clinker v0.0.11

Hotfix for locus resizing bug in Chromium based browsers

clinker v0.0.10

• Added ability to draw genes unscaled without intergenic gaps (#17)
• Added toggle for drawing links as lines instead of boxes
• Added toggle for straight/curved links
• Added toggle for colouring links by similarity group colour, not identity
• Added multiprocessing for cluster alignments using -j/--jobs flag (#22)
• Added GFF3/FASTA parser (#10)
• clinker now looks for file extensions: GenBank = .gb, .gbk, .genbank, .gbf or .gbff, GFF = .gtf, .gff, .gff3, FASTA = .fa, .faa, .fna, .fsa, .fasta
• Fixed some invalid SVG tags

clinker v0.0.9

Minor update to fix gene colours not changing when choosing colours from legend entries

clinker v0.0.8

• Reworked simlarity grouping (gamcil/clustermap.js@d44f094)
• Groups now shown in gene tooltips
• More gene qualifiers are saved and shown in gene tooltips
• Added ability to change gene labels in bulk from sidebar (#6)
• Added ability to show similarity scores on gene links

clinker v0.0.7

• Added session serialisation using -s/--session flag. Sessions can be loaded alongside new file paths to add them to the session without redoing all alignments
• Extended list of valid gene name qualifiers (fixes #4)
• Use uuid4 to generate object identifiers, not incrementing integers
• Added right-click menu to gene polygons for changing labels manually (#6)
• Fixed bug in cluster dragging where clusters would go below scale bar
• Added --use_file_order argument so cluster order can be determined by input rather than hierarchical clustering (#15)
• Added bioRxiv citation to web app

clinker v0.0.6

• Fixed clinker reading in and translating pseudo CDS features, which caused errors when aligning
• Added -na/--no_align flag to allow clinker to visualise clusters without performing alignments

clinker v0.0.4

• Visualisation is no longer generated automatically by default; use the -p/--plot argument to generate it (optional: pass a file name to generate a static HTML document)

clinker v0.0.2

Initial release of clinker