Version 2.3.0

• not backwards compatible. Files made by prepareref, and the report.tsv have changed.
• resfinder download using getref is fixed
• getref cleans up all temporary files (issue #135)
• getref has a new option --debug, which keeps all temporary files
• original sequence names are reported (issue #136)
• --force option added to the run task (issue #138)
• partial matches are reported by summary (issue #141)
• full codon change is reported in report.tsv (issue #142)
• uses $TMPDIR if it is set (issue #143)
• general improvements to reporting of samtools read depths and variant depths
• better filtering of read mapping before assembly
• extra checks to stop cases where extra copy of allele erroneously reported as partially present