Major overhaul and bug fixes

bug fixes

• yes, plenty. please upgrade!

snippy

• diploid mode to ensure mixed/het sites not used
• better BAM using fixmate and markdup
• filter soft clipped reads with samclip to avoid false positives
• better freebayes parameters to handle low complexity regions
• more bcftools and vt, less perl scripts
• parallel stack reports for --report (currently too slow for lots of SNPs)
• consistent --version reporting across tools
• cleaner categorised --help output
• new --targets option to focus on BED regions
• new --check option to validate installation
• new --minqual for VCF quality filtering

snippy-core

• complete rewrite
• --noref no longer supported
• ability to mask with a --mask BED file eg. phage regions from PHASTER
• more use of alphabet to denote SNPs and het sites

general

• better TRAVIS tests
• removed unused output files
• updated bundled binaries
• new dependencies vt and bcftools