T extends Feature> void runBenchmark(FeatureCodec<T> codec, FunctionToBenchmark<T> func) {
+    private <T extends Feature> void runBenchmark(FeatureCodec codec, FunctionToBenchmark<T> func) {
         // TODO -- update for new Tribble interface
 //        try {
 //            InputStream is = new ByteArrayInputStream(INPUT_STRING.getBytes());
@@ -129,7 +129,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
     public void timeV14(int rep) {
         for ( int i = 0; i < rep; i++ ) {
             FunctionToBenchmark<VariantContext> func = getV14FunctionToBenchmark();
-            FeatureCodec<VariantContext> codec = new VCFCodec();
+            final VCFCodec codec = new VCFCodec();
             runBenchmark(codec, func);
         }
     }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala b/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
index 73c4ccf64..5802faff2 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
@@ -31,14 +31,12 @@ import scala.io.Source._
 import net.sf.samtools.SAMFileReader
 import org.broadinstitute.variant.vcf.{VCFHeader, VCFCodec}
 import scala.collection.JavaConversions._
-import org.broad.tribble.{FeatureCodec, AbstractFeatureReader}
-import org.broadinstitute.variant.variantcontext.VariantContext
+import org.broad.tribble.AbstractFeatureReader
 
 object VCF_BAM_utilities {
 
   def getSamplesFromVCF(vcfFile: File): List[String] = {
-    val codec: FeatureCodec[VariantContext] = new VCFCodec().asInstanceOf[FeatureCodec[VariantContext]]
-    AbstractFeatureReader.getFeatureReader(vcfFile.getPath, codec).getHeader.asInstanceOf[VCFHeader].getGenotypeSamples.toList
+    AbstractFeatureReader.getFeatureReader(vcfFile.getPath, new VCFCodec()).getHeader.asInstanceOf[VCFHeader].getGenotypeSamples.toList
   }
 
   def getSamplesInBAM(bam: File): List[String] = {
diff --git a/settings/repository/net.sf/sam-1.96.1515.xml b/settings/repository/net.sf/sam-1.96.1515.xml
deleted file mode 100644
index 6c436926a..000000000
--- a/settings/repository/net.sf/sam-1.96.1515.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.96.1515" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.96.1515.jar b/settings/repository/net.sf/sam-1.96.1525.jar
old mode 100644
new mode 100755
similarity index 94%
rename from settings/repository/net.sf/sam-1.96.1515.jar
rename to settings/repository/net.sf/sam-1.96.1525.jar
index 391432b4a072011cecdb7176ef19a5f7a80dbe71..73dd0ee48385d71b86d9d0fb6dcf8d0b07744e4e
GIT binary patch
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diff --git a/settings/repository/net.sf/sam-1.96.1525.xml b/settings/repository/net.sf/sam-1.96.1525.xml
new file mode 100644
index 000000000..efc11ce6c
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.96.1525.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.96.1525" status="release" />
+</ivy-module>
diff --git a/settings/repository/org.broad/tribble-1.96.1525.jar b/settings/repository/org.broad/tribble-1.96.1526.jar
similarity index 93%
rename from settings/repository/org.broad/tribble-1.96.1525.jar
rename to settings/repository/org.broad/tribble-1.96.1526.jar
index 8e4deaa7a8cd13a9cbfb6ac2327ed2c1a4747088..0f45dbf5228aa1321764270812652f61dfbbb16e 100644
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diff --git a/settings/repository/org.broad/tribble-1.96.1525.xml b/settings/repository/org.broad/tribble-1.96.1526.xml
similarity index 76%
rename from settings/repository/org.broad/tribble-1.96.1525.xml
rename to settings/repository/org.broad/tribble-1.96.1526.xml
index b50fe7b2e..6f3c52e1b 100644
--- a/settings/repository/org.broad/tribble-1.96.1525.xml
+++ b/settings/repository/org.broad/tribble-1.96.1526.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="1.96.1525" status="integration" />
+    <info organisation="org.broad" module="tribble" revision="1.96.1526" status="integration" />
 </ivy-module>