Adding a function to give the canonical read name, defined as the
concatenation of the read group identifier and the read name.

DuplicateScoringStrategy: a class to help with picking a non-duplicate
from a set of candidate duplicates.

SAMRecordSetBuilder: many improvements to support more complex SAMRecord
creation.

Code cleanup in SortingCollectionTest

We are adding utilties to support Picard's MarkDuplicatesWithMateCigar,
   but put them here as they may be generally useful to folks.
   DiskBackedQueue: a queue for SAMRecords that stores the records in
   memory until a limit is reached, and then writes them to disk.  The
   queue returns records only when the consumer has set the given record
   as examined.  We also added other classes to support this utility.
Merge pull request #85 from samtools/bt_mark_duplicates

Bt mark duplicates
Fixes two issues related to compilation under jdk8:

1. make '-proc:none' the default for all compilation

Since cofoja is not used outside of 'variant', there is no need
for the processor to be run there (it had been excluded from
running in 'variant' as well to prevent contract processing).

Also, the version of cofoja used by htsjdk currently will not
run under java 8 due to api changes in oracle-private packages

2. compatibility with java 8 strictness regarding generics in poly expressions

see background in:
http://docs.oracle.com/javase/specs/jls/se8/html/jls-15.html#jls-15.25.3
http://stackoverflow.com/questions/22509488/generics-compilation-error-with-ternary-operator-in-java-8-but-not-in-java-7
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...
Fixes related to JDK8 in SamFileHeaderMergerTest

1. SAM test files had spaces as delimiters in
   some headers (spec requires tab delimiters)
2. The order of attributes in merged headers
   is non-deterministic (and turns out to be
   different in jdk8 than in earlier versions).
   This tests the headers independent of
   attribute order.
travis tests on oraclejdk8