From d44d5b827538789bae68c47c1634080e6c7d04c9 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Sun, 21 Oct 2012 01:29:59 -0400
Subject: [PATCH] Fix RawHapMapCodec so that it can build indexes.  Minor fixes
 to VCF codec.

---
 .../sting/utils/codecs/hapmap/RawHapMapCodec.java        | 9 +++++++++
 .../broadinstitute/sting/utils/codecs/vcf/VCFCodec.java  | 4 +---
 2 files changed, 10 insertions(+), 3 deletions(-)

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 916fb43ea..6b3fce966 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
@@ -25,8 +25,11 @@
 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 java.io.IOException;
 import java.util.Arrays;
@@ -116,4 +119,10 @@ public class RawHapMapCodec extends AsciiFeatureCodec<RawHapMapFeature> {
         }
         return headerLine;
     }
+
+    @Override
+    public FeatureCodecHeader readHeader(final PositionalBufferedStream stream) throws IOException {
+        final AsciiLineReader br = new AsciiLineReader(stream);
+        return new FeatureCodecHeader(readHeader(br), br.getPosition());
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
index 4df1efee7..f12f13dc7 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
@@ -2,8 +2,6 @@ package org.broadinstitute.sting.utils.codecs.vcf;
 
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
-import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.io.IOException;
 import java.util.*;
@@ -119,7 +117,7 @@ public class VCFCodec extends AbstractVCFCodec {
         // empty set for passes filters
         List<String> fFields = new LinkedList<String>();
         // otherwise we have to parse and cache the value
-        if ( filterString.indexOf(VCFConstants.FILTER_CODE_SEPARATOR) == -1 )
+        if ( !filterString.contains(VCFConstants.FILTER_CODE_SEPARATOR) )
             fFields.add(filterString);
         else
             fFields.addAll(Arrays.asList(filterString.split(VCFConstants.FILTER_CODE_SEPARATOR)));