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>();