Merged in .py stripped files from vcf2trees branch
Updated Docs and Setup.py with new script names
Updates.
Removed vcf2trees.py from this branch
Fixed buffered output error.
updated maptasksperchiled to 10000
Fixed GQ error
Added new filter command and minor txt revision
Fixed filter issue
Merge branch 'master' of github.com:ngcrawford/pypgen into vcf2trees
Merge SCC changes.

Merge branch 'vcf2trees' of github.com:ngcrawford/pypgen into vcf2trees

Conflicts:
	pypgen/parser/VCF.py
	scripts/vcfSNVfstats
Minor updates
Fixed setup.py
Merge branch 'vcf2trees' of github.com:ngcrawford/pypgen into vcf2trees

Conflicts:
	setup.py
updates.