faster and more stable
Pre-release
Pre-release
thierrygosselin
released this
08 Jul 21:01
·
532 commits
to master
since this release
v.0.3.0
- Update that makes my coding life easier.
- Several internal functions to convert from a tidy dataframe to:
vcf
,plink
,genind
,genlight
,gtypes
,hierfstat
,genepop
,structure
andbetadiv
are now separate modules available to users (look forwrite_...
with the outputformat) - New function
genomic_converter
: If you want the to convert from the supported
input file formats to many output formats, at once, this is the function.
With the new functiongenomic_converter
, import and imputations are only
done once, saving time if you were generating different output WITH imputations. - Change: all the
vcf2...
functions (excepvcf2dadi
) are now a shorcut ofgenomic_converter
.
This is particularly interesting and faster if you were generating different
output WITH imputations. This makes the functionsvcf2...
andgenomic_converter
easier to debug for me and more stable for users. - Deprecated: the
haplo2...
functions are all deprecated and replaced by
genomic_converter
, except haplo2colony that requires so many arguments that it
would be too complicated, for now, to integrate withgenomic_converter
. - New feature: when arguments
pop.select
,blacklist.id
andimputation.method
are used, the REF and ALT alleles are now re-computed to account for the filters
and imputations.