Instead of the SelfScopingFeatureCodec interface, pushed this functionality into Tribble itself. Now we can e.g. determine that a file can be parsed by the BedCodec on the fly.

public/java/src/org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.java

@@ -1,48 +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.gatk.refdata;
-
-import java.io.File;
-
-/**
- * An interface marking that a given Tribble codec can look at the file and determine whether the
- * codec specifically parsing the contents of the file.
- */
-public interface SelfScopingFeatureCodec {
-    /**
-     * This function returns true iff the File potentialInput can be parsed by this
-     * codec.
-     *
-     * The GATK assumes that there's never a situation where two SelfScopingFeaetureCodecs
-     * return true for the same file.  If this occurs the GATK splits out an error.
-     *
-     * Note this function must never throw an error.  All errors should be trapped
-     * and false returned.
-     *
-     * @param potentialInput the file to test for parsiability with this codec
-     * @return true if potentialInput can be parsed, false otherwise
-     */
-    public boolean canDecode(final File potentialInput);
-}

public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java

@@ -30,16 +30,12 @@ import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.NameAwareCodec;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.help.GATKDocUtils;
-import org.broadinstitute.sting.utils.help.HelpUtils;
 
-import javax.mail.Header;
 import java.io.File;
 import java.util.*;
 
@@ -159,10 +155,8 @@ public class FeatureManager  {
     public FeatureDescriptor getByFiletype(File file) {
         List<FeatureDescriptor> canParse = new ArrayList<FeatureDescriptor>();
         for ( FeatureDescriptor descriptor : featureDescriptors )
-            if ( descriptor.getCodec() instanceof SelfScopingFeatureCodec ) {
+            if ( descriptor.getCodec().canDecode(file) ) {
-                if ( ((SelfScopingFeatureCodec) descriptor.getCodec()).canDecode(file) ) {
+                canParse.add(descriptor);
-                    canParse.add(descriptor);
-                }
             }
 
         if ( canParse.size() == 0 )

public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java

@@ -249,4 +249,6 @@ public class BeagleCodec implements ReferenceDependentFeatureCodec<BeagleFeature
         return bglFeature;
     }
 
+    public boolean canDecode(final File potentialInput) { return false; }
+
 }

public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java

@@ -24,8 +24,8 @@
 
 package org.broadinstitute.sting.utils.codecs.hapmap;
 
+import org.broad.tribble.AbstractFeatureCodec;
 import org.broad.tribble.Feature;
-import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.annotation.Strand;
 import org.broad.tribble.readers.LineReader;
 
@@ -71,7 +71,7 @@ import java.util.Arrays;
  * @author Mark DePristo
  * @since 2010
  */
-public class RawHapMapCodec implements FeatureCodec {
+public class RawHapMapCodec extends AbstractFeatureCodec {
     // the minimum number of features in the HapMap file line
     private static final int minimumFeatureCount = 11;
 

public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java

@@ -9,6 +9,7 @@ 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;
 
 /**
@@ -138,4 +139,7 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec<RefSeqFeature
     public Class<RefSeqFeature> getFeatureType() {
         return RefSeqFeature.class;
     }
+
+    public boolean canDecode(final File potentialInput) { return false; }
+
 }

public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java

@@ -25,8 +25,8 @@
 
 package org.broadinstitute.sting.utils.codecs.sampileup;
 
+import org.broad.tribble.AbstractFeatureCodec;
 import org.broad.tribble.Feature;
-import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.exception.CodecLineParsingException;
 import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.ParsingUtils;
@@ -76,7 +76,7 @@ import static org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature.V
  * @author Matt Hanna
  * @since 2009
  */
-public class SAMPileupCodec implements FeatureCodec<SAMPileupFeature> {
+public class SAMPileupCodec extends AbstractFeatureCodec<SAMPileupFeature> {
     // the number of tokens we expect to parse from a pileup line
     private static final int expectedTokenCount = 10;
     private static final char fldDelim = '\t';

public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java

@@ -27,8 +27,8 @@ package org.broadinstitute.sting.utils.codecs.samread;
 import net.sf.samtools.Cigar;
 import net.sf.samtools.TextCigarCodec;
 import net.sf.samtools.util.StringUtil;
+import org.broad.tribble.AbstractFeatureCodec;
 import org.broad.tribble.Feature;
-import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.exception.CodecLineParsingException;
 import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.ParsingUtils;
@@ -52,7 +52,7 @@ import org.broad.tribble.util.ParsingUtils;
  * @author Matt Hanna
  * @since 2009
  */
-public class SAMReadCodec implements FeatureCodec<SAMReadFeature> {
+public class SAMReadCodec extends AbstractFeatureCodec<SAMReadFeature> {
     /* SL-XBC:1:10:628:923#0	16	Escherichia_coli_K12	1	37	76M	=	1	0	AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGA	B@>87<;A@?@957:>>@AA@B>@A9AB@B>@A@@@@@A;=AAB@BBBBBCBBBB@>A>:ABB@BAABCB=CA@CB */
 
     // the number of tokens we expect to parse from a read line

public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java

@@ -6,6 +6,7 @@ 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;
@@ -101,4 +102,7 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
         }
         return header;
     }
+
+    public boolean canDecode(final File potentialInput) { return false; }
+
 }

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java

@@ -8,7 +8,6 @@ import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.BlockCompressedInputStream;
 import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
@@ -20,7 +19,7 @@ import java.util.*;
 import java.util.zip.GZIPInputStream;
 
 
-public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, VCFParser, SelfScopingFeatureCodec {
+public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, VCFParser {
 
     protected final static Logger log = Logger.getLogger(VCFCodec.class);
     protected final static int NUM_STANDARD_FIELDS = 8;  // INFO is the 8th column

settings/repository/org.broad/tribble-41.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="40" status="integration" />
+    <info organisation="org.broad" module="tribble" revision="41" status="integration" />
 </ivy-module>