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"