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Record of Changes to PEDSTATS

ChangeLog

========================================================================================
CHANGES AFTER PUBLIC RELEASE OF PEDSTATS
========================================================================================

PEDSTATS 0.6.12
===============

   * Fixed problem with --rewrite function that caused original allele labels to be lost.

PEDSTATS 0.6.11
===============

   * Pedstats now always uses the exact Hardy-Weinberg equilibrium test for SNPs. In previous 
     versions, an approximate test was used whenever there were >5000 genotyped individuals.

PEDSTATS 0.6.10
===============

   * Noted that ChangeLog hand't been updated for a while...

   * Updated pedigree library to incorporate changes from recent versions of Merlin,
     including support for base-pair allele labels and .gzipped input files. 

PEDSTATS 0.6.3
==============

   * Unrelated sample Hardy-Weinberg test added (--checkUnrelated). When this option is 
     selected, Pedstats will select a reasonable sample of unrelated individuals from each family 
     to be used for all Hardy-Weinberg tests. Sampled individuals are reported to a log file. 

   * Data quality statistics. When more than 50 markers are present, Pedstats now
     prints a table summarizing marker quality and sends detailed marker information to 
     a separate file.

   * PDF output. When more than 50 markers are present, Pedstats will only produce 
     PDF summaries of each marker if they are specifically requested (--markerPDF)

   * Option to select significance cutoff for printing of Hardy-Weinberg test results added (--cutoff).


PEDSTATS 0.5.9
==============

   * Corrected bug that caused non-specific Mendelian inheritance errors to be erroneously reported for 
     some large family structures.

PEDSTATS 0.5.8
==============

   * Mendelian inheritance checks expanded to include a genotype elimination algorithm
     capable of identifying all errors within families without loops. Inheritance 
     checks now incorporate a first-pass nuclear family check followed by 
     a more thorough genotype elimination check if no errors are identified by the 
     nuclear family algorithm. 

   * Verbose output option added (--verbose). When this option is selected, 
     additional information on individuals comprising disconnected family groups 
     will be reported.

   * Option to output marker summary information to a separate text file added (--markerTables).

   * Filter log added. When filtering is done, persons excluded from summaries are
     reported in a text file.

   * Age checks now screen for large differences in sibling age or birth year values. 

   * Basic age checking algorithm updated to provide clearer error messaging and to 
     correct bug where missing data in leaf individuals occasionally caused an error 
     to be reported for parent/grandparent age values when no error existed.

   * Major revisions to make main code routines more modular.

   * Major revisions to charting classes to accomodate additional functionality. 

   * Capability to zero out founder parents after trimming added.

   * Multiple minor updates to improve readability of graphical and text output.  
 

PEDSTATS 0.5.4
==============

   * Fixed inverted labels for expected and observed number of heterozygotes in exact Hardy-Weinberg
     test output

   * Changes to String::printf() function to accomodate different structure for variable argument lists
     (valist) on amd64 and ppc.	

PEDSTATS 0.5.3
===============

   * Fast exact Hardy-Weinberg test added. When this option is requested,
     all tests for markers with two alleles and less than 5000 genotypes will be 
     computed using a fast exact calculation.

   * Graphical output for fast exact Hardy-Weinberg test added.

   * Updates to Hardy-Weinberg pooling algorithm to handle end case 
     where all alleles are classified as rare, provide better error messages 
     for other end cases. 

   * Code updates to eliminate compiler warnings generated for Unix CC

   * Age checking algorithm rewritten to improve performance and error 
     messaging.

    
PEDSTATS 0.4.6
==============

   * Version information added to program banner and Makefile. 

   * Option for sex-specific output added (--bySex). When this option is requested,
     all text output is broken down by gender. When combined with --pdf and --pairs options,
     all pairwise charts are broken down by gender.

   * Graphical output for Hardy-Weinberg tests added.

   * Option to print all results for Hardy-Weinberg tests added (--showAll)

   * Options to test age covariates for appropriate generation gaps added (--ageLabel
     --birthYear, --minGap, and --maxGap). 

   * Data structures for relative pair output rewritten to improve code performance
     on large data sets

   * Covariate and trait text output reorganized to include additional statistics

   * Family-based output added (--byFamily) When this option is requested, per-family
     summaries of traits, covariates, affection variables and marker genotypes are
     output to separate data files

   * Expanded text output for pairwise affection variables to include counts of
     discordant and unaffected relative pairs.

   * Added separate section for IBD statistics. When an ibd file is supplied (using
     the -i command line option), counts of families by generation structures
     that have ibd information provided in the ibd file are reported for each marker
     locus.

   * Pedigree filtering added. Filtering options (--minPhenos, --minGenos, --minCovariates, 
     and --affectedFor) can be used to remove from all summaries any individuals not 
     meeting filtering criteria.  

   * New options for pdf output added (--markerPDF, --traitPDF, --affPDF) to allow better 
     control over types of information written to pdf files.
 	
PEDSTATS 0.3.2
==============
   * pairs graphical output follows individual trait, affection and covariate variables 
     instead of being placed at end of the pdf file

   * Corrected bug that miscounted avuncular pairs in text output for some input files.

PEDSTATS 0.3.1
==============

   * Fixed bug where half-sibs were included in cousins count for --pairStatistics 
     graphical output.

PEDSTATS 0.3.0
===============

   * PDF output added for --pairStatistics option. When pair information
     is requested, pedstats generates a page of scatter plots for each 
     covariate and quantitative trait variable. One plot is generated for 
     each of 6 relative pair types (cousin, half-sib, sib, avuncular, parent-child
     and grandparent-grandchild pairs). In addition,  pairwise affection status 
     is summarized for each relative pair type, using one page of histogram plots per
     affection status variable.

   * Legends are replaced with labels on the x-axis for charts with categorical variables.

PEDSTATS 0.2.0
==============

  * Improved PDF Graph Layout. Graphs in PedStats now provide better handling
    of missing data. 

  * R^2 in the sib-sib trait and covariate plots has been
    replaced by the correlation coefficient r, which is expected to be half
    of the heritability for a simple genetic trait.

  * Fixed mislabelling of males and females in breakdown of phenotype scores by sex.


PEDSTATS 0.1.0
==============

February 21st, 2003 -- Version 0.1.0 Officially Released

=============================================================
OLDER VERSIONS OF PEDSTATS AVAILABLE WITH MERLIN & QTDT
=============================================================




 
 

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