Added a DiskBackedQueue and began alterations to MarkDuplicatesWithMateCigar. Much much work to do. Committing these changes in advance of move to git

Conflicts:
	src/java/net/sf/picard/sam/markduplicates/MarkDuplicatesWithMateCigarIterator.java
	src/java/net/sf/picard/sam/markduplicates/ReadEnds.java