fix coverage for reads with gaps

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14128 ee4ac58c-ac51-4696-9907-e4b3aa274f04

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

@@ -43,6 +43,7 @@ import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 
+import net.sf.samtools.AlignmentBlock;
 import net.sf.samtools.SAMRecord;
 
   public class CoveragePanel extends JPanel
@@ -147,8 +148,6 @@ import net.sf.samtools.SAMRecord;
         int offset = jamView.getSequenceOffset(thisRead.getReferenceName());
         offset = offset - jamView.getBaseAtStartOfView();
 
-        int length = thisRead.getReadLength();
-
         String fileName;
         if(bamList.size() > 1)
           fileName = bamList.get((Integer) thisRead.getAttribute("FL"));
@@ -164,11 +163,15 @@ import net.sf.samtools.SAMRecord;
           plots.put(fileName, coverage);
         }         
         
-        for(int j=0; j<length;j++)
+        List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
+        for(int j=0; j<blocks.size(); j++)
         {
-          int bin = 
-            (int)((thisRead.getAlignmentStart() + j + offset) / windowSize);
+          AlignmentBlock block = blocks.get(j);
  
+          for(int k=0; k<block.getLength(); k++)
+          {
+            int pos = block.getReferenceStart() + k + offset;
+            int bin = pos/windowSize;
             if(bin < 0 || bin > nBins-1)
               continue;
             
@@ -184,6 +187,7 @@ import net.sf.samtools.SAMRecord;
             }
           } 
         }
+      }
 
       int size = jamView.bamList.size();
       if(includeCombined)