* 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
0.5.0
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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
0.4.0
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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
0.3.0
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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
0.2.0
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* improved vcf to fasta sites method * renamed to snpgenie * use genbank as annotation file * added proximity filter * GUI works for any ref genome * text bam alignment viewer * add folders in gui * clean up files option * fastq quality report
0.1.0
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* first version * CLI workflow works for general microbial genomes * GUI works for mbovis so far * functions working so far: trimming, alignment, variant calling, snp matrix, tree building