Merge pull request vgteam#1313 from vgteam/release

Release

Merge pull request vgteam#733 from vgteam/runtime-perf

Increase the pair window by an alignment length

Merge pull request vgteam#199 from edawson/master

Incorporate new GFA parser + updated GFA spec

small updates: debugging, change in alignment viz, msga

Alignment viz now writes out the whole mapping object. This should be improved with the alignment text format TGAM here:

https://github.com/adamnovak/hgvm-aligner-bakeoff-compliance/blob/master/Text%20Graph%20Alignment%20Map%20Format.md

Also, (slow) but useful hash functions for getting the sha1sum of a vg graph.

add vg validate (resolves vgteam#126)

cleans up debugging file outputs

Merge branch 'dnanexus-rnd-mlin-find-remove-orphans'