start on proper post processor
Rename of utils

Coverage counter is now called freq_seq, `pp.c` renamed to post_processor (to
reflect it`s job)
Merge branch 'master' into validate

Move updated base_index_finder into validaton branch
remoced copy-pasted base_index finder
Merge branch 'master' into validate

Giving utils acess to helper functoins in headers
Basic logic of post processor in place

- Compiles (!)
- Collects summary data for all samplesi (class SiteData)
- Visitor then identifies mutant sample and mutant allele
- Now need to summarise data for each and spit it out
post processor compiles
all 'original' data now included in post-processor output
added include for numeric

(Needed to use accumulate, and for compilation of FreeBSD)
main loop now actually opens it's outstream
Visitor loops properly align

Lat commit was buggy - evaluating most of the loop for _all_
aligmnets it saw, rather only those matching the selected target
bug in Visitor (evaluating once per ali)
Redesign of post_processor

Hopefully this represents a cleaner approach...

-New classes represented site for one sample/whole experiment
-Appropriate classes suck up alignment data/call genotypes/export summary
-Visitor class now handles parsing BAM, only calls methods from other classes
to process the results
Post processor functional

- Correctly skipping non-target bases
- Printing data per site

NOTE:
As of this commit Vistior prints to stdout (makes debuggin easier for now)
Added mutant strain frequency to output
corrected bug in indexing mutant sample
Merge branch 'validate'
post-processor prints line fro inital data
Major re-write of post_processor

New approach writes all data required to calculate stats from Li 2014
(http://arxiv.org/abs/1404.0929) and Sung 2012 for validatoin.
clean up of error reporting for post processor