Information & Computational Sciences

New in Flapjack

By on 07/10/2020 in News

Flapjack has just been updated to version

  • NEW: Huge changes to Flapjack’s BrAPI codebase with the result that Flapjack is now BrAPI version 2.0 compliant.
  • NEW: BrAPI support includes downloading of data in both JSON and Flapjack (bulk file) formats.
  • NEW: Flapjack now uses the actual variant set name (from BrAPI) to name an imported data set, instead of just “BRAPI”.
  • NEW: Reworked many of the BrAPI import dialog’s controls so that everything is presented in a nicer way.
  • NEW: BrAPI import won’t allow the user to proceed unless either the number of expected lines or markers is greater than zero.
  • NEW: Implemented threshold settings for Ped Ver analyses (Lines and F1s).
  • NEW: Threshold variables can be tweaked in real-time with dynamic table updates.
  • NEW: The PedVerF1s table now colours the decision column based on the threshold/decision.
  • NEW: Added a new ‘Indexed Forward Breeding” analysis module, supporting single and batch runs. Requires GOBii-QTL files to work.
  • NEW: Added tablet cell rendering that attempts to heat-map colour 0-100 scale ranges on the summary table.
  • NEW: Expanded and enhanced the ‘GOBii’ QTL file format support within Flapjack. See
  • NEW: Added dynamic parsing of all GOBii-QTL column headers, so order doesn’t matter.
  • NEW: Added a new command-line version of CreateProject (CreateProjectBatch) that can be provided with an input file containing multiple map/genotype/trait/etc files for batch loading.
  • NEW: Implemented full batch analysis modules for each for the support ‘GOBii’ analysis/decision support modules.
  • NEW: A batch results summary tab is now available for all analysis runs (even if singular), showing per-dataset summary statistics.
  • NEW: Data shown in the batch results summary tab can be exported out as tab-delimited text.
  • NEW: Double-clicking a row in the Summary Table will jump to the main analysis results for that data set.
  • NEW: An imported QTL file can now be applied to all loaded data sets at once.
  • NEW: Added the ability to automatically select True F1s as part of the PedVerF1s analysis.
  • NEW: Added threshold and automated decision selection to the MABC analysis.
  • NEW: Added a dialog for finding data sets by name, initiated (only) by a right-click on a navpanel dataset node.
  • NEW: Added the ability to override trait data type by using _#NUM or _#CAT in the column headers of the input file.
  • NEW: CreateProject/CreateProjectBatch now support a -N parameter that forces Flapjack to use the nucleotide (0/1) colour scheme regardless of the underlying data type that was imported.
  • NEW: Added a QTL Allele Count (Average) column to the MABC batch summary stats.
  • NEW: Updated the line/marker DB encoding code to try and cope better with spaces and forward slashes in names.
  • NEW: Attempted to make single point QTL render better (basically ‘wider’).
  • NEW: Changed BrAPI import progress tracking to use alleles-read rather than bytes-read, as we can (usually) work out the total in advance via other BrAPI calls.
  • CHG: MABC/PedVerF1s batch analyses now automatically pick the best parents if pedigree headers are included in the input file.
  • CHG: Minor changes to the statistics and headers shown after a Pedigree Verification (F1) analysis.
  • CHG: Changed the Similarity to Parents colour scheme to work on an allele match basis versus each parent.
  • CHG: Renamed colour scheme “Similarity to Parents” to “Similarity to each Parent (alleles)”.
  • CHG: Renamed colour scheme “Parent Total Match” “Similarity to Either Parent (alleles)”.
  • CHG: Minor changes to the statistics and headers shown after a Pedigree Verification (Lines) analysis.
  • CHG: Changed the alternate fav_allele to favorable_alleles (plural) for the GOBii-QTL format.
  • CHG: Minor changes to the statistics and headers shown after a Forward Breeding analysis.
  • CHG: The similarity to favourable allele colour scheme now colours hets which match favourable or unfavourable alleles as matches to the favourable or unfavourable allele.
  • CHG: Removed the warning popup about multiple parents being available for MABC.
  • CHG: Tidied up the UI (title panes, etc) across the GOBii analysis dialogs.
  • CHG: Modified (globally) the background selection colour for tables.
  • CHG: Small update to the installers to handle the latest JRE bundles.
  • CHG: Dropped support for the -C CreateProject option, which has been (partially) replaced with -K.
  • BUG: Fixed an issue where favourable allele information wasn’t being properly stored in the project, causing a crash when attempting to run a forward breeding analysis.
  • BUG: Fixed an issue with float comparisons that was affecting Forward Breeding results.
  • BUG: Fixed select cases where multi-allelic homozygous alleles that were encoded as hets could be dealt with incorrectly when collapsing that allele.
  • BUG: Fixed lots of inconsistencies/errors with the defined keyboard accelerators across the various menus.
  • BUG: Some of the parameters for command-line execution (eg decimalEnglish) were being ignored if provided.
  • BUG: The ‘auto-fit columns’ checkbox on the PedVerF1s panel was showing the wrong background colour.
  • BUG: Fixed several colouring mismatches in the Similarity to Either Parent color scheme.
  • BUG: Added missing job-cancelled handling code to the GOBii analysis methods.
  • BUG: Fixed an issue that meant the first press of OK/Cancel on the Database Settings (Link) dialog had no effect.
  • BUG: Fixed a QTL display formatting problem with large numbers.
  • BUG: QTL at the extreme left/right hand side of maps should now render.
  • BUG: Fixed a display problem with some NaN double values when background cell colouring is used.

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