Snipgenie

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* changed calling step to now run mpileup and call separately
* now merge called vcfs at end, allows re-running pipeline much easier
* 16S plugin
* added calling_method option to use old method
* changed proximity filter to number, now default unless value is 0
* check for duplicates tool allows dups to be marked
* move fastq file option

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* fixes to RD plugin
* fixes to contam plugin
* added assembly plugin
* quality check in gui

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* fix to pair order in sample names when pivoted
* fix to keeping unmapped reads when not needed
* check samples match a previous raw.bcf file when running
* plugin system for gui
* gui - contam plugin added
* gui - testing plugin
* added manifest file option to cmd line
* removed get samples from bams during workflow, redundant

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* changed sample table format to single rows per sample
* fixes to RD analysis
* added minimap2 aligner for ont reads
* added platform keyword if using ont
* settings in gui saved
* mask in preset for gui
* redirect stdout to log in gui

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* changes to output files, snps and indels now output
* snps file made after filtering of calls
* make tree with snp branch lengths
* can save unmapped reads

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* can mask sites with bed file
* fix to use only core snps
* can remove uninformative sites from core
* can create qc report from cmd line
* more preset preset genomes
* can select species at command line
* added subread aligner
* map view for gui
* gui tree viewer
* spoligotyping tool to gui
* find heterozygous sites
* plot snp matrix
* changed name to snipgenie