From d7d8b8e38030bef5518055734f8992805cb28bdf Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 28 Nov 2011 14:18:28 -0500
Subject: [PATCH] Tribble v42 changes the Codec.canDecode method to take in a
 String instead of a File; this is something that Jim was adamant about
 (because Tribble can handle streams other than files).  I didn't want the
 next person who needed to rev Tribble to deal with this change additionally,
 so I took care of updating the GATK now.

---
 .../gatk/refdata/tracks/FeatureManager.java   |   2 +-
 .../walkers/diffengine/VCFDiffableReader.java |   3 +--
 .../utils/codecs/beagle/BeagleCodec.java      |   2 +-
 .../utils/codecs/refseq/RefSeqCodec.java      |   3 +--
 .../sting/utils/codecs/table/TableCodec.java  |   3 +--
 .../utils/codecs/vcf/AbstractVCFCodec.java    |   2 +-
 .../sting/utils/codecs/vcf/VCF3Codec.java     |   3 +--
 .../sting/utils/codecs/vcf/VCFCodec.java      |   3 +--
 .../{tribble-41.jar => tribble-42.jar}        | Bin 301217 -> 301131 bytes
 .../{tribble-41.xml => tribble-42.xml}        |   2 +-
 10 files changed, 9 insertions(+), 14 deletions(-)
 rename settings/repository/org.broad/{tribble-41.jar => tribble-42.jar} (93%)
 rename settings/repository/org.broad/{tribble-41.xml => tribble-42.xml} (51%)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
index c41444ef3..fcd85fd1d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
@@ -155,7 +155,7 @@ public class FeatureManager  {
     public FeatureDescriptor getByFiletype(File file) {
         List<FeatureDescriptor> canParse = new ArrayList<FeatureDescriptor>();
         for ( FeatureDescriptor descriptor : featureDescriptors )
-            if ( descriptor.getCodec().canDecode(file) ) {
+            if ( descriptor.getCodec().canDecode(file.getPath()) ) {
                 canParse.add(descriptor);
             }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
index efa57c0aa..3c0da8e9d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -33,7 +33,6 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileReader;
 import java.io.IOException;
 import java.util.Map;
 
@@ -135,6 +134,6 @@ public class VCFDiffableReader implements DiffableReader {
 
     @Override
     public boolean canRead(File file) {
-        return AbstractVCFCodec.canDecodeFile(file, VCFCodec.VCF4_MAGIC_HEADER);
+        return AbstractVCFCodec.canDecodeFile(file.getPath(), VCFCodec.VCF4_MAGIC_HEADER);
     }
 }
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 90d305d73..e4768fd5b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
@@ -249,6 +249,6 @@ public class BeagleCodec implements ReferenceDependentFeatureCodec<BeagleFeature
         return bglFeature;
     }
 
-    public boolean canDecode(final File potentialInput) { return false; }
+    public boolean canDecode(final String potentialInput) { return false; }
 
 }
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 9a899f9e7..efcd3ecf0 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
@@ -9,7 +9,6 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.io.File;
 import java.util.ArrayList;
 
 /**
@@ -140,6 +139,6 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec<RefSeqFeature
         return RefSeqFeature.class;
     }
 
-    public boolean canDecode(final File potentialInput) { return false; }
+    public boolean canDecode(final String potentialInput) { return false; }
 
 }
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 bab7e73c0..2557d70bb 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
@@ -6,7 +6,6 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -109,6 +108,6 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
         return header;
     }
 
-    public boolean canDecode(final File potentialInput) { return false; }
+    public boolean canDecode(final String potentialInput) { return false; }
 
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index 7cceaa008..3009c236b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -638,7 +638,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
         return position+Math.max(refLength - 1,0);
     }
 
-    public final static boolean canDecodeFile(final File potentialInput, final String MAGIC_HEADER_LINE) {
+    public final static boolean canDecodeFile(final String potentialInput, final String MAGIC_HEADER_LINE) {
         try {
             return isVCFStream(new FileInputStream(potentialInput), MAGIC_HEADER_LINE) ||
                     isVCFStream(new GZIPInputStream(new FileInputStream(potentialInput)), MAGIC_HEADER_LINE) ||
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
index 6f8e64e55..aaa2e63a7 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
@@ -5,7 +5,6 @@ import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.sting.utils.variantcontext.*;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.*;
 
@@ -193,7 +192,7 @@ public class VCF3Codec extends AbstractVCFCodec {
     }
 
     @Override
-    public boolean canDecode(final File potentialInput) {
+    public boolean canDecode(final String potentialInput) {
         return canDecodeFile(potentialInput, VCF3_MAGIC_HEADER);
     }
 }
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 407c4bc41..4c1bb1d9e 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
@@ -5,7 +5,6 @@ import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.sting.utils.variantcontext.*;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.*;
 
@@ -217,7 +216,7 @@ public class VCFCodec extends AbstractVCFCodec {
     }
 
     @Override
-    public boolean canDecode(final File potentialInput) {
+    public boolean canDecode(final String potentialInput) {
         return canDecodeFile(potentialInput, VCF4_MAGIC_HEADER);
     }
 }
diff --git a/settings/repository/org.broad/tribble-41.jar b/settings/repository/org.broad/tribble-42.jar
similarity index 93%
rename from settings/repository/org.broad/tribble-41.jar
rename to settings/repository/org.broad/tribble-42.jar
index 76903f007552b51d801c3b77e61623cbed774194..2c798364cee483735ed679f6504ce6a8c5845e4b 100644
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diff --git a/settings/repository/org.broad/tribble-41.xml b/settings/repository/org.broad/tribble-42.xml
similarity index 51%
rename from settings/repository/org.broad/tribble-41.xml
rename to settings/repository/org.broad/tribble-42.xml
index 6ee8bfb78..1c03ce1b1 100644
--- a/settings/repository/org.broad/tribble-41.xml
+++ b/settings/repository/org.broad/tribble-42.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="41" status="integration" />
+    <info organisation="org.broad" module="tribble" revision="42" status="integration" />
 </ivy-module>