Tweaking high-coverage branch thresholds, not final
sga-preqc now outputs JSON using the rapidjson library
Cleanup preqc python
Added fragment size distribution output
First pass at per-base quality score metrics
Cleaned up output
Revising gc composition stats
New gc plot
Added missing rapidjson headers to the makefile, minor formatting tweaks
Minor output changes
New 2D histogram of (gc, coverage) pairs
Fewer data points for gc distribution
Work-in-progress of finding overlaps using approximate seeds
Multiple approximate seeds/both strands now working.
Implemented a de bruijn graph haplotype builder that uses paired end data
Trying out idea of using read-coherent paths through the graph to constrain the haplotype search.
Do not expand guide/targets to new variant kmers.
Code cleanup and impose a minimum distance during paired dbg haplotype construction
Reverted to more conservative alignment criteria
Reenable all preqc metrics