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
Merge pull request #288 from broadinstitute/jt_move_field_type

Move the field_type checks to VariantHeader
Genotype: add convenience functions: snp, indel...

This is a tricky request from Louis which I anticipate to be a big hit
with the compbios. Everyone wants to query directly at the genotype what
kind of event it is. The problem is that doing so is expensive. One
should always strive to batch this kind of computation across all
samples using functionality like select_if or simple for_each loops.

However sometimes you want to just query one or two of these conditions
and it is nice to have such convenience functions. I strived here to
achieve as much performance as possible without increasing the state of
the Genotype object. To avoid string comparisons, all member functions
rely on an AlleleMask that pre-computes the string differences in the
alt/ref fields only once. All functions operate on key comparisons only.

Still, if you are going to use this for multiple comparisons such as:

```c++
if (genotype.insertion() || genotype.snp() && genotype.simple())
  do_something(genotype);
```

You will most likely be better off writing your own for loop instead of
paying for 3 passes on the data. But for quick queries in data with few
alleles (like diploids) this should be fine.

closes #204