Add htslib as a dependency of the gamgee target
Add an install target for Gamgee

Installs the Gamgee library and required header files using the CMake
install mechanism.

This is also useful for dependent projects to be able to easily find
Gamgee after building it.
Add option to install dependencies

When building a project that depends on Gamgee, we want to make sure we
also expose any libraries required to build and link with Gamgee. This
adds an option to install those dependencies during the build.

Note that this could conflict with existing packages if we're
installing to a system location, so it is off by default. This is
intended for use only by projects that depend on Gamgee.
Modify htslib.cmake to inherit number of jobs

Calling make using the $(MAKE) built-in variable will inherit the
number of simultaneous jobs to run when the parent project is being
built with make.

If the parent uses a different build system, because of the lack of job
control, building htslib in parallel is likely to be counter-productive
as the parent build system is likely running in parallel already.
Merge pull request #352 from nsubtil/cmake-fixes

CMake fixes for Firepony
Travis: add prebuilt cmake 3.1

* update the commented out code that was only for 2.8.7
Merge pull request #353 from broadinstitute/mc_travis_update_cmake

Travis: add prebuilt cmake 3.1
ReferenceBlockSplittingVariantIterator
- uses htslib hack to modify Variant (TODO: use VariantBuilder)
- TODO: test ref bases
MultipleVariantReader changes causes the test case for Issue #209 to pass
- but the issue still exists, so add a new test case
1. Modified ReferenceBlockSplittingVariantIterator to insert 'N' as the
reference allele for a split <NON_REF> GVCF interval. This is done by
introducing a function set_reference_allele() in Variant.
2. Uncommented the test cases for
ReferenceBlockSplittingVariantIteratorr reference allele
3. The problem*.vcf files failed because their headers did not declare
an END field. htslib assumes that fields which are not declared are of
type String. Declaring END as an integer field in these files solves the
problem.
Make temporary mutators private