Made sga-preqc-report.py deal with bad json gracefully.
Merge pull request #68 from deltadev/sga-preqc-py-patch

Made sga-preqc-report.py deal with bad json gracefully.
preqc: added mode to quickly output basic read stats. Closes #64
index: Only allow one of -a or -d to defined. Closes #67
new options to variant-filters

Conflicts:

	src/bin/sga-variant-filters.pl
used htslib instead of vcftools
Added an interactive mode to graphdiff for debugging
Added new alignment-based filters
Added AF filter and output file parameter
Merge branch 'master' of https://github.com/jts/sga