Python 0.5.7
Breaking Changes
- The VCF writing methods (
ts.write_vcf,ts.as_vcf) now error if a site with
position zero is encountered. The VCF spec does not allow zero position sites.
Suppress this error with theallow_position_zeroargument.
(@benjeffery, #2901, #2838)
Bugfixes
- Fix to the folded, expected allele frequency spectrum (i.e.,
TreeSequence.allele_frequency_spectrum(mode="branch", polarised=False),
which was half as big as it should have been. (@petrelharp,
@nspope, #2933)