Update find_near_exonjunction.m
Fix gc_count to actually count
Improve implementations

Especially improved are blast_check, as well as a helpful tester script,
find_near_exonjunction, and individual scoring.
I also added a .gitignore in order to allow me to keep some notes separate
from the main repo.
Fix comment in gc_count

This resolves recent pull request by Sarah.
Implement hairpin scoring
Clean up obsolete functions

These are no longer necessary, or the functionality if covered by other
functions.
Add preliminary blast_check function, test script
Implement basic individual oligo scoring
Start migrating oligo representation

Oligos are now being represented by an index and length that are to refer to
the forward coding sequence.
Reverse primers should be treated accordingly.
Start working on trunk function

The trunk function is now select_primers.
I also worked on a few of our branch functions to smooth out how they
represent data.
Debug Jason's sloppy trunk code