vcffilter,gtcheck: Added sanity checks; Extended help message; Changed the order of columns on gtcheck output
plot-vcfcheck: Produce the overlap by AF graphs
synced read and vcftools: Changed the -f, --apply-filters switch so that it accepts a list of allowed FILTERs. This is useful for example in cases when PASS has to be distinguished from "."
vcffilter: FILTER column of hard-filtered sites now lists failed filters; Unset the FILTER of skipped sites only with -u switch, not by default.
vcfcheck: Fixed a bug in initialization of frame-shift calculation; More detailed FS output
vcfnorm: Removed two assertions to allow realignment of MNPs