v0.7.0

• changed calling step to now run mpileup and call separately. now merge called vcfs at end, allows re-running pipeline much easier
• 16S species check plugin
• added calling_method option to allow use of old calling 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
• snp tables should now display better with vertical column header
• removed rtd docs - moved to wiki

v0.6.1

Last release using old mpileup/calling method.

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

v0.6.0

• 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

v0.5.0

• 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
• fixed spotyping

v0.4.0

• 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
• some gui fixes

v0.3.0

• 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

v0.2.0

• 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 qualities report

v0.1.0

• 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