Range inputRange = this.inputRangesIterator.next();
int prevReferenceIndex=-1;
int prevAlignmentStart=-1;
this.toAddToGraphList = new ThreadPoolLinkedList();
this.toAlignList = new ThreadPoolLinkedList();
this.graph = new Graph();
this.io.query(this.referenceDictionary.getSequence(inputRange.referenceIndex).getSequenceName(),
inputRange.startPosition,
inputRange.endPosition);