This fixes a null pointer exception was thrown when the cigar string

contains a deletion immediately prior to the intron. 

This is because the junction counting method required that the read
nucleotides flanking the junction are aligned to the genome. This
commit relaxes this requirement so that the null pointer exception is
not thrown.

IsoSCM/src/processing/FindSpliceJunctions.java

@@ -766,7 +766,10 @@ public static void updateJunctionCounts2(SAMRecord sr, MapFactory<Character, Map
 			if(cigarElement.getOperator().consumesReferenceBases()){
 				boolean consumesReadBases = cigarElement.getOperator().consumesReadBases();
 
-				if(consumesReadBases){
+				if(cigarElement.getOperator()==CigarOperator.N){
+					alignmentPosition+=cigarElement.getLength();
+				}
+				else{
 					for(int j=0; j<cigarElement.getLength(); j++){
 						if(lastAlignedPosition!=null){
 
@@ -797,9 +800,6 @@ else if(alignmentPosition-lastAlignedPosition!=1 && prevCigarElement.getOperator
 						alignmentPosition++;
 					}
 				}
-				else{
-					alignmentPosition+=cigarElement.getLength();
-				}
 			}			
 			prevCigarElement = cigarElement;
 		}