Major refactoring

Note important flag changes!

• OLD: --inbreedSites, NEW: --inbreed_sites
• OLD: --inbreedSamples, NEW: --inbreed_samples
• OLD: --minMaf, NEW: --maf

All EM algorithms now uses SqS3 acceleration scheme.

pcangsd v1.10

fix pip discrepancy

Last Python 2.7 support

Last release before going full Python 3.x. In upcoming update a lot will be reworked for better performance.

PCAngsd Cython based

v0.98

Delete python_packages.txt

PCAngsd 0.97

A lot of stability updates have been made. The genotype probabilities of negative inbreeding estimations have been fixed. Reduced some memory spikes.

PCAngsd 0.95

All inbreeding analyzes have now been multithreaded. The EM algorithms of method 2 in the estimations of both per-site and per-individual inbreeding coefficients have been stabilized.

PCAngsd

Fully functional release for genotype likelihoods and PLINK files. Tested a new NMF update for F. The kinship estimator still needs to be reworked and the code for individual inbreeding coefficients needs to heavily sped up.