htsjdk version 1.122

htsjdk version 1.122
Cleanups regarding temporary files in tests

Delete index files for temp files at the end of testing, and
do not write temp files within source directory.
Merge pull request #127 from bpow/testing-fixes

Prevent testing from leaving extra files around
htsjdk version 1.123

htsjdk version 1.123
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.
Added setOption and reapplyOptions methods to SamReaderFactory.
Deprecated truncated reader.
Exposed file extension from Type.
Added reference fasta to SamReaderFactory and SamWriterFactory to facilitate CRAM support.
Use SamReaderFactory makeDefault with reference sequence whenever possible to allow for CRAM support.

fixed the multiref slice building code.
Conflicts:
	src/java/htsjdk/samtools/cram/build/ContainerFactory.java

relaxed EOF marker by ignoring ITF8 hanging bits

initial commit of indexing for CRAM

added static methods for CRAI parsing and building in-memory index

added crai building methods that takes input stream

fix for pairing primary and secondary alignments separately when writing
CRAM
Conflicts:
	src/java/htsjdk/samtools/CRAMFileWriter.java