Prewas back on CRAN

prewas 1.1.1

• Prewas had been archived because a dependent package was archived. Now that the dependency is on CRAN prewas is also back on CRAN.
• Updated citation and description to reflect paper published in Microbial genomics
• No changes to how prewas functions.

Handling SnpEff annotations & indels

prewas 1.1.0

• Given updates to as.factor default behavior in R 4.0 code was changed to keep data correctly typed.
• New feature: prewas can now subset variants by SnpEff annotation.
• New feature: Added an optional flag, grp_nonref. Its value tells prewas whether keep all alleles at multiallelic sites separate or to collapse all non-reference alleles for multi-allelic sites.
• New feature: prewas can now handle bcftools-prepared indel vcf file and prepare these variants in the same manner as SNPs.

Initial release

prewas 1.0.0

Initial submission to CRAN