506d39f751a77d29e54686b87eb106c629c7d4bd,java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java,BaseTransitionTableCalculatorJavaWalker,initialize,#,58

Before Change


        UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
        uac.baseModel = BaseMismatchModel.THREE_STATE;
        uac.ALL_BASES = true;
        ug = UnifiedGenotyper.getUnifiedCalculationArguments(getToolkit(), uac);
        // refWindow = new ReferenceContextWindow(nPreviousBases);
        usePreviousBases = new ArrayList<Boolean>();
        previousBaseLoci = new ArrayList<GenomeLoc>();

After Change


        if ( nPreviousBases > 3 || ( nPreviousReadBases > 3 && readBasesMustMatchRef ) ) {
            throw new StingException("You have opted to use a number of previous bases in excess of 3. In order to do this you must change the reference window size in the walker itself.");
        }
        UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
        uac.baseModel = BaseMismatchModel.THREE_STATE;
        uac.ALL_BASES = true;
        ug = new UnifiedGenotyperEngine(getToolkit(), uac);
        // refWindow = new ReferenceContextWindow(nPreviousBases);
        usePreviousBases = new ArrayList<Boolean>();
        previousBaseLoci = new ArrayList<GenomeLoc>();