CampagneLaboratory/variationanalysis: Release 1.2.2

This release includes the following changes: Fix frequency of bases when indels are also present. Now correctly removes bases that support the flanking sequence of the indel and do not double count. Many changes to how we store varmaps introduced to support indels (vcf-to-varmap). The serialization format is incompatible with previous versions, so make sure you regenerate varmaps from VCF. Adjust VCF output for compatibility with REF/ALT conventions. This makes it possible to measure performance with standard tools such as RTG vcfeval (http://realtimegenomics.com/products/rtg-tools/). Keep counts of indels separately for forward and reverse strand. vcf-to-varmap mode: improved semantic of --chromosome-prefix option allows removing (e.g., -chr) or adding (+chr) prefix to chromosome name