HATCHet fails with new version of bcftools 1.21

[simozacca]

The new version of bcftools 1.21 requires to specify that the AD field is in INFO in the query command used by HATCHet in

https://github.com/raphael-group/hatchet/blob/783058042cc3ef78b3f46ff7478edb5b6dfd9f44/src/hatchet/utils/count_alleles.py#L236C22-L236C53

Specifically, the following command of bcftools called by HATCHet fails and hang with the new version of bcftools 1.21:

bcftools mpileup ${BAM} -Ou -f ${REF} --skip-indels -a INFO/AD -q 13 -Q 13 -d 30 | bcftools query -f '%CHROM\\t%POS\\t%REF,%ALT\\t%AD\\n' -i 'SUM(AD)<=1000 & SUM(AD)>=1' > output

failing with the message:

[mpileup] 1 samples in 1 input files
Error: ambiguous filtering expression, both INFO/AD and FORMAT/AD are defined in the VCF header.

The temporary solution is to install HATCHet with a previous version of samtools/bcftools, like 1.19, after correct setting up of bioconda channells:

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

conda create -n hatchet hatchet "bcftools==1.19" "samtools==1.19"

In the meanwhile, @mmyers1 can we please fix this by making the bcftools command compatible, or changing bioconda recipe of HATCHet to only use a compatible version of bcftools/samtools please?