New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@355 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -105,7 +105,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
      */
     private static Logger logger = Logger.getLogger(GenomeAnalysisTK.class);
 
-    public static ArrayList<String> ROD_BINDINGS = null;
+    public static ArrayList<String> ROD_BINDINGS = new ArrayList<String>();
 
 
     /**
@@ -143,9 +143,11 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         m_parser.addOptionalArg("daughter", "KID", "Daughter's genotype (SAM pileup)", "DAUGHTER_GENOTYPE_FILE");
 
         // --rodBind <name> <type> <file>
+        //m_parser.addOptionalArg("rods", "B", "Bind rod with <name> and <type> to <file>", "ROD_BINDINGS");
+
         Option rodBinder = OptionBuilder.withArgName("rodBind")
                                         .hasArgs()
-                                        .withDescription( "Bind rod with <name> and <type> to <file>" )
+                                        .withDescription( "" )
                                         .create("B");
         m_parser.addOptionalArg(rodBinder, "ROD_BINDINGS");
     }
@@ -187,48 +189,38 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         start(Instance, argv);
     }
 
+    /**
+     * Convenience function that binds RODs using the old-style command line parser to the new style list for
+     * a uniform processing.
+     * 
+     * @param name
+     * @param type
+     * @param file
+     */
+    private static void bindConvenienceRods(final String name, final String type, final String file )
+    {
+        ROD_BINDINGS.add(name);
+        ROD_BINDINGS.add(type);
+        ROD_BINDINGS.add(file);
+    }
+
     protected int execute() {
         final boolean TEST_ROD = false;
         List<ReferenceOrderedData<? extends ReferenceOrderedDatum> > rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum> >();
 
-        if ( ROD_BINDINGS != null ) {
+        //
-            System.out.printf("ROD BINDINGS are %s%n", Utils.join(":", ROD_BINDINGS));
+        // please don't use these in the future, use the new syntax
-        }
+        //
-
+        if ( DBSNP_FILE != null )               bindConvenienceRods("dbSNP", "dbsnp", DBSNP_FILE);
-
+        if ( HAPMAP_FILE != null )              bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", HAPMAP_FILE);
-        if ( TEST_ROD ) {
+        if ( HAPMAP_CHIP_FILE != null )         bindConvenienceRods("hapmap-chip", "GFF", HAPMAP_CHIP_FILE);
-            ReferenceOrderedData<rodGFF> gff = new ReferenceOrderedData<rodGFF>("test", new File("trunk/data/gFFTest.gff"), rodGFF.class );
+        //TODO: remove when walkers can ask for tracks
-            gff.testMe();
+        if ( MOTHER_GENOTYPE_FILE != null )     bindConvenienceRods("mother", "SAMPileup", MOTHER_GENOTYPE_FILE);
-
+        if ( FATHER_GENOTYPE_FILE != null )     bindConvenienceRods("father", "SAMPileup", FATHER_GENOTYPE_FILE);
-            //ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("trunk/data/dbSNP_head.txt"), rodDbSNP.class );
+        if ( DAUGHTER_GENOTYPE_FILE != null )   bindConvenienceRods("daughter", "SAMPileup", DAUGHTER_GENOTYPE_FILE);
-            ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>("dbSNP", new File("/Volumes/Users/mdepristo/broad/ATK/exampleSAMs/dbSNP_chr20.txt"), rodDbSNP.class );
-            //dbsnp.testMe();
-            rods.add(dbsnp); // { gff, dbsnp };
-        } else {
-            if ( DBSNP_FILE != null ) {
-                ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>("dbSNP", new File(DBSNP_FILE), rodDbSNP.class );
-                //dbsnp.testMe();
-                rods.add(dbsnp); // { gff, dbsnp };
-            }
-            if ( HAPMAP_FILE != null ) {
-                ReferenceOrderedData<HapMapAlleleFrequenciesROD> hapmap = new ReferenceOrderedData<HapMapAlleleFrequenciesROD>("hapmap", new File(HAPMAP_FILE), HapMapAlleleFrequenciesROD.class );
-                //dbsnp.testMe();
-                rods.add(hapmap); // { gff, dbsnp };
-            }
-            if ( HAPMAP_CHIP_FILE != null ) {
-                ReferenceOrderedData<rodGFF> hapmapChip = new ReferenceOrderedData<rodGFF>("hapmap-chip", new File(HAPMAP_CHIP_FILE), rodGFF.class );
-                rods.add(hapmapChip);
-            }
-            //TODO: remove when walkers can ask for tracks
-            if ( MOTHER_GENOTYPE_FILE != null ) 
-                rods.add( new ReferenceOrderedData<rodSAMPileup>("mother", new File(MOTHER_GENOTYPE_FILE), rodSAMPileup.class ) );
-            if ( FATHER_GENOTYPE_FILE != null ) 
-                rods.add( new ReferenceOrderedData<rodSAMPileup>("father", new File(FATHER_GENOTYPE_FILE), rodSAMPileup.class ) );
-            if ( DAUGHTER_GENOTYPE_FILE != null ) 
-                rods.add( new ReferenceOrderedData<rodSAMPileup>("daughter", new File(DAUGHTER_GENOTYPE_FILE), rodSAMPileup.class ) );
-            
-       }
 
+        ReferenceOrderedData.parseBindings(logger, ROD_BINDINGS, rods);
+        
         initializeOutputStreams();
 
         Walker<?,?> my_walker = null;
@@ -281,7 +273,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         // Prepare the sort ordering w.r.t. the sequence dictionary
         if (REF_FILE_ARG != null) {
             final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG);
-            GenomeLoc.setupRefContigOrdering(refFile);
+            //GenomeLoc.setupRefContigOrdering(refFile);
         }
 
         // Determine the validation stringency.  Default to ValidationStringency.STRICT.

java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java

@@ -7,11 +7,20 @@ import java.util.List;
 import java.util.Collection;
 
 /**
- * Created by IntelliJ IDEA.
+ * This class represents the Reference Metadata available at a particular site in the genome.  It can be
+ * used to conveniently lookup the RODs at this site, as well just getting a list of all of the RODs
+ *
+ * The standard interaction model is:
+ *
+ * Traversal system arrives at a site, which has a bunch of rods covering it
+ * Traversal calls tracker.bind(name, rod) for each rod in rods
+ * Traversal passes tracker to the walker
+ * walker calls lookup(name, default) to obtain the rod values at this site, or default if none was
+ *   bound at this site.
+ *
  * User: mdepristo
  * Date: Apr 3, 2009
  * Time: 3:05:23 PM
- * To change this template use File | Settings | File Templates.
  */
 public class RefMetaDataTracker {
     final HashMap<String, ReferenceOrderedDatum> map = new HashMap<String, ReferenceOrderedDatum>();
@@ -26,29 +35,65 @@ public class RefMetaDataTracker {
      */
     public ReferenceOrderedDatum lookup(final String name, ReferenceOrderedDatum defaultValue) {
         //logger.debug(String.format("Lookup %s%n", name));
-        if ( map.containsKey(name) )
+        final String luName = canonicalName(name);
-            return map.get(name);
+        if ( map.containsKey(luName) )
+            return map.get(luName);
         else
             return defaultValue;
     }
 
+    /**
+     * @see this.lookup
+     * @param name
+     * @param defaultValue
+     * @return
+     */
     public Object lookup(final String name, Object defaultValue) {
-        if ( map.containsKey(name) )
+        final String luName = canonicalName(name);
-            return map.get(name);
+        if ( map.containsKey(luName) )
+            return map.get(luName);
         else
             return defaultValue;
     }
 
-    public Object hasROD(final String name) {
+    /**
-       return map.containsKey(name);
+     * Returns the canonical name of the rod name
+     * @param name
+     * @return
+     */
+    private final String canonicalName(final String name)
+    {
+        return name.toLowerCase();
     }
 
+    /**
+     * Is there a binding at this site to a ROD with name?
+     *
+     * @param name
+     * @return
+     */
+    public Object hasROD(final String name) {
+       return map.containsKey(canonicalName(name));
+    }
+
+    /**
+     * Get all of the RODs at the current site
+     * 
+     * @return
+     */
     public Collection<ReferenceOrderedDatum> getAllRods() {
         return map.values();
     }
 
+    /**
+     * Binds the reference ordered datum ROD to name at this site.  Should be used only but the traversal
+     * system to provide access to RODs in a structured way to the walkers.
+     *
+     * @param name
+     * @param rod
+     */
     public void bind(final String name, ReferenceOrderedDatum rod) {
         //logger.debug(String.format("Binding %s to %s%n", name, rod));
-        map.put(name, rod);
+        map.put(canonicalName(name), rod);
     }
 }

java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java

@@ -4,9 +4,7 @@ import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.FileNotFoundException;
-import java.util.Iterator;
+import java.util.*;
-import java.util.ArrayList;
-import java.util.Collections;
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
 
@@ -14,6 +12,7 @@ import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.xReadLines;
 import org.broadinstitute.sting.utils.Utils;
+import org.apache.log4j.Logger;
 
 /**
  * Class for representing arbitrary reference ordered data sets
@@ -28,6 +27,98 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
     private File file = null;
     private Class<ROD> type = null; // runtime type information for object construction
 
+    // ----------------------------------------------------------------------
+    //
+    // Static ROD type management
+    //
+    // ----------------------------------------------------------------------
+    public static class RODBinding {
+        public final String name;
+        public final Class<? extends ReferenceOrderedDatum> type;
+        public RODBinding(final String name, final Class<? extends ReferenceOrderedDatum> type) {
+            this.name = name;
+            this.type = type;
+        }
+    }
+
+    public static HashMap<String, RODBinding> Types = new HashMap<String, RODBinding>();
+    public static void addModule(final String name, final Class<? extends ReferenceOrderedDatum> rodType) {
+        System.out.printf("* Adding rod class %s%n", name);
+        Types.put(name.toLowerCase(), new RODBinding(name, rodType));
+    }
+
+    static {
+        // All known ROD types
+        addModule("GFF", rodGFF.class);
+        addModule("dbSNP", rodDbSNP.class);
+        addModule("HapMapAlleleFrequencies", HapMapAlleleFrequenciesROD.class);
+        addModule("SAMPileup", rodSAMPileup.class);
+    }
+
+
+    /**
+     * Parse the ROD bindings.  These are of the form of a single list of strings, each triplet of the
+     * form <name> <type> <file>.  After this function, the List of RODs contains new RODs bound to each of
+     * name, of type, ready to read from the file.  This function does check for the strings to be well formed
+     * and such.
+     *
+     * @param logger
+     * @param bindings
+     * @param rods
+     */
+    public static void parseBindings(Logger logger, ArrayList<String> bindings, List<ReferenceOrderedData<? extends ReferenceOrderedDatum> > rods)
+    {
+        logger.info("Processing ROD bindings: " + bindings.size() + " -> " + Utils.join(" : ", bindings));
+        if ( bindings.size() % 3 != 0 )
+            Utils.scareUser(String.format("Invalid ROD specification: requires triplets of <name> <type> <file> but got %s", Utils.join(" ", bindings)));
+
+        // Loop over triplets
+        for ( int i = 0; i < bindings.size(); i += 3) {
+            final String name = bindings.get(i);
+            final String typeName = bindings.get(i+1);
+            final String fileName = bindings.get(i+2);
+
+            ReferenceOrderedData<?> rod = parse1Binding(logger, name, typeName, fileName);
+
+            // check that we're not generating duplicate bindings
+            for ( ReferenceOrderedData rod2 : rods )
+                if ( rod2.getName().equals(rod.getName()) )
+                    Utils.scareUser(String.format("Found duplicate rod bindings", rod.getName()));
+
+            rods.add(rod);
+        }
+    }
+
+    /**
+     * Helpful function that parses a single triplet of <name> <type> <file> and returns the corresponding ROD with
+     * <name>, of type <type> that reads its input from <file>.
+     * 
+     * @param logger
+     * @param trackName
+     * @param typeName
+     * @param fileName
+     * @return
+     */
+    private static ReferenceOrderedData<?> parse1Binding( Logger logger, final String trackName, final String typeName, final String fileName )
+    {
+        // Gracefully fail if we don't have the type
+        if ( ReferenceOrderedData.Types.get(typeName.toLowerCase()) == null )
+            Utils.scareUser(String.format("Unknown ROD type: %s", typeName));
+
+        // Lookup the type
+        Class rodClass = ReferenceOrderedData.Types.get(typeName.toLowerCase()).type;
+
+        // Create the ROD
+        ReferenceOrderedData<?> rod = new ReferenceOrderedData<ReferenceOrderedDatum>(trackName.toLowerCase(), new File(fileName), rodClass );
+        logger.info(String.format("Created binding from %s to %s of type %s", trackName.toLowerCase(), fileName, rodClass));
+        return rod;
+    }
+
+    // ----------------------------------------------------------------------
+    //
+    // Constructors
+    //
+    // ----------------------------------------------------------------------
     public ReferenceOrderedData(final String name, File file, Class<ROD> type ) {
         this.file = file;
         this.type = type;

java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java

@@ -24,18 +24,6 @@ public class PrepareROD extends CommandLineProgram {
     @Option(shortName="RODNAME", doc="Name of the data") public String ROD_NAME = null;
     @Option(shortName="RODTYPE", doc="Referenced Ordered Data type") public String ROD_TYPE = null;
 
-    public static HashMap<String, Class<? extends ReferenceOrderedDatum>> Types = new HashMap<String,Class<? extends ReferenceOrderedDatum>>();
-    public static void addModule(final String name, final Class<? extends ReferenceOrderedDatum> rodType) {
-        System.out.printf("* Adding rod class %s%n", name);
-        Types.put(name.toLowerCase(), rodType);
-    }
-
-    static {
-        addModule("GFF", rodGFF.class);
-        addModule("dbSNP", rodDbSNP.class);
-        addModule("HapMapAlleleFrequencies", HapMapAlleleFrequenciesROD.class);
-    }
-
     /** Required main method implementation. */
     public static void main(String[] argv) {
         System.exit(new PrepareROD().instanceMain(argv));
@@ -47,7 +35,7 @@ public class PrepareROD extends CommandLineProgram {
         final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG);
         GenomeLoc.setupRefContigOrdering(refFile);
 
-        Class<? extends ReferenceOrderedDatum> rodClass = Types.get(ROD_TYPE.toLowerCase());
+        Class<? extends ReferenceOrderedDatum> rodClass = ReferenceOrderedData.Types.get(ROD_TYPE.toLowerCase()).type;
 
         ReferenceOrderedData<? extends ReferenceOrderedDatum> rod = new ReferenceOrderedData("ROD", new File(ROD_FILE), rodClass );
         try {

java/src/org/broadinstitute/sting/utils/GenomeLoc.java

@@ -99,9 +99,9 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
             return false;
         }  else {
             contigInfo = seqDict;
-            logger.info(String.format("Prepared reference sequence contig dictionary%n  order ->"));
+            logger.debug(String.format("Prepared reference sequence contig dictionary"));
             for (SAMSequenceRecord contig : seqDict.getSequences() ) {
-                logger.info(String.format(" %s (%d bp)", contig.getSequenceName(), contig.getSequenceLength()));
+                logger.debug(String.format(" %s (%d bp)", contig.getSequenceName(), contig.getSequenceLength()));
             }
         }
         
@@ -225,7 +225,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
             Collections.sort(locs);
             //logger.info(String.format("Going to process %d locations", locs.length));
             locs = mergeOverlappingLocations(locs);
-            logger.info("  Locations are:\n" + Utils.join("\n", Functions.map(Operators.toString, locs)));
+            logger.info("Locations are:" + Utils.join(", ", Functions.map(Operators.toString, locs)));
             return locs;
         } catch (Exception e) {
             e.printStackTrace();
@@ -235,7 +235,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
     }
 
     public static ArrayList<GenomeLoc> mergeOverlappingLocations(final ArrayList<GenomeLoc> raw) {
-        logger.info("  Raw locations are:\n" + Utils.join("\n", Functions.map(Operators.toString, raw)));        
+        logger.debug("  Raw locations are:\n" + Utils.join("\n", Functions.map(Operators.toString, raw)));        
         if ( raw.size() <= 1 )
             return raw;
         else {