set compilation flags on load


Former-commit-id: dd7edb4ca21b875b9e5b0f4c1d7346f850d4db62
move test data to own directory, use robust data paths


Former-commit-id: 5badf6c066f1194befa97823091454799d28038d
handle situation where we run out of sequences for Nx


Former-commit-id: 8286a2f3fc0cc87491905e22b93a2bec4d9441cd
set GCC flags to empty for inline compilation


Former-commit-id: bce704a2b134fc675cfd2847231c0677c52d4ba5
remove unneeded logging


Former-commit-id: 8efa17fef71e9092bf7ec3c8e104f1b41b5eee20
add test-unit to fix weird shoulda errors


Former-commit-id: 2f22733b84f473efd86f8cd8ebdf8a9393daee8a
remove more logging


Former-commit-id: 78f5650021109a8971cd2d2c24b807615a5dc015
merge in master
create new contig class
move to contig WIP
add bindeps for blast and bowtie2 dependencies
add deps for bindeps, update travis install script
fix travis build script
Merge branch 'master' into samtools
ignore blast test output files
contig fully implemented with tests
fix enumeration of contig bases
bring contig metrics in line with new contig model
fix test data filename in ComparativeMetrics test
update inline tests for new Contig model, cleanup style