adding methods to help set mate cigars and mate information given a
queryname sorted iterator.  This is useful when we want to fix or update
the mate information, including the mate cigar.
removed an old 'addPair' function on which others relied: add it back
output '.' when uniquing interval lists and merging their names
a couple of comment tweaks
test DiskBackedQueue switching to read-only mode
Removed cofoja as a dependency and simply removed all references to it. This allows building under Java 8, which has been out for a while. The old annotations can be replaced with javax.validation annotations later.
removed cofoja from IDE config files
remove cofoja-related items from build.xml and IDE config files
Added an option to VCFWriter to write the entire FORMAT field, even if the trailing values are missing and could therefore be trimmed.  Also fixed ParsingUtils.split() to correctly handle the case where the only delimiter is the first character
Release 1.120
README.md points to the HTSJDK documentation github pages site
The SamReaderFactory needs to expose a way to set the default validation
stringency
do not enforce by default that intervals that will be merged have the
same strand
Adding copyrights to some recently added classes
added methods to check for readability/writability of list of files
Merge pull request #103 from samtools/nh_really_fix_supplementals

adding a method to help set mate cigars and mate information given a
Merge branch 'master' of https://github.com/samtools/htsjdk