CLI frontend: set conf.setClassLoader

Appears to be necessary at least in CDH 4.2.0.
LazyBAMRecord: fix bad old copy-pasto
LazyBAMRecord: invalidate name cache correctly
BAMSplitGuesser: accept EOF only after a good read
Twiddle whitespace
BAMSplitGuesser: separate pre- and mid-read EOF
Merge remote-tracking branch 'upstream/master'