Added ROD for parsing hapmap3 genotype files.

Tweak to TabularROD to allow HapMapGenotypeROD to work.
Added HapMapGenotypeROD to list of RODs in ReferenceOrderedData.java.
Modified MultiSampleCaller to return a single object with most of the relvant information.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1169 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,44 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import java.util.*;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+
+public class HapMapGenotypeROD extends TabularROD 
+{
+    public HapMapGenotypeROD(final String name) 
+	{
+        super(name);
+    }
+
+    public GenomeLoc getLocation() 
+	{
+		//System.out.printf("chrom: %s; pos: %s\n", this.get("chrom"), this.get("pos"));
+       
+		return GenomeLocParser.createGenomeLoc(this.get("chrom").replaceAll("chr", ""), Long.parseLong(this.get("pos")));
+    }
+
+	public String[] getSampleIDs()
+	{
+		ArrayList<String> header = this.getHeader();
+		String[] sample_ids = new String[header.size()-11];
+		for (int i = 11; i < header.size(); i++)
+		{
+			sample_ids[i-11] = header.get(i);
+		}
+		return sample_ids;
+	}
+
+	public String[] getGenotypes()
+	{
+		ArrayList<String> header = this.getHeader();
+		String[] genotypes = new String[header.size()-11];
+		for (int i = 11; i < header.size(); i++)
+		{
+			genotypes[i-11] = this.get(header.get(i));
+		}
+		return genotypes;
+	}
+
+}

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

@@ -68,6 +68,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         addModule("PooledEM", PooledEMSNPROD.class);
         addModule("1KGSNPs", KGenomesSNPROD.class);
         addModule("SangerSNP", SangerSNPROD.class);
+        addModule("HapMapGenotype", HapMapGenotypeROD.class);
         addModule("Intervals", IntervalRod.class);
         addModule("Variants", rodVariants.class);
     }
@@ -309,22 +310,22 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
     // Parsing
     //
     // ----------------------------------------------------------------------
+	private Constructor<ROD> parsing_constructor;
     private ROD newROD( final String name, final Class<ROD> type ) {
         try {
-            Constructor<ROD> c = type.getConstructor(String.class);
+            return (ROD)parsing_constructor.newInstance(name);
-            return (ROD)c.newInstance(name);
         } catch ( java.lang.InstantiationException e ) {
             throw new RuntimeException(e);
         } catch ( java.lang.IllegalAccessException e ) {
             throw new RuntimeException(e);
-        } catch ( java.lang.NoSuchMethodException e ) {
-            throw new RuntimeException(e);
         } catch ( InvocationTargetException e ) {
             throw new RuntimeException(e);
         }
     }
 
     private Object initializeROD(final String name, final File file, final Class<ROD> type) {
+		try { parsing_constructor = type.getConstructor(String.class); }
+		catch (java.lang.NoSuchMethodException e) { throw new RuntimeException(e); }
         ROD rod = newROD(name, type);
         try {
             return rod.initialize(file);

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

@@ -51,7 +51,7 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
     public static String DELIMITER_REGEX = DEFAULT_DELIMITER_REGEX;
 
     private static int MAX_LINES_TO_LOOK_FOR_HEADER = 1000;
-    private static Pattern HEADER_PATTERN = Pattern.compile("^\\s*((HEADER)|(loc)).*");
+    private static Pattern HEADER_PATTERN = Pattern.compile("^\\s*((HEADER)|(loc)|(rs#)).*");
     private static Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
 
     private static int parsedRecords = 0;
@@ -91,7 +91,7 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
 
     private static boolean headerIsGood(final ArrayList<String> header) {
         if ( header.size() == 0 ) return false;
-        if ( ! header.get(0).equals("HEADER") ) return false;
+        //if ( ! header.get(0).equals("HEADER") ) return false;
         return true;
     }
 
@@ -304,4 +304,4 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
 
         return true;
     }
-}
+}

java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java

@@ -21,7 +21,7 @@ import java.io.*;
 // Beta iterative multi-sample caller
 // j.maguire 6-11-2009
 
-public class MultiSampleCaller extends LocusWalker<String,String>
+public class MultiSampleCaller extends LocusWalker<MultiSampleCaller.MultiSampleCallResult,String>
 {
     @Argument(required=false, shortName="fractional_counts", doc="should we use fractional counts?") public boolean FRACTIONAL_COUNTS = false;
     @Argument(required=false, shortName="max_iterations", doc="Maximum number of iterations for EM") public int MAX_ITERATIONS = 10;
@@ -36,6 +36,41 @@ public class MultiSampleCaller extends LocusWalker<String,String>
 	PrintStream individual_output_file;
 	PrintStream discovery_output_file;
 
+
+	class MultiSampleCallResult
+	{
+		char ref;
+		char alt;
+		EM_Result em_result;
+		double lod;
+		double strand_score;
+		double pD;
+		double pNull;
+		String in_dbsnp;
+		int n_ref;
+		int n_het;
+		int n_hom;
+		int EM_N;
+		double alt_freq;
+		public MultiSampleCallResult(char ref, char alt, EM_Result em_result, double lod, double strand_score, double pD, double pNull, String in_dbsnp, int n_ref, int n_het, int n_hom, int EM_N, double alt_freq)
+		{
+			this.ref = ref;
+			this.alt = alt;
+			this.em_result = em_result;
+			this.lod = lod;
+			this.strand_score = strand_score; 
+			this.pD = pD;
+			this.pNull = pNull;
+			this.in_dbsnp = in_dbsnp;
+			this.n_ref = n_ref;
+			this.n_het = n_het;
+			this.n_hom = n_hom;
+			this.EM_N = EM_N;
+			this.alt_freq = alt_freq;
+		}
+	}
+
+
 	/////////
 	// Walker Interface Functions 
     public void initialize() 
@@ -76,15 +111,13 @@ public class MultiSampleCaller extends LocusWalker<String,String>
         } 
     }
 
-	public String in_dbsnp = "novel";
 
-    public String map(RefMetaDataTracker tracker, char ref, LocusContext context) 
+    public MultiSampleCallResult map(RefMetaDataTracker tracker, char ref, LocusContext context) 
 	{
 		if (ref == 'N') { return null; }
 		this.ref = ref;
-		if (tracker.lookup("DBSNP", null) != null) { in_dbsnp = "known"; } else { in_dbsnp = "novel"; }
+		MultiSampleCallResult result = this.MultiSampleCall(tracker, ref, context, sample_names);
-		this.MultiSampleCall(context, sample_names);
+		return result;
-		return null;
 	}
 
     public void onTraversalDone(String sum) 
@@ -98,7 +131,7 @@ public class MultiSampleCaller extends LocusWalker<String,String>
 		return null;
 	}
 
-    public String reduce(String record, String sum) 
+    public String reduce(MultiSampleCallResult record, String sum) 
 	{
 		return null;
 	}
@@ -273,11 +306,15 @@ public class MultiSampleCaller extends LocusWalker<String,String>
 
 	class EM_Result
 	{
+		String[] sample_names;
 		GenotypeLikelihoods[] genotype_likelihoods;
 		double[] allele_likelihoods;
 		int EM_N;
-		public EM_Result(GenotypeLikelihoods[] genotype_likelihoods, double[] allele_likelihoods)
+
+		public EM_Result(List<String> sample_names, GenotypeLikelihoods[] genotype_likelihoods, double[] allele_likelihoods)
 		{
+			this.sample_names = new String[1];
+			this.sample_names = sample_names.toArray(this.sample_names);
 			this.genotype_likelihoods = genotype_likelihoods;
 			this.allele_likelihoods = allele_likelihoods;
 
@@ -317,7 +354,7 @@ public class MultiSampleCaller extends LocusWalker<String,String>
 			}
 		}
 
-		return new EM_Result(G, allele_likelihoods);
+		return new EM_Result(sample_names, G, allele_likelihoods);
 	}
 
 	// Hacky global variables for debugging.
@@ -429,8 +466,11 @@ public class MultiSampleCaller extends LocusWalker<String,String>
 	}
 
 	// This should actually return a GLF Record
-	String MultiSampleCall(LocusContext context, List<String> sample_names) 
+	MultiSampleCallResult MultiSampleCall(RefMetaDataTracker tracker, char ref, LocusContext context, List<String> sample_names) 
 	{
+		String in_dbsnp;
+		if (tracker.lookup("DBSNP", null) != null) { in_dbsnp = "known"; } else { in_dbsnp = "novel"; }
+
 		LocusContext[] contexts = filterLocusContextBySample(context, sample_names, 0);
 		double lod = LOD(contexts);		
 		double strand_score = StrandScore(context);
@@ -472,7 +512,7 @@ public class MultiSampleCaller extends LocusWalker<String,String>
 			individual_output_file.printf("\n");
 		}
 
-		return null;
+		return new MultiSampleCallResult(ref, alt, em_result, lod, strand_score, pD, pNull, in_dbsnp, n_ref, n_het, n_hom, em_result.EM_N, alt_freq);
 	}
 
 	// END Calling Functions