Version 4.0, 21 August 2007


  • added support for HapMap PHASE format data
  • added support for phased HapMap downloads
  • added support for PLINK output files including plotting functionality
  • added a number of Tagger features to coincide with the Tagger website functionality
  • added 2-marker aggressive tagging from the command line
  • added log file functionality to command line mode
  • added proxy support
  • added table sorting to Tagger configuration
  • added numerous minor display and interface tweaks
  • added export options for Mendel errors and male heterozygotes on x chromosome
  • added command line HapMap info track download
  • added case control frequencies to command line association output
  • added ld values selection to command line image export
  • added citation information to the "About" dialog
  • added "Uncapture All" button to Tagger
  • added build 36 option to HapMap info track downloads
  • added http:// loading for files on the command line and initial load screen
  • changed some labelling in Tagger and made pairwise the default option
  • changed obsHet calculation to use founders only
  • changed HW and het calculations to show as "NA" in X data with too few individuals
  • enhanced GUI design with tabbed pane for initial loading dialog
  • fixed bug with haplotype associations for extended trios and x chromosome
  • fixed bug with case control counts for certain zeroed out markers
  • fixed Mendel error reporting bug on x chromosome
  • fixed Tagger bug affecting maximum number of tags input
  • fixed bug when left-clicking on the LD plot
  • fixed bug when changing tabs after multiple file loads
  • fixed bug when changing tabs after running tagger and changing check marker thresholds
  • fixed bug when loading custom association test file with multi-marker tests but no alleles
  • fixed bug with long windows filenames in command line mode
  • fixed bug with display when resizing the window to a very small size
  • fixed bug with 'h' alleles in haps files not being properly calculated
  • fixed bug with check panel export not accounting for user threshold adjustments
  • fixed bug with LD display where some r^2 values were invisible against the background
  • fixed bug with integer overflow when loading files with tens of thousands of individuals
  • fixed bug where HapMap info track would turn black if it was too wide
  • fixed bug with null pointer exception on failed hapmap info track downloads
  • fixed bug with null pointer exception when using Export Options Dialog
  • fixed bug with LD Plot now showing the correct markers when changing marker ratings and using table sorting in the check panel
  • fixed tagger results reporting of % captured when specifying alleles to capture
  • fixed bug with marriage loops in pedigree files causing StackOverflow errors
  • fixed bug with exception being thrown for certain input files with no markers
  • fixed bug with multimarker tags showing in the tagger results even though they don't capture anything
  • fixed bug with command line error handling
  • fixed bug with loading improperly formatted info files from "Load marker data"