added some (currently commented out) code that might reduce artifacts caused by alignment segmentation
added some (currently commented out) code that might reduce artifacts caused by alignment segmentation

jts/nanopolish,mateidavid/nanopolish,mateidavid/nanopolish,mateidavid/nanopolish,mateidavid/nanopolish,jts/nanopolish,mateidavid/nanopolish,jts/nanopolish,jts/nanopolish,jts/nanopolish