Sam: add insert_size member function

fixes #224
Merge pull request #225 from broadinstitute/mc_insert_size

Sam: add insert_size member function
Sam: rename next => mate
Add eclipse project files to .gitignore
Merge pull request #229 from broadinstitute/jt_gitignore

Add eclipse project files to .gitignore
Added vim backup directories (.vimbup/) to .gitignore.
Merge pull request #231 from broadinstitute/bh_vimbup_gitignore

Added vim backup directories (.vimbup/) to .gitignore.
updating hom_ref and hom_var to work with alternate ploidies
adding tests for non diploid hom_var, hom_ref
Merge pull request #230 from lbergelson/lb_homozygous_works_on_all_purities

updating hom_ref and hom_var to work with alternate ploidies
HTSLIB: move to broad branch
SyncedVariantReader/Iterator
- variant_reader_test refactoring
Add .vcf.gz test to VariantReader/Iterator and MultipleVariantReader/Iterator
Add warnings to incomplete identity checks
Merge pull request #232 from broadinstitute/jt_synced

SyncedVariantReader/Iterator
Enable the use of SyncedVariantReader with no intervals
Merge pull request #236 from broadinstitute/jt_sync_no_intervals

Enable the use of SyncedVariantReader with no intervals
Cache headers instead of deep copying every time
Merge pull request #238 from broadinstitute/jt_sync_cache_headers

Cache headers instead of deep copying every time
Rename Genotype::alleles_keys to allele_keys
Merge pull request #241 from broadinstitute/lb_rename_alleles_keys

Rename Genotype::alleles_keys to allele_keys