update ycm files for new directory structure
Setters for the simple members of the Sam API

only those whose data can be accessed independently inside the bam1_t
and bam_core_t structs. Basically the ones with fixed length.

* add simple members for alignment fields
* add simple flags
* add tests to all functions

this closes #13
Merge pull request #19 from MauricioCarneiro/mc_simple_setter_api

Setters for the simple members of the Sam API
add simple setters as described on issue #13
Reduce code duplication in Sam API

make Sam inherit from both SamHeader and SamBody to avoid the
duplication of code and simplify writer and all other APIs.

This closes issue #16