Preliminary commit of performance changes
Interim commit to merge with main branch
Merge branch 'master' of https://github.com/mgarber/scriptureV2

Conflicts:
	src/java/nextgen/core/programs/ConvertBamToPairedEnd.java
Moved scan statistics computations to its own class to simplify its access and make things a bit more clear and easier to find
Cleaned up paired alignment writer a bit before pushing