fix drawPairedStackView() for reads on different contig

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@12332 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/alignment/BamView.java

@@ -1243,7 +1243,8 @@ public class BamView extends JPanel
       }
       else
       {
-        if(!pr.sam1.getMateUnmappedFlag())
+        if(!pr.sam1.getMateUnmappedFlag() &&
+            pr.sam1.getMateReferenceName().equals(pr.sam1.getReferenceName()))
         {
           int prStart;
           
@@ -1965,7 +1966,7 @@ public class BamView extends JPanel
     menu.add(maxHeightMenu);
 
     final String hgts[] =
-       {"500", "800", "1000", "1500", "2500", "5000"};
+       {"500", "800", "1000", "1500", "2500", "5000", "50000"};
     
     ButtonGroup bgroup = new ButtonGroup();
     for(int i=0; i<hgts.length; i++)