Merge pull request #103 from samtools/nh_really_fix_supplementals

adding a method to help set mate cigars and mate information given a
Fixes related to JDK8 in SamFileHeaderMergerTest

1. SAM test files had spaces as delimiters in
   some headers (spec requires tab delimiters)
2. The order of attributes in merged headers
   is non-deterministic (and turns out to be
   different in jdk8 than in earlier versions).
   This tests the headers independent of
   attribute order.
3. jdk8 tearDown complains when tmpDir is empty
   in SortingCollectionTest, earlier jdks
   ignored this.
travis tests on oraclejdk8
Merge pull request #89 from bpow/SAMFileHeaderMergerTest-order

SAMFileMergerTest relies on HashMap ordering produced by jdk6/7
Add the option of using original quality scores for determining the encoding scheme.
Merge pull request #104 from samtools/kt_revert_sam_use_oq_for_detection

Add the option of using original quality scores for determining the enco...
Master rebase and fixups for deprecations.
initial cram code base commit
added lossy options to CRAMFileWriter;
force lossless mode by default if no policies are given
lazy init of qs preservation with "*8"
Updated htsjdk to use SamReader instead of the deprecated SAMFileReader.
Also fixed a bug in the tlen calculation for cram compression records.
Master rebase and fixups for deprecations.