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.