v2.2.0
Pre-release
Pre-release
Improved phase set/block analysis
- vcfdist now skips unphased variants by default
- add phasing info from
PS
tag - switch "errors" only counted if they occur within phase sets
- added phase set count and NG50 (inputs)
- calculated phase block NG50 (break on switches) and NGC50 (break on flips and switches)
- reorganization and variable renaming in
phase.cpp
General improvements
- VCF parsing and warnings are more concise/consistent
- allow variant selection by
FILTER
- truth and query variants are no longer realigned by default
- removed unnecessary data copying from
sort_superclusters()
which significantly improves overall runtime and fixes uncounted runtime