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