Releases: marbl/gingr
Releases · marbl/gingr
Gingr v1.3
New features
- VCF annotations - When annotations are loaded, there are new INFO fields in VCF output indicating what CDS locus, if any, each variant lies in, the amino acid changes for each allele, and whether all alleles are synonymous.
- Clade internal variants - Right click on a tree clade to export a VCF with only positions that differ within the clade (columns will be restricted to genomes in the clade).
- Clade signature variants - Right click on a tree clade to export a VCF with only positions that are consistent within the clade and different outside of it (all columns will be included).
- Top level zoom - Return the tree and alignment to their original zoom levels from the View menu or with [CMD/CTRL]+T.
Changes
- GenBank annotations are now reconciled with fasta reference sequences using accessions rather than GIs, due to the retirement of GIs by NCBI.
v1.2
Bug fixes
- Large alignments will no longer run into serialization size limits when creating Gingr files, thanks to the Cap'n Proto library. Older Gingr files in the Protocol Buffer format can still be read, but will not be written (and may eventually be phased out).
- Exported trees will no longer have bootstrap or branch length values for the root node, which was not standard Newick and could cause crashes when loading them back in.
- Exported Fasta reference files will no longer have an extra space between the ID and description in their tags.
v1.1.1
New features
- Adjust branch lengths - This toggle (on by default) shows adjusted branch lengths to account for trees generated on only variant columns, rather than entire multi-alignments (only Gingr files generated with Parsnp v1.1 or with HarvestTools v1.1 using the -u option will have this feature available).
v1.1
Features
- The Import menu options have been combined into a single Open dialog. Formats are inferred from file extensions. If a format is unknown or a reference can be provided, a new import window allows specification of the format and a reference.
- If tree leaf names don't match alignment track names (when importing either), there will now be a prompt to clear the existing data, rather than always canceling the load of the new data.
- LCB boundaries are now drawn in the Annotation View, allowing boundaries between directly adjacent LCBs (which were formerly invisible) to be seen. The boundaries will fade when zoomed out if they are too crowded.
- VCF import now supports indels. See the documentation for details and caveats.
- MAF alignments can now be imported. See the documentation for details and caveats.
- Information about Gingr (including its version) can now be seen after the splash screen is gone from the About menu item (under Help or Gingr, depending on the OS).
Bug fixes
- Non-wrapped Fasta files (with each full sequence on one line) no longer cause hangs when importing as references.
- XMFA output when the final LCB contains no variants will no longer crash or produce infinite output.
- Synteny view can now be zoomed to the nucleotide level without glitches.
- Low SNP counts no longer cause slowness & graphical artifacts when zoomed out.
- The ruler markings around indels have been fixed.
