JCSCache configuration updated. 
Integer keys are now used.
functions using Annotation.trim() are updated to allow for trim()
returning an Annotation instead of updating itself.
functions using Annotation.trim() are updated to allow for trim()
returning an Annotation instead of updating itself.
functions using Annotation.trim() are updated to allow for trim()
returning an Annotation instead of updating itself.
AlignmentPair is corrected to write record correctly using the NH flag.
For a multi-mapped read, the pair is appropriately if the next mapping
in on a different chromosome.
functions using Annotation.trim() are updated to allow for trim()
returning an Annotation instead of updating itself.
functions using Annotation.trim() are updated to allow for trim()
returning an Annotation instead of updating itself.
Small bug in Scripture to connect is corrected so that does not loop
unnecessarily and functions using Annotation.trim() are updated to allow
for trim() returning an Annotation instead of updating itself.
functions using Annotation.trim() are updated to allow for trim()
returning an Annotation instead of updating itself.
Bug in PairedEndWriter is fixed and memory reduced as tempCollection is
maintained correctly, and purged appropriately. The distance-related fix
is not committed. 
~25% faster than older implementation.
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git