Variant: add filter field functionality

* add has_filter() to the public API
* add filters() member function to the public API
* add tests

closes #80
Merge pull request #86 from broadinstitute/mc_filter_field

Variant: add filter field functionality
VariantReader: add subsetting samples constructor

you can now use this iterator to discard samples in your iteration (this
significantly speeds up iteration over a vcf and bcf file.

* add test case for sites only vcf
* add test case for different levels of subsetting
VariantField: fix size() member function for sites with no genotypes

closes #88
Merge pull request #90 from broadinstitute/mc_sites_only_variant_reader

VariantReader: add subsetting samples constructor
addressing simple gcc warnings
Merge pull request #92 from broadinstitute/mc_fix_warnings_on_sam_builder

addressing simple gcc warnings
SamBuilder: zero out TLEN field

Since we can't generally calculate a value for the TLEN field, always
set it to 0 in SamBuilder (which in the SAM spec means that the information
is unavailable)
Merge pull request #94 from broadinstitute/dr_sam_builder_handle_tlen

SamBuilder: zero out TLEN field
Update README

Remove --remote from the submodule recommendations.
Travis: move doxygen updates to it's own script
Travis: move boost-build to /Users/carneiro/build
Travis: move GCC to it's own script
Travis: move CLANG to it's own script
Travis: move BOOST to it's own script
Merge pull request #100 from broadinstitute/mc_travis_updates

Travis: overhaul script to call out to scripts #64
ref/alt alleles
Merge pull request #101 from broadinstitute/ak_refalt_persite_issue98

ref/alt alleles
Variant: ref/alt unpack only what's necessary

* move ref test to the top of the list to make sure no other unpacking  was happening and it still works
* add a BCF version of the vcf to the test (vcfs are fully unpacked anyway)
Merge pull request #102 from broadinstitute/ak_refalt_persite_issue98

Variant: ref/alt unpack only what's necessary