Information & Computational Sciences

New in Flapjack 1.18.06.13

By on 13/06/2018 in News

Flapjack has just been updated to version 1.18.06.13.

  • NEW: Flapjack is now BrAPI (https://www.brapi.org) enabled.
  • NEW: Added a new menu option to import via BrAPI to the File menu.
  • NEW: Added a new analysis module to perform line-based pedigree verification.
  • NEW: Added an option to use a SOCKS proxy rather than a normal HTTP proxy.
  • NEW: Added a new colour scheme to handle markers with favourable and unfavourable allele information (see http://flapjack.readthedocs.io/en/latest/favalleles.html).
  • NEW: Added a parental colour scheme, matching lines against (total) match to either of two selected parental lines.
  • NEW: Added an option to filter markers by the percentage of heterozygous alleles they have.
  • NEW: Added the ability to filter out lines based on a percentage of missing data.
  • NEW: Added the ability to filter lines by percentage of heterozygous and homozygous alleles.
  • NEW: Line ranking can now be performed for PedVer as well as MABC analyses.
  • NEW: Added a new line similarity colour scheme (any match), and renamed the existing ones to allele-match and genotype-match.
  • NEW: It is now possible to truncate long line names via the right click menu on the ListPanel.
  • NEW: Added support for holding basic pedigree information for a line (see http://flapjack.readthedocs.io/en/latest/pedigrees.html).
  • NEW: Pedigree information is parsed (including ‘*’ special case) and stored both internally and in the .flapjack project files.
  • NEW: Tweaked the chromosome-combo selector/box to render maps with QTLs in a red colour.
  • NEW: Added a (right-click) option to copy line names to the clipboard.
  • NEW: The UI for MABC now filters the lines list based on known RP or DP information.
  • NEW: Added an option to exclude parents not being used for the analysis from MABC results.
  • NEW: If create-all-chromosomes is selected Flapjack now auto-select the all-chromosomes view after data import.
  • NEW: Flapjack will now warn if pedigree information is known, but multiple RP or DP lines are available for an MABC analysis.
  • NEW: For MABC analysis, without pedigree information, Flapjack reverts to the original UI where all lines are available and the 1st and 2nd indices are pre-selected for the RP and DP lines respectively.
  • NEW: Textual trait information can now be displayed alongside the list of line names (and aligned against the graphical genotype view).
  • NEW: Visible trait selection has been split into two sets; one for the existing heatmap and a new one for the textual display.
  • NEW: Textual trait information is saved as part of the project.
  • NEW: After importing trait data, the first three trait columns found in the file are auto-assigned to both the heatmap and the textual displays.
  • NEW: Modified the top-level menus to split trait selection into two submenus (heatmap/text).
  • NEW: Added a new context menu to the lines list to select its traits.
  • NEW: Modified the line list’s context menu so that selection of linked table (eg MABC) table results is always visible, but may be disabled.
  • NEW: Added an option (on by default) to truncate the width of textual traits so that more columns of data can be shown at once.
  • NEW: Added alternating column colour highlighting for the traits (and/or MABC table results) display.
  • NEW: Added support for .fjzip files (zipped containers of tab-delimited input files).
  • NEW: Improved the responsiveness of cancelling remote jobs by ensuring the UI disappears as soon as Cancel is pressed.
  • NEW: Many changes and improvements to the command-line tools, especially with regards to the available options and parameters that can be passed.
  • NEW: Galaxy wrappers are now available for Flapjack’s command-line tools (search https://testtoolshed.g2.bx.psu.edu/ for ‘flapjack’).
  • NEW: Added an additional command-line CreateProject parameter to allow the user to specify a name for the dataset being imported into Flapjack.
  • NEW: Added an option to include phenotypic trait information in the exported output file from an analysis run.
  • NEW: Added the ability to specify whether or not to allow duplicate line names when creating projects.
  • NEW: Added the ability to adjust the lengths of chromosomes that contain QTL with a maximum length beyond that of the chromosome.
  • NEW: Added .rpm and .deb installers.
  • CHG: Reworked the code for collapsing A/T:T/A situations to run significantly faster on cases with a lot of duplicates.
  • CHG: Any QTL that have been “unticked” in the UI will now be skipped during an MABC analysis run.
  • CHG: Updated HapMap conversion code to be more memory efficient.
  • CHG: Removed the option to import via an HDF5 file.
  • BUG: Removed over-enthusiastic trimming of whitespace from file parsers that meant double-tab blank entries would throw errors.
  • BUG: The Traits/QTL panel wasn’t remembering the active tab after the user selected another view.
  • BUG: Fixed an issue with clearing the text box for entering the path to a map file.
  • BUG: Running F1 PedVer with a simulated F1 and imported traits was broken.
  • BUG: Fixed issue where alleles with a space at the end wouldn’t match the same allele without the space at the end.
  • BUG: Fixed issue where the Export View as Text dialog’s radio buttons weren’t behaving properly.
  • BUG: Dragging in a genotype file on its own (with no map file) wasn’t working.
  • BUG: The simulation of an F1 (PedVer) was incorrect if markers had been filtered or reordered.
  • BUG: Analysis results tables with checkboxes weren’t rendering correctly on Linux.

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