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Record of Changes to PEDSTATS
ChangeLog
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CHANGES AFTER PUBLIC RELEASE OF PEDSTATS
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PEDSTATS 0.6.12
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* Fixed problem with --rewrite function that caused original allele labels to be lost.
PEDSTATS 0.6.11
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* 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
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* 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
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* 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
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* Corrected bug that caused non-specific Mendelian inheritance errors to be erroneously reported for
some large family structures.
PEDSTATS 0.5.8
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* 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
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* 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
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* 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
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* 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
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* 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
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* Fixed bug where half-sibs were included in cousins count for --pairStatistics
graphical output.
PEDSTATS 0.3.0
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* 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
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* 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
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February 21st, 2003 -- Version 0.1.0 Officially Released
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OLDER VERSIONS OF PEDSTATS AVAILABLE WITH MERLIN & QTDT
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