Copied str method from foghorn.
Merge pull request #278 from broadinstitute/lb_277_move_interval_changes_to_gamgee

Copied str method from foghorn interval
Add reference_iterator.h and reference_map.h
Merge pull request #279 from broadinstitute/jt_gamgee_h

Add reference_iterator.h and reference_map.h
Mark tsca_tiling as const
- needed by oligo_designer in foghorn
Merge pull request #280 from broadinstitute/jt_tsca_tiling_const

Mark tsca_tiling as const
Adding current interval accessor to indexed_sam_iterator.
Travis: add precompiled packages for our tools

* add doxygen 1.8 binary package
* add clang-3.5 + clang modernize
* add gcc 4.9

I also have a boost package compiled with gcc 4.9 but the current clang
package depends on gcc 4.8 (for stdlibc++) and resolving this was a
dependency nightmare that I decided to postpone. Boost-155 is currently
being used from a PPA.

I also added clang-format and clang-modernize #56 but I will only close
that item when we actually use them in the build process. It's available
now.

closes #57
Merge pull request #281 from broadinstitute/mc_travis_experiments

Travis: add precompiled packages for our tools
Merge pull request #282 from broadinstitute/lb_276_add_interval_accessor

Adding current interval accessor to indexed_sam_iterator.
Move the field_type checks to VariantHeader
- necessary when merging variants: not all variants will have all fields,
  but the merged header will
rev htslib
ReferenceBlockSplittingVariantIterator
- uses htslib hack to modify Variant (TODO: use VariantBuilder)
- TODO: test ref bases
VariantBuilder
Remove VariantBuilder signed-unsigned comparisons