Revise PairedEndAlignment .  Now the  toSAMFile() function report the
correct position.

Add BamToPairedEndIterator class in src/java/nextgen.core.reader
and test class BamToPairedEndIteratorTest  in
src/test/nextgen.core.reader
Merge branch 'master' of https://github.com/mgarber/scriptureV2