better printing in VE2. Added support for TiTv analysis

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2766 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/varianteval2/TiTvVariantEvaluator.java

@@ -0,0 +1,65 @@
+package org.broadinstitute.sting.oneoffprojects.variantcontext.varianteval2;
+
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
+import org.broadinstitute.sting.oneoffprojects.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.StingException;
+
+import java.util.List;
+import java.util.Arrays;
+
+public class TiTvVariantEvaluator extends VariantEvaluator {
+    long nTi = 0, nTv = 0;
+    long nTiInStd = 0, nTvInStd = 0;
+
+    private double ratio(long num, long denom) {
+        return ((double)num) / (Math.max(denom, 1));
+    }
+
+    public String getName() {
+        return "titv";
+    }
+
+    public int getComparisonOrder() {
+        return 2;   // we only need to see each eval track
+    }
+
+    public void updateTiTv(VariantContext vc, boolean updateStandard) {
+        if ( vc != null && vc.isSNP() && vc.isBiallelic() ) {
+            if ( vc.isTransition() ) {
+                if ( updateStandard ) nTiInStd++; else nTi++;
+            } else {
+                if ( updateStandard ) nTvInStd++; else nTv++;
+            }
+        }
+    }
+
+    public void update2(VariantContext vc1, VariantContext vc2, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( vc1 != null ) updateTiTv(vc1, false);
+        if ( vc2 != null ) updateTiTv(vc2, true);
+    }
+
+    public String toString() {
+        return getName() + ": " + summaryLine();
+    }
+
+    private String summaryLine() {
+        return String.format("%d %d %.2f %d %d %.2f",
+                nTi, nTv, ratio(nTi, nTv),
+                nTiInStd, nTvInStd, ratio(nTiInStd, nTvInStd));
+    }
+
+    private static List<String> HEADER =
+            Arrays.asList("nTi", "nTv", "TiTvRatio", "nTiStandard", "nTvStandard", "TiTvRatioStandard");
+
+    // making it a table
+    public List<String> getTableHeader() {
+        return HEADER;
+    }
+
+    public List<List<String>> getTableRows() {
+        return Arrays.asList(Arrays.asList(summaryLine().split(" ")));
+    }
+}

java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/varianteval2/VariantEval2Walker.java

@@ -69,13 +69,15 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
                 for ( VariantContextUtils.MatchExp e : selectExps ) {
                     addNewContext(d.getName(), d.getName() + "." + e.name, e);
                 }
-                addNewContext(d.getName(), d.getName(), null);
+                addNewContext(d.getName(), d.getName() + ".all", null);
             } else if ( d.getName().startsWith("dbsnp") || d.getName().startsWith("hapmap") || d.getName().startsWith("comp") ) {
                 compNames.add(d.getName());
             } else {
                 logger.info("Not evaluating ROD binding " + d.getName());
             }
         }
+
+        determineContextNamePartSizes();
     }
 
     private void determineAllEvalations() {
@@ -144,7 +146,7 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
                     // now call the single or paired update function
                     switch ( evaluation.getComparisonOrder() ) {
                         case 1:
-                            if ( vc != null ) evaluation.update1(vc, tracker, ref, context);
+                            if ( evalWantsVC && vc != null ) evaluation.update1(vc, tracker, ref, context);
                             break;
                         case 2:
                             for ( VariantContext comp : comps.values() ) {
@@ -249,16 +251,59 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
         return null;
     }
 
-    public <T extends Comparable<T>> List<T> sorted(Collection<T> c ) {
+    private <T extends Comparable<T>> List<T> sorted(Collection<T> c ) {
         List<T> l = new ArrayList<T>(c);
         Collections.sort(l);
         return l;
     }
 
+    private final static String CONTEXT_HEADER = "track.subset.novelty.filter";
+    private final static int N_CONTEXT_NAME_PARTS = CONTEXT_HEADER.split("\\.").length;
+    private static int[] nameSizes = new int[N_CONTEXT_NAME_PARTS];
+    static {
+        int i = 0;
+        for ( String elt : CONTEXT_HEADER.split("\\.") )
+            nameSizes[i++] = elt.length();
+    }
+
+    private void determineContextNamePartSizes() {
+        for ( String contextName : sorted(contexts.keySet()) ) {
+            EvaluationContext group = contexts.get(contextName);
+            for ( String evalSubgroupName : sorted(group.keySet()) ) {
+                String keyWord = contextName + "." + evalSubgroupName;
+                String[] parts = keyWord.split("\\.");
+                if ( parts.length != N_CONTEXT_NAME_PARTS ) {
+                    throw new StingException("Unexpected number of eval name parts " + keyWord + " length = " + parts.length + ", expected " + N_CONTEXT_NAME_PARTS);
+                } else {
+                    for ( int i = 0; i < parts.length; i++ )
+                        nameSizes[i] = Math.max(nameSizes[i], parts[i].length());
+                }
+            }
+        }
+    }
+    
+    private String formatKeyword(String keyWord) {
+        //System.out.printf("keyword %s%n", keyWord);
+
+        StringBuilder s = new StringBuilder();
+        int i = 0;
+        for ( String part : keyWord.split("\\.") ) {
+            //System.out.printf("part %s %d%n", part, nameSizes[i]);
+            s.append(String.format("%"+nameSizes[i]+"s ", part));
+            i++;
+        }
+
+        return s.toString();
+    }
+
     public void onTraversalDone(Integer result) {
+        // todo -- this really needs to be pretty printed; use some kind of table organization
+        // todo -- so that we can load up all of the data in one place, analyze the widths of the columns
+        // todo -- and pretty print it
         for ( String evalName : variantEvaluationNames ) {
             boolean first = true;
             out.printf("%n%n");
+            // todo -- show that comp is dbsnp, etc. is columns
             for ( String contextName : sorted(contexts.keySet()) ) {
                 EvaluationContext group = contexts.get(contextName);
 
@@ -267,13 +312,14 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
                     Set<VariantEvaluator> evalSet = group.get(evalSubgroupName);
                     VariantEvaluator eval = getEvalByName(evalName, evalSet);
                     String keyWord = contextName + "." + evalSubgroupName;
+
                     if ( first ) {
-                        out.printf("%20s\t%40s\t%s%n", evalName, "context", Utils.join("\t\t", eval.getTableHeader()));
+                        out.printf("%20s %s %s%n", evalName, formatKeyword(CONTEXT_HEADER), Utils.join("\t\t", eval.getTableHeader()));
                         first = false;
                     }
 
                     for ( List<String> row : eval.getTableRows() )
-                        out.printf("%20s\t%40s\t%s%n", evalName, keyWord, Utils.join("\t\t", row));
+                        out.printf("%20s %s %s%n", evalName, formatKeyword(keyWord), Utils.join("\t\t", row));
                 }
             }
         }