Merge pull request #3 from chmille4/master

fix fragment length calculation
Included jansson-2.5 into the source tree
Starting to create separate classes for stats collecting
The BasicStatsCollector for scalar statistics is working
Broken the original logics into three collectors
Broken the original logics into three collectors
Merge branch 'yq-develop'

Conflicts:
	AbstractStatCollector.h
class comment of AbstractStatCollector is improved
Introduced the "isSatisfied" function to deal with smart termination
Added the Change Monitor base class and Delta Average Ratio monitor
Moved DeltaAverage monitor inline to use template
Added a new, standard deviation based change monitor
Using Stddev Monitor in BasicStatsCollector.
Other collectors are temp.ly turned off for debugging purpose
Using precompiled header for freq. used ones
Ignoring .DS_Store now
Disabled debug output, and started using unique_ptr
Fragment Length calc. checks if two mates are mapped to the same chr
Merge branch 'yq-develop'
Coverage Histogram, and bug fixes
A critical initialization bug is fixed in CoverageMapStatsCollector

Also, a few dumb pointers are replaced by c++11 unique_ptr
Got rid of the c++11 stuffs