CHANGES IN VERSION 1.12.0 ----------------------- CHANGES IN VERSION 1.10.0 ----------------------- NEW FEATURES o minFreqFilt and minCountFilt SIGNIFICANT USER-VISIBLE CHANGES o The Phase2Genotype function now treats phase 0 as the ref allele and phase 1 as the alternative allele. CHANGES IN VERSION 1.8.0 ----------------------- NEW FEATURES o genotype accessor requires reference and alternative allele information o genotype setter requires reference allele information o reference fraction is now accessed through fraction(ASEset, top.allele.criteria="ref") o for a more robust performance unit tests are now covering the most crucial calculations, such as e.g. fraction, frequency, summary, mapbias and phase specific calculations. CHANGES IN VERSION 1.6.0 ----------------------- NEW FEATURES o ASEset slot for Phase information o generation of masked reference genomes o calculation of reference fraction 'refFraction' CHANGES IN VERSION 1.2.0 ----------------------- NEW FEATURES o Faster getAlleleCounts() BUG FIXES o Fixed bug in the "realCigarPosition" function, that otherwise could generate an error.