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