use genotype phred likelihood to determine if heterozygous

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15535 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/variant/VCFRecord.java

@@ -117,11 +117,26 @@ class VCFRecord
     return null;
   }
   
+  protected String getFormatValue(String key)
+  {
+    String fmts[] = getFormat().split(":");
+    for(int i=0; i<fmts.length; i++)
+    {
+      if(fmts[i].equals(key))
+      {
+        String vals[] = getSampleDataString().split(":");
+        if(vals.length == fmts.length)
+          return vals[i];
+      }
+    }
+    return null;
+  }
+  
   /**
    * Return the sample data as a tab-delimited string
    * @return
    */
-  private String getSampleDataString()
+  protected String getSampleDataString()
   {
     if(data == null)
       return "";
@@ -470,6 +485,14 @@ class VCFRecord
     {
       if(VCFRecord.MULTI_ALLELE_PATTERN.matcher(alt).matches())
         return true;
+      
+      // look at probability of each genotype (PL) information as well
+      String pl;
+      if((pl = getFormatValue("PL")) != null && 
+          pl.split(",").length == 3 &&
+          pl.split(",")[1].equals("0")) // middle value is zero, e.g. 
+        return true;
+
       return false;
     }
     

uk/ac/sanger/artemis/components/variant/VCFview.java

@@ -128,7 +128,7 @@ public class VCFview extends JPanel
   private int seqLength;
   private EntryGroup entryGroup;
   private String chr;
-  private String mouseOverVCFline;
+  private VCFRecord mouseVCF;
   private int mouseOverIndex = -1;
   
   private boolean vcf_v4 = false;
@@ -695,17 +695,18 @@ public class VCFview extends JPanel
   
   public String getToolTipText()
   {
-    if(mouseOverVCFline == null)
+    if(mouseVCF == null)
       return null;
 
-    String parts[] = tabPattern.split(mouseOverVCFline, 0);
     String msg = 
-           "Seq: "+parts[0]+"\n";
-    msg += "Pos: "+parts[1]+"\n";
-    msg += "ID:  "+parts[2]+"\n";
-    msg += "Variant: "+parts[3]+" -> "+parts[4]+"\n";
-    msg += "Qual: "+parts[5]+"\n";
-    
+           "Seq: "+mouseVCF.getChrom()+"\n";
+    msg += "Pos: "+mouseVCF.getPos()+"\n";
+    msg += "ID:  "+mouseVCF.getID()+"\n";
+    msg += "Variant: "+mouseVCF.getRef()+" -> "+mouseVCF.getAlt().toString()+"\n";
+    msg += "Qual: "+mouseVCF.getQuality()+"\n";
+    String pl;
+    if((pl = mouseVCF.getFormatValue("PL")) != null && pl.split(",").length > 1)
+      msg += "PL: "+pl+"\n";
     return msg;
   }
   
@@ -755,7 +756,7 @@ public class VCFview extends JPanel
   protected void paintComponent(Graphics g)
   {
     super.paintComponent(g);
-    mouseOverVCFline = null;
+    mouseVCF = null;
 
     float pixPerBase = getPixPerBaseByWidth();
     int start = getBaseAtStartOfView();
@@ -1013,19 +1014,16 @@ public class VCFview extends JPanel
         g.setColor(Color.gray);
       else if(record.getAlt().isInsertion(vcf_v4))
         g.setColor(Color.yellow);
-      else if(record.getAlt().length() == 1 && record.getRef().length() == 1)
-        g.setColor(getColourForSNP(record, features, basePosition));
-      else
-      {
-        if(record.getAlt().isMultiAllele())
+      else if(record.getAlt().isMultiAllele())
       {
         g.setColor(Color.orange);
         g.fillArc(pos[0]-3, pos[1]-LINE_HEIGHT-3, 6, 6, 0, 360);
       }
+      else if(record.getAlt().length() == 1 && record.getRef().length() == 1)
+        g.setColor(getColourForSNP(record, features, basePosition));
       else
         g.setColor(Color.pink);
     }
-    }
 
     if(markAsNewStop)
       g.fillArc(pos[0]-3, pos[1]-(LINE_HEIGHT/2)-3, 6, 6, 0, 360);
@@ -1081,7 +1079,7 @@ public class VCFview extends JPanel
     else if(variant.equals("T"))
       return Color.black;
     else
-      return Color.magenta;
+      return Color.magenta; // non-variant
   }
   
   /**
@@ -1229,7 +1227,7 @@ public class VCFview extends JPanel
        mousePoint.getX() > pos[0]-3 &&
        mousePoint.getX() < pos[0]+3)
      {
-       mouseOverVCFline = record.toString();
+       mouseVCF = record;
        mouseOverIndex = i;
      }
   }
@@ -1477,34 +1475,33 @@ public class VCFview extends JPanel
          if(showDetails != null)
            popup.remove(showDetails);
          
-         if( mouseOverVCFline != null )
+         if( mouseVCF != null )
          {
-           final String parts[] = tabPattern.split(mouseOverVCFline, 0);
-      
-           showDetails = new JMenuItem("Show details of : "+parts[0]+":"+parts[1]+" "+parts[2]);
+           showDetails = new JMenuItem("Show details of : "+
+               mouseVCF.getChrom()+":"+mouseVCF.getPos()+" "+mouseVCF.getID());
            showDetails.addActionListener(new ActionListener()
            {
              public void actionPerformed(ActionEvent e) 
              {
-               FileViewer viewDetail = new FileViewer(parts[0]+":"+parts[1]+" "+parts[2], true, false);
+               FileViewer viewDetail = new FileViewer(
+                   mouseVCF.getChrom()+":"+mouseVCF.getPos()+" "+mouseVCF.getID(), true, false);
                
                viewDetail.appendString(header[mouseOverIndex]+"\n", Level.INFO);
                
-               viewDetail.appendString("Seq   : "+parts[0]+"\n", Level.DEBUG);
-               viewDetail.appendString("Pos   : "+parts[1]+"\n", Level.DEBUG);
-               viewDetail.appendString("ID    : "+parts[2]+"\n", Level.DEBUG);
-               viewDetail.appendString("Ref   : "+parts[3]+"\n", Level.DEBUG);
-               viewDetail.appendString("Alt   : "+parts[4]+"\n", Level.DEBUG);
-               viewDetail.appendString("Qual  : "+parts[5]+"\n", Level.DEBUG);
-               viewDetail.appendString("Filter: "+parts[6]+"\n", Level.DEBUG);
-               viewDetail.appendString("Info  : "+parts[7]+"\n", Level.DEBUG);
+               viewDetail.appendString("Seq   : "+mouseVCF.getChrom()+"\n", Level.DEBUG);
+               viewDetail.appendString("Pos   : "+mouseVCF.getPos()+"\n", Level.DEBUG);
+               viewDetail.appendString("ID    : "+mouseVCF.getID()+"\n", Level.DEBUG);
+               viewDetail.appendString("Ref   : "+mouseVCF.getRef()+"\n", Level.DEBUG);
+               viewDetail.appendString("Alt   : "+mouseVCF.getAlt().toString()+"\n", Level.DEBUG);
+               viewDetail.appendString("Qual  : "+mouseVCF.getQuality()+"\n", Level.DEBUG);
+               viewDetail.appendString("Filter: "+mouseVCF.getFilter()+"\n", Level.DEBUG);
+               viewDetail.appendString("Info  : "+mouseVCF.getInfo()+"\n", Level.DEBUG);
                
-               if(parts.length > 8)
+               if(mouseVCF.getFormat() != null)
                {
                  viewDetail.appendString("\nGenotype information:\n", Level.INFO);
-                 viewDetail.appendString("Format: "+parts[8]+"\n", Level.DEBUG);
-                 for(int i=9; i<parts.length; i++)
-                   viewDetail.appendString(parts[i]+"\n", Level.DEBUG);
+                 viewDetail.appendString("Format: "+mouseVCF.getFormat()+"\n", Level.DEBUG);
+                 viewDetail.appendString(mouseVCF.getSampleDataString()+"\n", Level.DEBUG);
                }
                
                viewDetail.getTextPane().setCaretPosition(0);