Merge pull request #90 from bpow/jdk8-ternary

Jdk8 ternary
removed an old 'addPair' function on which others relied: add it back
Merge pull request #92 from samtools/nh_samfiletester_fix

removed an old 'addPair' function on which others relied: add it back
output '.' when uniquing interval lists and merging their names
Merge pull request #93 from samtools/nh_bed_to_interval_list

output '.' when uniquing interval lists and merging their names
a couple of comment tweaks
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.
test DiskBackedQueue switching to read-only mode
Merge pull request #94 from ryan-williams/comments

a couple of comment tweaks
removed cofoja from IDE config files
remove cofoja-related items from build.xml and IDE config files
Merge pull request #1 from bpow/nocofoja

removed cofoja from IDE config files
Merge pull request #95 from dmyersturnbull/master

Removed Cofoja as a dependency.
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
Merge pull request #96 from pdexheimer/pd_trailing_format_fields

Added an option to VCFWriter to write the entire FORMAT field, even if t...
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
Merge pull request #100 from samtools/nh_readme_doc_update

README.md points to the HTSJDK documentation github pages site
Merge pull request #101 from samtools/nh_bugfix_validation_stringency_on_sam_reader_factory

The SamReaderFactory needs to expose a way to set the default validation
do not enforce by default that intervals that will be merged have the
same strand