Version 0.13.3

• When clustering VCF records (as used by minos) proper handling of heterozygous genotypes. Previously if GT was N/M, N!=M, and N and M both non-zero, then the record would not get used. Now both alleles are added to the output.
• Fix to only use alleles that comprise A,C,G,T characters only. Other alleles now ignored, instead of making it to the output and breaking minos. This stops in particular alleles like <foo> getting used, which are allowed in the VCF spec.

Version 0.13.2

Bug fix: whitespace in fasta header lines resulted in no calls being output after merging.

Version 0.13.1

• update to use either vcflib foo (which is installed by apt install libvcflib-tool), or existing separated vcf* scripts (which is what gets built when installing vcflib from source). Code now first looks for vcflib in $PATH and if not found, falls back to looking for vcfbreakmulti, vcfallelicprimitives, vcfuniq.
• remove warning from bitarray about deprecated length funtion

Version 0.13.0

Adds support for reading BCF files

Version 0.12.4

Better at finding and removing duplicated paths when clustering VCF, at the cost of run time. Add option to use multiple CPUs when clustering.

Version 0.12.3

Another fix to remove duplicate allele paths

Version 0.12.2

Bug fix from previous release. Some allele combinations were missed.

Version 0.12.1

Fix to prevent allele combinations across VCF records that result in the same sequence.

Version 0.12.0

Improved merging and clustering of VCFs, as part of rewrite of minos regenotyping pipeline to handle huge numbers of samples.

Version 0.11.1

When clustering, always try to remove duplicate records (instead of only trying if total number of records <1000). This fixed bug in minos regenotyping pipeline.