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)
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
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 ...