a) consensus goes to week queue

b) New experimental TechnologyComposition annotation
c) SelectVariants fixes

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java

@@ -0,0 +1,77 @@
+package org.broadinstitute.sting.gatk.walkers.annotator;
+
+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.annotator.interfaces.ExperimentalAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.IndelUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: delangel
+ * Date: 6/29/11
+ * Time: 3:14 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class TechnologyComposition implements ExperimentalAnnotation,InfoFieldAnnotation {
+    private String nSLX = "NumSLX";
+    private String n454 ="Num454";
+    private String nSolid = "NumSOLiD";
+    private String nOther = "NumOther";
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
+        int readsIllumina = 0;
+        int readsSolid = 0;
+        int reads454 = 0;
+        int readsOther = 0;
+
+        for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
+            AlignmentContext context = sample.getValue();
+
+            ReadBackedPileup pileup = null;
+            if (context.hasExtendedEventPileup())
+                pileup = context.getExtendedEventPileup();
+            else if (context.hasBasePileup())
+                pileup = context.getBasePileup();
+
+            if (pileup != null) {
+                for (PileupElement p : pileup ) {
+                    if(ReadUtils.is454Read(p.getRead()))
+                        reads454++;
+                    else if (ReadUtils.isSOLiDRead(p.getRead()))
+                        readsSolid++;
+                    else if (ReadUtils.isSLXRead(p.getRead()))
+                        readsIllumina++;
+                    else
+                        readsOther++;
+                }
+            }
+        }
+
+        Map<String, Object> map = new HashMap<String, Object>();
+        map.put(nSLX, String.format("%d", readsIllumina));
+        map.put(n454, String.format("%d", reads454));
+        map.put(nSolid, String.format("%d", readsSolid));
+        map.put(nOther, String.format("%d", readsOther));
+            return map;
+    }
+
+     public List<String> getKeyNames() { return Arrays.asList(nSLX,n454,nSolid,nOther); }
+
+     public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(nSLX, 1, VCFHeaderLineType.Integer, "Number of SLX reads"),
+             new VCFInfoHeaderLine(n454, 1, VCFHeaderLineType.Integer, "Number of 454 reads"),
+             new VCFInfoHeaderLine(nSolid, 1, VCFHeaderLineType.Integer, "Number of SOLiD reads"),
+             new VCFInfoHeaderLine(nOther, 1, VCFHeaderLineType.Integer, "Number of Other technology reads")); }
+
+}

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@@ -303,13 +304,20 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                                     String[] afs = afo.split(",");
                                     afs[0] = afs[0].substring(1,afs[0].length());
                                     afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
-                                    af = Double.valueOf(afs[0]);
+
+                                    double[] afd = new double[afs.length];
+
+                                    for (int k=0; k < afd.length; k++)
+                                        afd[k] = Double.valueOf(afs[k]);
+
+                                    af = MathUtils.arrayMax(afd);
+                                    //af = Double.valueOf(afs[0]);
 
                                 }
                                 else
                                     af = Double.valueOf(afo);
 
-                                System.out.format("%s .. %4.1f\n",afo.toString(), af);
+                                //System.out.format("%s .. %4.4f\n",afo.toString(), af);
                                 if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom * af)
                                     vcfWriter.add(sub, ref.getBase());
                             }