Some support for VCF v4.2 files added:
Handles "Number=R" for INFO fileds in the header.
Other VCF v4.2 specific additions (Eg: Source and Version fields in INFO header lines) are not handled, but appear to be silently ignored.
Tested on output of samtools mpileup | bcftools call (1.0-17-gfaf4dd6, 1.0-55-gc661821, using htslib 1.0-11-g830ea73)
Fixed the behavior of BCF2Utils.toList() when it's given an array
 * Old version return a List with a single element, which was the provided array.  This broke BCF writing, in particular when a FORMAT annotation used arrays instead of Lists
 * Made toList generic, rather than returning a List<Object>
 * Removed the redundant BCF2FieldEncoder.toList()
 * Added unit tests
Merge pull request #126 from travc/master

Some support for VCF v4.2 files added
Merge pull request #129 from pdexheimer/pd_bcf_attrib_arrays

Fixed the behavior of BCF2Utils.toList() when it's given an array
Added ability to open SamReader from string, specifying either a URL or a file path.
This will make it easier treat INPUT parameters in Picard tools uniformly regardless of whether they designate a file or URL resoures.
Url detection and decision of whether the resource is file based on url based is done in SamInputResource.
Merge pull request #125 from iliat/ga4gh-work

Added ability to open SamReader from string, specifying either a URL or ...
htsjdk version 1.124

htsjdk version 1.124
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