Single positional arguments are now treated as names unless they actually match a tribble feature

public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java

@@ -317,38 +317,45 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             String tribbleType = null;
             Tags tags = getArgumentTags(matches);
             // must have one or two tag values here
-            if ( tags.getPositionalTags().size() == 2 ) { // -X:name,type style
+            if ( tags.getPositionalTags().size() > 2 ) {
+                throw new UserException.CommandLineException(
+                        String.format("Unexpected number of positional tags for argument %s : %s. " +
+                                "Rod bindings only suport -X:type and -X:name,type argument styles",
+                                value, source.field.getName()));
+            } if ( tags.getPositionalTags().size() == 2 ) {
+                // -X:name,type style
                 name = tags.getPositionalTags().get(0);
                 tribbleType = tags.getPositionalTags().get(1);
             } else {
-                if ( tags.getPositionalTags().size() == 1 ) {
+                // case with 0 or 1 positional tags
+                FeatureManager manager = new FeatureManager();
+
                 // -X:type style is a type when we cannot determine the type dynamically
-                    tribbleType = tags.getPositionalTags().get(0);
+                String tag1 = tags.getPositionalTags().size() == 1 ? tags.getPositionalTags().get(0) : null;
+                if ( tag1 != null ) {
+                    if ( manager.getByName(tag1) != null ) // this a type
+                        tribbleType = tag1;
+                    else
+                        name = tag1;
                 }
 
+                if ( tribbleType == null ) {
                     // try to determine the file type dynamically
-                FeatureManager manager = new FeatureManager();
                     File file = new File(value);
                     if ( file.canRead() && file.isFile() ) {
                         FeatureManager.FeatureDescriptor featureDescriptor = manager.getByFiletype(file);
                         if ( featureDescriptor != null ) {
                             tribbleType = featureDescriptor.getName();
                             logger.warn("Dynamically determined type of " + file + " to be " + tribbleType);
-
+                        }
-                        if ( tags.getPositionalTags().size() == 1 ) {
-                            // -X:type style is a name when we can determine the type dynamically
-                            name = tags.getPositionalTags().get(0);
                     }
                 }
             }
 
-                // now, if we haven't found a type
+            if ( tribbleType == null ) // error handling
-                if ( tribbleType == null )
                 throw new UserException.CommandLineException(
-                            String.format("Unexpected number of positional tags for argument %s : %s. " +
+                        String.format("Could not parse argument %s with value %s",
-                                    "Rod bindings only suport -X:type and -X:name,type argument styles",
+                                defaultDefinition.fullName, value));
-                                    value, source.field.getName()));
-            }
 
             Constructor ctor = (makeRawTypeIfNecessary(type)).getConstructor(Class.class, String.class, String.class, String.class, Tags.class);
             Class parameterType = getParameterizedTypeClass(type);

public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java

@@ -24,26 +24,16 @@
 
 package org.broadinstitute.sting.gatk;
 
-import org.broad.tribble.Feature;
 import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.testng.Assert;
 import org.testng.annotations.Test;
 
-import java.util.List;
-
 /**
  *
  */
 public class EngineFeaturesIntegrationTest extends WalkerTest {
     private void testBadRODBindingInput(String type, String name, Class c) {
-        WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -L 1:1 --variants:" + type + " "
+        WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -L 1:1 --variants:variants," + type + " "
                 + b37dbSNP132 + " -R " + b37KGReference + " -o %s",
                 1, c);
         executeTest(name, spec);
@@ -65,26 +55,3 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
         testBadRODBindingInput("bedXXX", "Unknown input to VCF expecting walker", UserException.UnknownTribbleType.class);
     }
 }
-
-//class TestRodBindings extends RodWalker<Integer, Integer> {
-//    @Input(fullName="req", required=true)
-//    public RodBinding<Feature> required;
-//
-//    @Input(fullName="optional", required=false)
-//    public RodBinding<Feature> optional = RodBinding.makeUnbound(Feature.class);
-//
-//    @Input(fullName="rodList", shortName="RL", doc="A list of ROD types that we will convert to a table", required=true)
-//    public List<RodBinding<Feature>> variantsList;
-//
-//    public void initialize() {
-//        // bound values
-//        Assert.assertEquals(required.isBound(), true);
-//
-//
-//        System.exit(0);
-//    }
-//
-//    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; }
-//    public Integer reduceInit() { return 0; }
-//    public Integer reduce(Integer counter, Integer sum) { return counter + sum; }
-//}

public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java

@@ -11,7 +11,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
         return "-T ReadBackedPhasing" +
                 " -R " + reference +
                 " -I " + validationDataLocation + reads +
-                " -B:variant,VCF " + validationDataLocation + VCF +
+                " --variants " + validationDataLocation + VCF +
                 " --cacheWindowSize " + cacheWindowSize +
                 " --maxPhaseSites " + maxPhaseSites +
                 " --phaseQualityThresh " + phaseQualityThresh +

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java

@@ -72,7 +72,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
 
     public void combinePLs(String file1, String file2, String md5) {
          WalkerTestSpec spec = new WalkerTestSpec(
-                 "-T CombineVariants -NO_HEADER -o %s -R " + b36KGReference + " -priority v1,v2 -B:v1,VCF " + validationDataLocation + file1 + " -B:v2,VCF " + validationDataLocation + file2,
+                 "-T CombineVariants -NO_HEADER -o %s -R " + b36KGReference + " -priority v1,v2 -V:v1 " + validationDataLocation + file1 + " -V:v2 " + validationDataLocation + file2,
                  1,
                  Arrays.asList(md5));
          executeTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);

public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java

@@ -17,11 +17,11 @@ public class VCFIntegrationTest extends WalkerTest {
 
         String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
 
-        String test1 = baseCommand + "-T VariantAnnotator --variants:vcf " + testVCF + " -BTI variants";
+        String test1 = baseCommand + "-T VariantAnnotator --variants " + testVCF + " -BTI variants";
         WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF));
         List<File> result = executeTest("Test Variant Annotator with no changes", spec1).getFirst();
 
-        String test2 = baseCommand + "-T VariantsToVCF --variants:vcf " + result.get(0).getAbsolutePath();
+        String test2 = baseCommand + "-T VariantsToVCF --variants " + result.get(0).getAbsolutePath();
         WalkerTestSpec spec2 = new WalkerTestSpec(test2, 1, Arrays.asList(md5ofInputVCF));
         executeTest("Test Variants To VCF from new output", spec2);
     }