Product Updates

Progeny 6 Release Notes

PROGENY 6.9.04 UPDATE
Enhancements

The Custom Genotype Export now has an option to specify a character to export in place of No Call

Fixes

A fix was made to the display of the Minor Allele for SNPs
A change was made in the Spreadsheet for updating SNP data
A fix was made in Markers to prevent incorrect name for markers
A fix for the PLINK export was made to prevent missing data for targeted regions
An update for the PLINK export was made

PROGENY 6.9.03 UPDATE
Enhancements

The Custom Genotype Export now has an option for one row per marker
The PLINK export now has break options for chromosome and additional breaks for base pairs, cM, and number of markers
An additional option was added in Mendelian Error Checking to allow the clearing of genotype data for the specifc call

Fixes

A fix was made to the Hardy Weinberg calculation to handle markers with no data
An update was made to allow for querying on Folder Name for analysis exports
The program now prevents the Symbol Legend from displaying off of the viewable space
An update was made for the display of discrepancies values
A display change was made for the retrieval of search criteria for tables
Import module will now accurately report on the prevention of overwriting existing pedigrees
A fix was made in the Import to handle the Autobuild of Marker fields
An update was made to the Import to allow inferred alleles
A fix was made in the individual query for Haploview exports
A change was made to disallow invalid characters in marker set imports
A update was made for genotype imports to handle cases in which the marker name is blank

PROGENY 6.9.02 UPDATE
Enhancements

SNP fields display NoCall for display and update in spreadsheets, data sheets and pedigrees
The user can now choose between Pedigree ID and Pedigree Name for Haploview and PLINK exports

Fixes

A fix was made to the ordering of Haploview exports
An update was made to the internal p-value calculation
PLINK export defaults to 0 for motherid and fatherid
A fix was made to the PLINK export to handle the filtering of markers
An update was made to the Sample Status system field for smartlists

PROGENY 6.9.01 UPDATE
New Features

A custom marker set import with preview window and ability to import and update additional marker fields is now available

PROGENY 6.8.02 UPDATE
New Features

A new import module is now available for Pedigrees, Individuals, and Samples
A new individual level system field contains the status of sample, plate, genotyped

Enhancements

Tables rows in spreadsheet searches use an improved algorithm
PLINK exports are optimized for speed
The Quick Find window can now be accessed via CTRL-Q
Custom genotype exports now use the same recoding technique as linkage exports
The show field on all tabs option is included in the Japanese version dialog's individual data sheet
Right click option for spreadsheets is available for individuals
Rejected and discrepancies now use a filter to allow browsing of large result sets
An option to toggle polymorphic markers is available for all association exports
Marker spreadsheet imports for a single match column are optimized for performance.

Fixes

A fix was made to the edit control for manually entering marker data
Fixes were made to PLINK exports
Linkage exports no longer export a blank map file
Hyperlink field now allows the user to select the hyperlink value
The data sheet properties window allows keyboard entry into the heading column in all cases
The user is able to change between raw calls and recoded alleles in the custom genotype export
The ability to right click to plates from the pedigree is available
The ability to right click to access Find Sample is available
The genotype imports rejected tab is now loading correctly in all cases

PROGENY 6.8.01 UPDATE
New Features

Maternal-Paternal system field is now available
A marker filter is available in analysis
Administrators can view the connected users
New analysis server contains the ability to link to analysis server peers
A new analysis server monitor now includes progress bars and status for multiple servers
PLINK export option is included in analysis

Enhancements

Changes were made to the conversion process to improve the performance
Analysis recodes SNP fields for non polymorphic markers (B is recoded to 1)
Samples can be created if the Find Sample function does not find a match
Sample lookup tables include an option to allow keystrokes
Individual level fields are now available in the sample smart list
The affection status chooser in analysis now supports checkboxes and lookup table field types
Individual name is a field choice for any unique ID field chooser
Do not allow non admin users to upgrade the database server to a new version
Discrepancies displays the file name and line number

Fixes

The summary field type is now an option in analysis queries
The individual import module includes fixes to format correctly
Scrolling is now working properly in the lookup table viewer in the datasheets
Problems with the BRCA process inside the pedigree are resolved
Analysis no longer allows duplicate export names
Lookup table maintenance problems with delete row are resolved
Lookup table maintenance problems with lookup tables are resolved
The spreadsheet printing now correctly handles all cases for columns in the second horizontal page
Merlin now exports the correct map file when all chromosomes are exported

PROGENY 6.8.00 UPDATE
New Features

Allele counts, call rates, pvalues, minor allele frequency, minor allele, and degree of heterozygosity are now available in marker navigation and analysis filters
A custom genotype import with preview window and ability to import wide file formats is now available
Lookup tables are now available for sample level fields
A find sample dialog was added to the sample navigation to assist with barcoding

Enhancements

XML imports are now threaded and display progress
If pedigrees are being replaced in mobile the audit status now does not change
Performance enhancements were made to the marker navigation
The linkage export now includes filters on pvalue, MAF, degree of heterozygosity, and call rate
Haploview now includes file break options for chromosome and position
The Phase export now includes filters on pvalue, MAF, degree of heterozygosity, and call rate
The Phase export now contains file break options
The analysis server now supports Phase
Changes were made to the Merlin export. The dat file was changed and the map file was added.
Genotype Exports and Haploview now support alphanumeric ID numbers and Affection Status
Hardy Weinberg was optimized for performance
Hardy Weinberg results can now be exported to text files
Columns were added to Hardy Weinberg as well as the ability to sort by chromosome and position
cM can now be updated in the marker set import
Plate imports are no longer case sensitive
The sample spreadsheet import now includes progress bars
The focus is initially set to the Find edit box in the Find/Replace dialog
cM was extended to 4 decimal places
Sample audit status was added to the sample data sheet and grid
Rejects now handle multiple rejects per import file row
Rejects do not repeat missing markers and samples within the same file
The user now has the ability to delete a marker from the database when a set is selected
Progeny Link fields are now compatible with SQL Server
The IP address and the port for batch Phase exports are now stored
There is a new option to delete a linkage run via right click
The NoCall processing in the genotype import was improved
The spreadsheet will now maintain widths for resized columns over runs
Repeat discrepancies are now displayed in the genotype import rejects
Field defaults are no longer limited in character length

Fixes

Copy features now copies PDS table default formats
A problem with XML checksum validation is fixed
Problems launching the XML import from the import module were resolved
Image files created from the pedigree can now be stored in the format x.y.z.jpg
Progeny Link fields now save correctly in spreadsheets
When discrepancies are resolved the correct column is immediately updated
A fix was made to the Phase Export to display the correct individuals list
The genotype export Unique ID field is disabled if the export does not use Unique ID
Discrepancies in the second open database can now be resolved
The space bar now correctly disables fields for XML import
Browsing for the export analysis folder now supports increased length
A problem with find/replace in the last row of a spreadsheet was resolved
The vertical and horizontal icons were changed in the align palette
A fix was made to prevent a pedigree or field from being lost via security settings
A marker set import problem with chromosome name case sensitivity was resolved
Copy pedigree now correctly sets the default PDS table formats
Batch pedigree print now supports the linkage and genotype indicators
A problem with selecting pedigrees in the Clear Genotypes function was resolved
A problem with icon symbols in the XML exports was resolved
A problem with the population of smart list columns was resolved
Problems with LOD score imports were resolved
A problem with annotated text editing in the PDS was resolved
Fixed a problem with the rejected tab showing the wrong import file
Copy features now includes icon markers
Copy pedigree now includes the inferred genotype status

PROGENY 6.7.06 UPDATE
Enhancements

System fields are now available in Haploview, Phase, and association exports
The database history can be erased from the login screen
The marker set import progress bar is enhanced
A hard return was added to Mega2 exports
The first intermarker distance was added to linkage exports
The field warehouse now can be resized in spreadsheets and pedigrees

Fixes

Displaying Mendelian errors no longer requires the user to refresh the icon markers
A problem with the XML export for specific field configurations is fixed
The default date in the table data sheet is now the current date
A problem with the XML export for markers is fixed
The plate export formats are now displaying correctly
A problem with computed fields containing very long paths is fixed
A problem with saving field positions in the individual data sheet is fixed
A problem adding samples via the pedigree is fixed
A problem with deleting table rows in the individual data sheet is fixed
A problem with checkboxes inside tables in the data sheet is fixed
Individual import formats are now displayed correctly
Pedigrees can be saved to XML format from the pedigree navigation tab
A problem with user access to the individual spreadsheets is fixed
A problem with marker set imports that contain empty columns is fixed
A problem with adding individuals to pedigrees is fixed
The sample import progress bar is enhanced
The spreadsheet import progress bar is enhanced
A problem with Haploview handling blank or invalid values is fixed
A problem with Haploview while using the folder system field is fixed

PROGENY 6.7.04 UPDATE
Fixes

NOTE: A database update will be performed.
A fix was made to marker set imports
A fix was made in the pedigree to handle drawing issues related to line width
A fix was made to allow the user to use the keyboard delete key when renaming fields
A fix was made to allow the user to use the keyboard enter key while editing pedigree text annotations
A fix was made to the conversion process from Progeny 5 to Progeny 6.
A fix was made to XML export to handle empty tables and invalid computational fields.
A fix was made to correctly handle haplotyping when no markers are selected.

PROGENY 6.7.00 UPDATE
New Features

A filter is now available throughout the software for selecting markers
The marker navigation tab is redesigned to be easier to use
Links to Ensembl, dbSNP, HapMap , and UCSC are one click away
A new analysis option for genotype export is now available
A web knowledge base is now available
Erase the genotypes for selected pedigrees and markers
Select specific fields to include in an XML export
Markers and SNPs from different chromosomes can be displayed on the pedigree

Enhancements

Adding markers to pedigree subtext is redesigned to be easier to use
Security for genotypes is available at the user level
The genotyping tabs (Mendelians, Discrepancies, Rejects) include an export option
Open a sample data sheet from the plate viewer
Open a pedigree or pedigree data sheet from the pedigree spreadsheet
Open an individual data sheet from the individual spreadsheet
Open a pedigree or individual from the sample navigation tab
Spreadsheet data import has the option to overwrite or skip empty cells
Open an individual data sheet from the individual spreadsheet for a single individual
The navigation tab for a subpedigree now displays the name of the subpedigree instead of the pedigree name
The query windows in analysis now support system fields
Association TDT and CC options are now available in Haploview
The user now has the ability to rename spreadsheet formats
The current format is now the default for a save format operation
A progress bar is now displayed during spreadsheet data imports
Genotype import now reports rejects of invalid SNP characters
The BRCAPRO processing is now limited to individuals within 2 degrees of relation
The user can now drag plates into folders
A progress bar is now displayed during copy features
The login screen now displays the version number
A progress bar is now displayed during sample import
The haplotyping default color selection is improved

Fixes

A bug related to exporting single individuals in Phase and Haploview is now fixed
A bug related to importing marker sets with a header row is now fixed
A bug related to printing large pedigrees is fixed
A bug related to SmartDraw selection in copy features is now fixed
A bug related to table field security in individual spreadsheets is now fixed
A memory leak related to haplotyping is now fixed
A bug related to pedigree spreadsheet system field widths is now fixed
Linkage exports run from the pedigree now handle single individuals
A bug related to using the keyboard delete key is now fixed
A bug related to printers/plotters with large page sizes is now fixed
A bug related to changing static text in data sheets is now fixed

PROGENY 6.6.05 UPDATE
New Features

Allow the user to include subfolders in a copy features operation

Enhancements

Made improvements to the haplotyping algorithm inside the pedigree
Made improvement to the haplotype bar coloring algorithm inside the pedigree

Fixes

Fixed a problem with window positioning during startup
Fixed a problem with resolve discrepancies in the genotype import
Prevent loss of features during a copy features operation
Fixed a problem with "unselect all" (fields) when copying across databases
Fixed a problem with the Haploview analysis
Do not allow discrepancies to load duplicate rows
Include data for pedigree table fields during copy pedigree
Made improvements to the import module algorithm for very wide pedigrees
Fixed a problem with table formats when copying pedigrees across databases
Fixed a problem with missing table subfields when copying pedigrees across databases
Fixed a problem resulting from repeating values in the genotype import

PROGENY 6.6.04 UPDATE
Fixes

A fix was made to prevent users from deleting format folders
A fix was made to the genotype import Affymetrix CHP format

PROGENY 6.6.03 UPDATE
New Features

Added the ability to import Affymetrix GTYPE formats
Improve the performance for saving large individual data sheets

Fixes

A fix was made to linkage ped file exports from sub pedigrees
A fix was made for field selection when copying pedigrees across databases

PROGENY 6.6.02 UPDATE
New Features - Lab Only

Added the ability to import genotypes in ACGT format

Fixes

Batch printing of pedigrees includes legend option
Fixed a problem with table fields in individual spreadsheets run from a pedigree
Fixed a problem retrieving the correct Individual Data Sheet for new individuals
Only prompt for deleting a format folder if the delete key is pressed
Fix a column problem in the standard spreadsheet data import

PROGENY 6.6.01 UPDATE
New Features - Lab Only

Built an Analysis Server to run exports on a Computational Server
New Analysis Options:
Can launch samples from the plate module.
Import samples can now automatically create new individuals
Now when adding a sample manually you can automatically create the individual
Now allow Linkage to export markers that only have one allele
Added ACGT support and direct import of Allele A and Allele B from marker files

New Features - All Versions

Added the ability to display more graphic types in all data sheets (JPG, TIF, PNG, GIF)
Added Lookup Tables at the Pedigree level
Added the ability to display Pedigree Level Fields In the Individual SS
Added an Import Module for Individuals
Now can import into tables in Pedigree spreadsheet
Added the ability to directly import .FAM files
Mouse wheel scroll now available in all data sheets
Added the ability to insert fields into all search windows
Expanded the size of drop down boxes in spreadsheets and data sheets
Can now launch the data sheet from any given row in a spreadsheet
Can launch pedigree from pedigree spreadsheet.

Fixes

Fixed a problem with Page Numbering in the pedigree
Set the starting point of the cursor inside the data sheet (on the first field)
Fixed an issue in Genotype imports that rejects markers with different capitalization
XML export reactivated from Pedigree navigation
Users can now search on all system fields in pedigree spreadsheet
Fixes to import module
Smart List fixes
Fix to large data values in PDS table rows
Locks are announced if an operation fails
Fixed a relationship problem adding a parent to a single child

PROGENY 6.5.01 UPDATE
Enhancements:

Add class based security at the folder and sample folder level
Performance enhancements in visual controls
Default marker conversion into a marker set

Fixes:

Add pedigree level system fields that were missing in warehouse
Datafolder security was blocking access and not displaying some fields
Marker conversion window was reformatted to provide clear instructions
Fixes were made to the copy individuals functions
Fix to jump from mendelian errors to pedigree for large SNP arrays
Fix to spreadsheets for large SNP arrays
Fix to find marker in pedigree
Change "Back to Pedigree" graphics for sub pedigrees
Individual shortcut is now using the correct shortcut name
Fix to recombination fractions calculations for linkage exports
Formatting fixes to MEGA2 linkage export
Fix to linkage export using cM
Table summary fixes in the create and change functions
Table summary fixes for is not null operator

PROGENY 6.5.00 UPDATE
Note: Progeny 6.5.00 is a substantial update. Major new features may be viewed here.