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In lieu of knowing the actual chromosome name, I think using '1' seems to be convention.
In augur's case, a VCF is read upstream of this so we should be able to use the chromsome name provided there, either by making TreeTime aware of it and exposing it within get_tree_dict, or as another argument to write_vcf.
I'm happy to implement this, but any suggestions on the best solution are welcome!
The text was updated successfully, but these errors were encountered:
This is only used if provided, otherwise we fall back to the default
ploidy of haploid (unchanged) and chromosome name of "1" (changed from
the previously hardcoded "MTB_anc"). Note that the spec states that
no-call genotypes should be encoded to reflect the ploidy (e.g. "./."
for diploid and "." only for haploid) which is a change from previous
behaviour.
Closes#262
The VCF chromosome is hardcoded as "MTB_anc":
treetime/treetime/vcf_utils.py
Line 497 in 9fdceaa
In lieu of knowing the actual chromosome name, I think using '1' seems to be convention.
In augur's case, a VCF is read upstream of this so we should be able to use the chromsome name provided there, either by making TreeTime aware of it and exposing it within
get_tree_dict
, or as another argument towrite_vcf
.I'm happy to implement this, but any suggestions on the best solution are welcome!
The text was updated successfully, but these errors were encountered: