add view method
view method

works on small files
unplugged all ffi code, setup for rewrite

dropping FFI basis, moving to new code base. Renamed old class files
for bio Sam
add view method
new Bio::DB::Alignment class
add fetch and fetch with function methods
add mpileup method
add chromosome_coverage method
add fetch_reference method
add faidx method
test skeletons
updated .gitignore
added sorted.bam
added reheader method
added gitignore for gem
Updated faidx method to run with no options
Added code for calmd
Added methods for targetcut and phase
added tests for index_stats, etch_with_function, fetch_reference, sort, mpileup, depth and index
Added test data and code for fixmate, flatstat and merge