<key>=<value> tagging support for command-line arguments. Unfortunately, still

very hard to validate and still very hard to use (requires core hacking to 
support additional tags).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5038 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java

@@ -51,7 +51,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
     /**
      * An ordered, freeform collection of tags.
      */
-    public final List<String> tags;
+    public final Tags tags;
 
     /**
      * Create a new argument match, defining its properties later.  Used to create invalid arguments.
@@ -65,10 +65,10 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
      * @param label Label of the argument match.  Must not be null.
      * @param definition The associated definition, if one exists.  May be null.
      */
-    private ArgumentMatch(String label,ArgumentDefinition definition) {
+    private ArgumentMatch(final String label, final ArgumentDefinition definition) {
         this.label = label;
         this.definition = definition;
-        this.tags = Collections.emptyList();
+        this.tags = new Tags();
     }
 
     /**
@@ -78,7 +78,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
      * @param index Position of the argument.  Must not be null.
      * @param tags ordered freeform text tags associated with this argument.
      */
-    public ArgumentMatch( String label, ArgumentDefinition definition, int index, List<String> tags ) {
+    public ArgumentMatch(final String label, final ArgumentDefinition definition, final int index, final Tags tags) {
         this( label, definition, index, null, tags );
     }
 
@@ -90,7 +90,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
      * @param value Value for the argument at this position.
      * @param tags ordered freeform text tags associated with this argument.
      */
-    private ArgumentMatch( String label, ArgumentDefinition definition, int index, String value, List<String> tags ) {
+    private ArgumentMatch(final String label, final ArgumentDefinition definition, final int index, final String value, final Tags tags) {
         this.label = label;
         this.definition = definition;
 
@@ -102,6 +102,26 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
         this.tags = tags;
     }
 
+    /**
+     * Check to see whether two ArgumentMatch objects are equal.
+     * @param other Object to which this should be compared.
+     * @return True if objects are equal, false if objects are not equal or incomparable.
+     */
+    @Override
+    public boolean equals(Object other) {
+        // this clearly isn't null, since this.equals() when this == null would result in an NPE.
+        if(other == null)
+            return false;
+        if(!(other instanceof ArgumentMatch))
+            return false;
+        ArgumentMatch otherArgumentMatch = (ArgumentMatch)other;
+        return this.definition.equals(otherArgumentMatch.definition) &&
+                this.label.equals(otherArgumentMatch.label) &&
+                this.indices.equals(otherArgumentMatch.indices) &&
+                this.tags.equals(otherArgumentMatch.tags);
+    }
+
+
     /**
      * Reformat the given entries with the given multiplexer and key.
      * TODO: Generify this.

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

@@ -213,10 +213,12 @@ public abstract class ArgumentTypeDescriptor {
      * @param matches The matches for the given argument.
      * @return The value of the argument if available, or null if not present.
      */
-    protected List<String> getArgumentTags(ArgumentMatches matches) {
+    protected Tags getArgumentTags(ArgumentMatches matches) {
-        List<String> tags = new ArrayList<String>();
+        Tags tags = new Tags();
-        for( ArgumentMatch match: matches ) {
+        for(ArgumentMatch match: matches) {
-                tags.addAll(match.tags);
+            if(!tags.isEmpty() && !match.tags.isEmpty())
+                throw new ReviewedStingException("BUG: multiple conflicting sets of tags are available, and the type descriptor specifies no way of resolving the conflict.");
+            tags = match.tags;
         }
         return tags;
     }
@@ -303,7 +305,7 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         ArgumentDefinition defaultDefinition = createDefaultArgumentDefinition(source);
         String value = getArgumentValue( defaultDefinition, matches );
         Object result;
-        List<String> tags = getArgumentTags( matches );
+        Tags tags = getArgumentTags(matches);
 
         // lets go through the types we support
         try {
@@ -383,7 +385,7 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     public Object parse(ParsingEngine parsingEngine,ArgumentSource source, Class type, ArgumentMatches matches) {
         Class componentType;
         Object result;
-        List<String> tags = new ArrayList<String>();
+        Tags tags;
 
         if( Collection.class.isAssignableFrom(type) ) {
 
@@ -414,8 +416,10 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
 
             for( ArgumentMatch match: matches ) {
                 for( ArgumentMatch value: match ) {
-                    collection.add( componentArgumentParser.parse(parsingEngine,source,componentType,new ArgumentMatches(value)) );
+                    Object object = componentArgumentParser.parse(parsingEngine,source,componentType,new ArgumentMatches(value));
-                    tags.addAll(value.tags);
+                    collection.add( object );
+                    // WARNING: Side effect!
+                    parsingEngine.addTags(object,value.tags);
                 }
             }
 
@@ -436,16 +440,15 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
 
             int i = 0;
             for( ArgumentMatch value: values ) {
-                Array.set( result,i++,componentArgumentParser.parse(parsingEngine,source,componentType,new ArgumentMatches(value)));
+                Object object = componentArgumentParser.parse(parsingEngine,source,componentType,new ArgumentMatches(value));
-                tags.addAll(value.tags);
+                Array.set(result,i++,object);
+                // WARNING: Side effect!
+                parsingEngine.addTags(object,value.tags);
             }
         }
         else
             throw new ReviewedStingException("Unsupported compound argument type: " + type);
 
-        // WARNING: Side effect!
-        parsingEngine.addTags(result,tags);
-
         return result;
     }
 

java/src/org/broadinstitute/sting/commandline/ParsingEngine.java

@@ -72,7 +72,7 @@ public class ParsingEngine {
     /**
      * List of tags associated with the given instantiation of the command-line argument.
      */
-    private final Map<Object,List<String>> tags = new IdentityHashMap<Object,List<String>>();    
+    private final Map<Object,Tags> tags = new IdentityHashMap<Object,Tags>();    
 
     /**
      * our log, which we want to capture anything from org.broadinstitute.sting
@@ -291,7 +291,7 @@ public class ParsingEngine {
      * @param key The key created.
      * @param tags List of tags, or empty list if no tags are present.
      */
-    public void addTags(Object key, List<String> tags) {
+    public void addTags(Object key, final Tags tags) {
         this.tags.put(key,tags);        
     }
 
@@ -300,9 +300,9 @@ public class ParsingEngine {
      * @param key Key for which to find a tag.
      * @return List of tags associated with this key.
      */
-    public List<String> getTags(Object key)  {
+    public Tags getTags(Object key)  {
         if(!tags.containsKey(key))
-            return Collections.emptyList();
+            return new Tags();
         return tags.get(key);
     }    
 

java/src/org/broadinstitute/sting/commandline/ParsingMethod.java

@@ -80,16 +80,31 @@ public abstract class ParsingMethod {
 
         String argument = matcher.group(1).trim();
 
-        List<String> tags = new ArrayList<String>();
+        Tags tags = new Tags();
-        if(matcher.group(2) != null)
+        if(matcher.group(2) != null) {
-            tags.addAll(Utils.split(matcher.group(2),","));
+            for(String tag: Utils.split(matcher.group(2),",")) {
+                // Check for presence of an '=' sign, indicating a key-value pair in the tag line.
+                int equalDelimiterPos = tag.indexOf('=');
+                if(equalDelimiterPos >= 0) {
+                    // Sanity check; ensure that there aren't multiple '=' in this key-value pair.
+                    if(tag.indexOf('=',equalDelimiterPos+1) >= 0)
+                        throw new ArgumentException(String.format("Tag %s passed to argument %s is malformed.  Please ensure that " +
+                                                                  "key-value tags are of the form <key>=<value>, and neither key " +
+                                                                  "nor value contain the '=' character", tag, argument));
+                    tags.addKeyValueTag(tag.substring(0,equalDelimiterPos),tag.substring(equalDelimiterPos+1));
+                }
+                else
+                    tags.addPositionalTag(tag);
+
+            }
+        }
 
         // Find the most appropriate argument definition for the given argument.
         ArgumentDefinition argumentDefinition = definitions.findArgumentDefinition( argument, definitionMatcher );
 
         // Try to find a matching argument.  If found, label that as the match.  If not found, add the argument
         // with a null definition.
-        ArgumentMatch argumentMatch = new ArgumentMatch( argument, argumentDefinition, position, tags );
+        ArgumentMatch argumentMatch = new ArgumentMatch(argument,argumentDefinition,position,tags);
 
         return argumentMatch;
     }
@@ -102,7 +117,7 @@ public abstract class ParsingMethod {
     /**
      * Tags, on the other hand, can start with any word character.
      */
-    private static final String TAG_TEXT = "[\\w\\-\\.]*";
+    private static final String TAG_TEXT = "[\\w\\-\\.\\=]*";
 
     public static ParsingMethod FullNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*--(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)),
                                                                           ArgumentDefinitions.FullNameDefinitionMatcher) {};

java/src/org/broadinstitute/sting/commandline/Tags.java

@@ -0,0 +1,102 @@
+/*
+ * 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.commandline;
+
+import java.util.*;
+
+/**
+ * Models the tags that can appear after command-line arguments
+ * in the GATK.
+ */
+public class Tags {
+    /**
+     * Storage for the ordered, unkeyed, positional tags.
+     */
+    private final List<String> positionalTags = new ArrayList<String>();
+
+    /**
+     * Storage for key-value tags of the form <key>=<value>
+     */
+    private Map<String,String> keyValueTags = new HashMap<String,String>();
+
+    /**
+     * Tests to see whether two tag sets are equal.
+     * @param other Other object to test for equality.
+     * @return True if objects are the same.  False if objects differ.
+     */
+    @Override
+    public boolean equals(Object other) {
+        if(other == null)
+            return false;
+
+        if(!(other instanceof Tags))
+            return false;
+
+        Tags otherTags = (Tags)other;
+        return this.positionalTags.equals(otherTags.positionalTags) && this.keyValueTags.equals(otherTags.keyValueTags);
+    }
+
+    /**
+     * Returns whether any tags are specified on the command-line for this operation.
+     * @return True if the tags are empty; false otherwise.
+     */
+    public boolean isEmpty() {
+        return positionalTags.isEmpty() && keyValueTags.isEmpty();
+    }
+
+    /**
+     * Retrieves the list of all positional tags associated with this argument.
+     * @return A list of positional tags.
+     */
+    public List<String> getPositionalTags() {
+        return Collections.unmodifiableList(positionalTags);
+    }
+
+    /**
+     * Gets the value associated with a given <key>=<value> argument tag.
+     * @param key The key for which to retrieve the value.
+     * @return The value paired with the given key, or null if no such element exists.
+     */
+    public String getValue(final String key) {
+        return keyValueTags.get(key);
+    }
+
+    /**
+     * Adds positional tag(s) to the tag object.
+     * @param tags The tag strings to add.
+     */
+    protected void addPositionalTag(final String... tags) {
+        positionalTags.addAll(Arrays.asList(tags));
+    }
+
+    /**
+     * Adds a <key>-<value> tag to this tag library.
+     * @param key key tag to add.
+     * @param value value to associate with this key.
+     */
+    protected void addKeyValueTag(final String key, final String value) {
+        keyValueTags.put(key,value);
+    }
+}

java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk;
 
+import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
@@ -206,7 +207,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
     private List<SAMReaderID> unpackBAMFileList(GATKArgumentCollection argCollection) {
         List<SAMReaderID> unpackedReads = new ArrayList<SAMReaderID>();
         for( String inputFileName: argCollection.samFiles ) {
-            List<String> inputFileNameTags = parser.getTags(inputFileName);
+            Tags inputFileNameTags = parser.getTags(inputFileName);
             inputFileName = expandFileName(inputFileName);
             if (inputFileName.toLowerCase().endsWith(".list") ) {
                 try {
@@ -239,27 +240,28 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
     private Collection<RMDTriplet> unpackRODBindings(GATKArgumentCollection argCollection) {
         Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();
 
-
         for (String fileName: argCollection.RODBindings) {
-            List<String> parameters = parser.getTags(fileName);
+            Tags tags = parser.getTags(fileName);
             fileName = expandFileName(fileName);
 
-            RMDStorageType storageType = null;
+            List<String> positionalTags = tags.getPositionalTags();
-            if(argCollection.rodInputType != null)
+            if(positionalTags.size() != 2)
-                storageType = argCollection.rodInputType;
-            else if(fileName.toLowerCase().endsWith("stdin"))
-                storageType = RMDStorageType.STREAM;
-            else
-                storageType = RMDStorageType.FILE;
-
-            if(parameters.size() != 2)
                 throw new UserException("Invalid syntax for -B (reference-ordered data) input flag.  " +
                         "Please use the following syntax when providing reference-ordered " +
                         "data: -B:<name>,<type> <filename>.");
             // Assume that if tags are present, those tags are name and type.
             // Name is always first, followed by type.
-            String name = parameters.get(0);
+            String name = positionalTags.get(0);
-            String type = parameters.get(1);
+            String type = positionalTags.get(1);
+
+            RMDStorageType storageType = null;
+            if(tags.getValue("storage") != null)
+                storageType = Enum.valueOf(RMDStorageType.class,tags.getValue("storage"));
+            else if(fileName.toLowerCase().endsWith("stdin"))
+                storageType = RMDStorageType.STREAM;
+            else
+                storageType = RMDStorageType.FILE;
+
             rodBindings.add(new RMDTriplet(name,type,fileName,storageType));
         }
 

java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -212,11 +212,6 @@ public class GATKArgumentCollection {
     @Input(fullName = "read_group_black_list", shortName="rgbl", doc="Filters out read groups matching <TAG>:<STRING> or a .txt file containing the filter strings one per line.", required = false)
     public List<String> readGroupBlackList = null;
 
-    @Element(required=false)
-    @Argument(fullName="rod_input_type",shortName="rit",doc="Indicates whether to use a file approach or a streaming approach to loading ROD data",required=false)
-    @Hidden
-    public RMDTriplet.RMDStorageType rodInputType = null;
-
     @Element(required=false)
     @Argument(fullName="processingTracker",shortName="C",doc="A lockable, shared file for coordinating distributed GATK runs",required=false)
     @Hidden
@@ -392,9 +387,6 @@ public class GATKArgumentCollection {
                 (other.processingTrackerFile != null && !other.processingTrackerFile.equals(this.processingTrackerFile)))
             return false;
 
-        if(rodInputType != other.rodInputType)
-            return false;
-
         if ( restartProcessingTracker != other.restartProcessingTracker )
             return false;
 

java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMReaderID.java

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
+import org.broadinstitute.sting.commandline.Tags;
+
 import java.io.File;
 import java.util.List;
 import java.util.Collections;
@@ -20,14 +22,14 @@ public class SAMReaderID {
     /**
      * A list of tags associated with this BAM file.
      */
-    protected final List<String> tags;
+    protected final Tags tags;
 
     /**
      * Creates an identifier for a SAM file based on read.
      * @param samFile The source file for SAM data.
      * @param tags tags to use when creating a reader ID.
      */
-    public SAMReaderID(File samFile, List<String> tags) {
+    public SAMReaderID(File samFile, Tags tags) {
         this.samFile = samFile;
         this.tags = tags;
     }
@@ -37,7 +39,7 @@ public class SAMReaderID {
      * @param samFileName The source filename for SAM data.
      * @param tags tags to use when creating a reader ID.
      */
-    public SAMReaderID(String samFileName, List<String> tags) {
+    public SAMReaderID(String samFileName, Tags tags) {
         this(new File(samFileName),tags);        
     }
 
@@ -45,8 +47,8 @@ public class SAMReaderID {
      * Gets the tags associated with the given BAM file.
      * @return A collection of the tags associated with this file.
      */
-    public List<String> getTags() {
+    public Tags getTags() {
-        return Collections.unmodifiableList(tags);
+        return tags;
     }
 
     /**

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java

@@ -30,6 +30,7 @@ import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.filters.*;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
@@ -272,13 +273,13 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
         int nNorm = 0;
         int nTum = 0;
         for ( SAMReaderID rid : getToolkit().getReadsDataSource().getReaderIDs() ) {
-             List<String> tags = rid.getTags() ;
+             Tags tags = rid.getTags() ;
-             if ( tags.isEmpty() && call_somatic )
+             if ( tags.getPositionalTags().isEmpty() && call_somatic )
                  throw new UserException.BadInput("In somatic mode all input bam files must be tagged as either 'normal' or 'tumor'. Untagged file: "+
                          getToolkit().getSourceFileForReaderID(rid));
              boolean normal = false;
              boolean tumor = false;
-             for ( String s : tags ) { // we allow additional unrelated tags (and we do not use them), but we REQUIRE one of Tumor/Normal to be present if --somatic is on
+             for ( String s : tags.getPositionalTags() ) { // we allow additional unrelated tags (and we do not use them), but we REQUIRE one of Tumor/Normal to be present if --somatic is on
                  if ( "NORMAL".equals(s.toUpperCase()) ) {
                      normal = true;
                      nNorm++;
@@ -469,9 +470,9 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
 
             if ( call_somatic ) {
 
-                List<String> tags =  getToolkit().getReaderIDForRead(read).getTags();
+                Tags tags =  getToolkit().getReaderIDForRead(read).getTags();
                 boolean assigned = false;
-                for ( String s : tags ) {
+                for ( String s : tags.getPositionalTags() ) {
                     if ( "NORMAL".equals(s.toUpperCase()) ) {
                         normal_context.add(read,ref.getBases());
                         assigned = true;

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceUnitTest.java

@@ -4,6 +4,7 @@ import static org.testng.Assert.fail;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy;
 import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory;
@@ -87,7 +88,7 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
         logger.warn("Executing testLinearBreakIterateAll");
 
         // setup the data
-        readers.add(new SAMReaderID(new File(validationDataLocation+"/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
+        readers.add(new SAMReaderID(new File(validationDataLocation+"/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),new Tags()));
 
         // the sharding strat.
         SAMDataSource data = new SAMDataSource(readers,genomeLocParser);
@@ -131,7 +132,7 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
         logger.warn("Executing testMergingTwoBAMFiles");
 
         // setup the test files
-        readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
+        readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),new Tags()));
 
         // the sharding strat.
         SAMDataSource data = new SAMDataSource(readers,genomeLocParser);
@@ -171,8 +172,8 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
 
         // setup the data and the counter before our second run
         readers.clear();
-        readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
+        readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),new Tags()));
-        readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
+        readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),new Tags()));
 
         count = 0;
         // the sharding strat.

java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.traversals;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
@@ -61,7 +62,7 @@ import java.util.Collections;
 public class TraverseReadsUnitTest extends BaseTest {
 
     private ReferenceSequenceFile seq;
-    private SAMReaderID bam = new SAMReaderID(new File(validationDataLocation + "index_test.bam"),Collections.<String>emptyList()); // TCGA-06-0188.aligned.duplicates_marked.bam");
+    private SAMReaderID bam = new SAMReaderID(new File(validationDataLocation + "index_test.bam"),new Tags()); // TCGA-06-0188.aligned.duplicates_marked.bam");
     private File refFile = new File(validationDataLocation + "Homo_sapiens_assembly17.fasta");
     private List<SAMReaderID> bamList;
     private Walker countReadWalker;

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java

@@ -54,11 +54,11 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
         inputStream.close();
 
         WalkerTestSpec spec = new WalkerTestSpec(
-            "-T SelectVariants " +
+            "-T SelectVariants" +
-                    "-R " + b36KGReference + " " + 
+                    " -R " + b36KGReference +
-                    "-B:variant,vcf " + tmpFifo.getAbsolutePath() + " " +
+                    " -B:variant,vcf,storage=STREAM " + tmpFifo.getAbsolutePath() +
-                    "-rit STREAM --NO_HEADER " + 
+                    " --NO_HEADER" +
-                    "-o %s",
+                    " -o %s",
             1,
             Arrays.asList("2cae3d16f9ed00b07d87e9c49272d877")
         );
@@ -78,12 +78,12 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
 
         // Output select to FIFO
         WalkerTestSpec selectTestSpec = new WalkerTestSpec(
-            "-T SelectVariants " +
+            "-T SelectVariants" +
-            "-R " + b36KGReference + " " +
+            " -R " + b36KGReference +
-            "-B:variant,vcf " + testFile + " " +
+            " -B:variant,vcf,storage=STREAM " + testFile +
-            "--NO_HEADER " +
+            " --NO_HEADER" +
-            "-select 'QD > 2.0' " +
+            " -select 'QD > 2.0'" +
-            "-o " + tmpFifo.getAbsolutePath(),
+            " -o " + tmpFifo.getAbsolutePath(),
             0,
             Collections.<String>emptyList()
         );
@@ -91,13 +91,12 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
 
         // Eval compare the full set to the subselection.
         selectTestSpec = new WalkerTestSpec(
-            "-T VariantEval " +
+            "-T VariantEval" +
-            "-R " + b36KGReference + " " +
+            " -R " + b36KGReference +
-            "-B:eval,vcf " + testFile + " " +
+            " -B:eval,vcf " + testFile +
-            "-B:comp,vcf " + tmpFifo.getAbsolutePath() + " " +
+            " -B:comp,vcf,storage=STREAM " + tmpFifo.getAbsolutePath() +
-            "-E CompOverlap -noStandard " +
+            " -E CompOverlap -noStandard" +
-            "-rit STREAM " +
+            " -reportType CSV -o %s",
-            "-reportType CSV -o %s",
             1,
             Arrays.asList("f7df3ac0777b1a45aa7a58228a290600")
         );