Fixed Bug 254: stranded merge of BedPlus records w/ strand. Added strand to default output for stranded merge. Added and updated unit tests.

Added distinct_sort_num and distinct_sort_num desc to VectorOps (and groupBy) and KeyListOps. Added -delim to groupBy.

Completed #181, GFF can have extra fields. Also, SVlen in VCF takes max of more than two numbers (as opposed to min)

Addressed >2 numbers in VCF SVLEN, can appear at endl w/ tab, semi-co…

Removed accidental copy in BinTree to fix speed

Changed common help to remove -names, -filenames, and -sortout from all tools but intersect and closest.

Addressed BinTree memory blow-up; -m in fisher (w/ unit tests)

Getfasta fixes

If modification time of a FASTA index file is less than modification
time of its FASTA file, then the warning message is shown; resolves
#228.

fixed sample and coverage unit tests, fixed up CommonHelp for all PFM tools