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.

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);
             }
 

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);
     }
 }

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; }
 
 }

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; }
 
 }

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; }
 
 }

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) ||

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);
     }
 }

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);
     }
 }

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>