changes in three files to make the HapMap RODs work:

- HapMapAlleleFrequenciesROD.java - the referenceOrderedDatum implementation
 - PrepareROD.java - has a static block that loads the known ROD classes, had to add the above
 - GenomeAnalysisTK.java - when supplied a hapmap argument... loads the ROD

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@265 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -10,6 +10,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.refdata.rodGFF;
+import org.broadinstitute.sting.gatk.refdata.HapMapAlleleFrequenciesROD;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -26,7 +27,6 @@ import java.io.File;
 import java.io.PrintStream;
 import java.io.FileNotFoundException;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
 
 public class GenomeAnalysisTK extends CommandLineProgram {
@@ -83,7 +83,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
      * Used by the walker.
      */
     public PrintStream err = System.err;
-    
+
     /**
      * our log, which we want to capture anything from this class
      */
@@ -103,7 +103,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         m_parser.addOptionalArg("genome_region", "L", "Genome region to operation on: from chr:start-end", "REGION_STR");
         m_parser.addRequiredArg("analysis_type", "T", "Type of analysis to run", "Analysis_Name");
         m_parser.addOptionalArg("DBSNP", "D", "DBSNP file", "DBSNP_FILE");
-        m_parser.addOptionalArg("Hapmap", "H", "Hapmap file", "HAPMAP_FILE");
+        m_parser.addOptionalArg("hapmap", "H", "Hapmap file", "HAPMAP_FILE");
         m_parser.addOptionalFlag("threaded_IO", "P", "If set, enables threaded I/O operations", "ENABLED_THREADED_IO");
         m_parser.addOptionalFlag("unsafe", "U", "If set, enables unsafe operations, nothing will be checked at runtime.", "UNSAFE");
         m_parser.addOptionalArg("sort_on_the_fly", "sort", "Maximum number of reads to sort on the fly", "MAX_ON_FLY_SORTS");
@@ -113,7 +113,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         m_parser.addOptionalArg("all_loci", "A", "Should we process all loci, not just those covered by reads", "WALK_ALL_LOCI");
         m_parser.addOptionalArg("out", "o", "An output file presented to the walker.  Will overwrite contents if file exists.", "outFileName" );
         m_parser.addOptionalArg("err", "e", "An error output file presented to the walker.  Will overwrite contents if file exists.", "errFileName" );
-        m_parser.addOptionalArg("outerr", "oe", "A joint file for 'normal' and error output presented to the walker.  Will overwrite contents if file exists.", "outErrFileName");        
+        m_parser.addOptionalArg("outerr", "oe", "A joint file for 'normal' and error output presented to the walker.  Will overwrite contents if file exists.", "outErrFileName");
     }
 
     /**
@@ -142,7 +142,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
 
     @Override
     protected String getArgumentSourceName( Class argumentSource ) {
-        return WalkerManager.getWalkerName( (Class<Walker>)argumentSource );    
+        return WalkerManager.getWalkerName( (Class<Walker>)argumentSource );
     }
 
     /**
@@ -157,23 +157,27 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         final boolean TEST_ROD = false;
         List<ReferenceOrderedData> rods = new ArrayList<ReferenceOrderedData>();
 
-        if (TEST_ROD) {
+
-            ReferenceOrderedData gff = new ReferenceOrderedData(new File("single.gff"), rodGFF.class);
+
+        if ( TEST_ROD ) {
+            ReferenceOrderedData gff = new ReferenceOrderedData(new File("trunk/data/gFFTest.gff"), rodGFF.class );
             gff.testMe();
 
             //ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("trunk/data/dbSNP_head.txt"), rodDbSNP.class );
-            ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("/Volumes/Users/mdepristo/broad/ATK/exampleSAMs/dbSNP_chr20.txt"), rodDbSNP.class);
+            ReferenceOrderedData dbsnp = new ReferenceOrderedData(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) {
+        } else {
-            ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File(DBSNP_FILE), rodDbSNP.class);
+            if ( DBSNP_FILE != null ) {
-            //dbsnp.testMe();
+                ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File(DBSNP_FILE), rodDbSNP.class );
-            rods.add(dbsnp); // { gff, dbsnp };
+                //dbsnp.testMe();
-        }
+                rods.add(dbsnp); // { gff, dbsnp };
-
+            }
-        if (HAPMAP_FILE != null) {
+            if ( HAPMAP_FILE != null ) {
-            ReferenceOrderedData gff = new ReferenceOrderedData(new File(HAPMAP_FILE), rodGFF.class);
+                ReferenceOrderedData hapmap = new ReferenceOrderedData(new File(HAPMAP_FILE), HapMapAlleleFrequenciesROD.class );
-            rods.add(gff);
+                //dbsnp.testMe();
+                rods.add(hapmap); // { gff, dbsnp };
+            }
         }
 
         initializeOutputStreams();

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

@@ -0,0 +1,105 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.Utils;
+
+import java.util.List;
+import java.util.Arrays;
+
+import edu.mit.broad.picard.util.SequenceUtil;
+
+/**
+ * ReferenceOrderedDatum class to hold HapMap AlleleFrequency Data
+ */
+public class HapMapAlleleFrequenciesROD extends ReferenceOrderedDatum {
+    public GenomeLoc loc;       // genome location of SNP
+                                // Reference sequence chromosome or scaffold
+                                // Start and stop positions in chrom
+
+    public String rsNumber;     // dbsnp rsNumber for this site
+
+    public String hgBuild;
+
+    public char Strand;         // strand of the supplied alleles
+
+    public char refAllele;
+    public char varAllele;
+
+    public double refFreq;
+    public double varFreq;
+
+
+    public String strand;   // maybe we don't need these?
+    public String alleles;  // maybe we don't need these?
+    public Integer refCounts; // maybe we don't need these?
+    public Integer varCounts; // maybe we don't need these?
+    public Integer totalCounts; // maybe we don't need these?
+
+
+    public GenomeLoc getLocation() { return loc; }
+
+    public String toString() {
+        //rs11511647      HG18    chr10   62765   +       T/C     T       C       21      97      0.178   0.822   118
+
+        return String.format(
+                "%s\t%s\t%s\t%d\t%s\t%s\t%s\t%s\t%d\t%d\t%1.3f\t%1.3f\t%d",
+                rsNumber, hgBuild, getContig(), getStart(), strand, alleles, refAllele, varAllele,
+                refCounts, varCounts, refFreq, varFreq, totalCounts);
+    }
+
+    public String toSimpleString() {
+        return String.format("%s:%s:%s:%1.3f", rsNumber, alleles, strand, varFreq);
+    }
+
+    public String repl() {
+        return toString();
+    }
+
+    public void parseLine(final String[] parts) {
+        try {
+            // rs11511647 <=> HG18 <=> chr10 <=> 62765 <=> + <=> T/C <=> T <=> C <=> 21 <=> 97 <=> 0.178 <=> 0.822 <=> 118
+
+            rsNumber = parts[0];    //rs#
+            hgBuild = parts[1];     // build
+
+            String contig = parts[2];   // chrom
+            long start = Long.parseLong(parts[3]); // The final is 1 based
+            long stop = start;
+
+            strand = parts[4];                   // strand
+            alleles = parts[5];                       //alleles
+            refAllele = parts[6].charAt(0); // ref_allele
+            varAllele = parts[7].charAt(0); // var_allele
+            refCounts = Integer.parseInt(parts[8]); // CEU_ref
+            varCounts = Integer.parseInt(parts[9]); // CEU_var
+            refFreq = Double.parseDouble(parts[10]); // CEU_ref_freq
+            varFreq = Double.parseDouble(parts[11]); // CEU_var_freq
+            totalCounts = Integer.parseInt(parts[12]); // CEU_var
+
+            loc = new GenomeLoc(contig, start, stop);
+
+        } catch ( RuntimeException e ) {
+            System.out.printf("  Exception caught during parsing HapMap Allele Freq %s%n", Utils.join(" <=> ", parts));
+            throw e;
+        }
+    }
+
+    public double getVarAlleleFreq() { return this.varFreq; }
+
+    public List<String> getAllelesFWD() {
+        List<String> alleleList;
+        if ( onFwdStrand() )
+            alleleList = Arrays.asList(alleles.split("/"));
+        else
+            alleleList = Arrays.asList(SequenceUtil.reverseComplement(alleles).split("/"));
+
+        return alleleList;
+    }
+
+    public boolean onFwdStrand() {
+        return strand.equals("+");
+    }
+
+
+
+}

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

@@ -8,10 +8,7 @@ import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
 import edu.mit.broad.picard.reference.ReferenceSequenceFile;
 
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
+import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.refdata.rodGFF;
 
 import java.io.*;
 import java.util.HashMap;
@@ -36,6 +33,7 @@ public class PrepareROD extends CommandLineProgram {
     static {
         addModule("GFF", rodGFF.class);
         addModule("dbSNP", rodDbSNP.class);
+        addModule("HapMapAlleleFrequencies", HapMapAlleleFrequenciesROD.class);
     }
 
     /** Required main method implementation. */