Added function writeSFF to create a .sff file from a SFFContainer object.
Added function qualityReportSFF to create a pdf quality report for SFF files.
Fixed a bug in the function to subset SFFContainers.
Added ability to read in data from Roche's latest Amplicon Variant Analyzer (v2.7).
New method ava2vcf to write the variants in an AVA-Set to a file in VCF format.
Multiple bugfixes.
Added new graphical components, options and annotations to the plotVariants function.
Added method readSFF to read-in Roche's .sff (Standard Flowgram Format) files.
Added functions for quality control on unaligned sequences in SFFContainer, ShortReadQ and QualityScaledDNAStringSet format.
Added a function to write files in FASTQ format from SFFContainer.
Added method for calculating Ti/Tv ratios.
Fixed bug in plotAmpliconCoverage().