Canary v1.0.0

This is the initial public release of Canary.
Canary is an efficient amplicon aligner, variant caller and annotator which transforms sequencer generated FASTQ files into VCF files annotated with HGVS nomenclature and Refseq transcripts. Implemented as a single JAR file, it is readily deployable onto any platform supporting Java runtime execution. All variants identified by Canary are 3’ shifted and represented in their most parsimonious form to provide a consistent representation irrespective of how the reads represent base changes. Further, proximate in-phase variants are additionally represented as a single HGVS ‘delins’ variant. This allows for correct nomenclature and consequences to be ascribed to complex MNPs which are otherwise difficult to interpret.