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GeneticsBase
Correct storing/retrieving bitArrays that span storage-cell boundaries
Correct storing/retrieving bitArrays that span storage-cell boundaries

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GeneticsBase
Add numbers to code chunks in SummaryTables.Rnw to make errors easier to locate

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GeneticsBase
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

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GeneticsBase
Change maintainer to R Genetics Project, with the mailing list email address

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GeneticsBase
removed quotes from do.call

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GeneticsBase
Fix typos and minor reformatting
Add vignette 'tutorial' from BioC2007 tutorial session.
Add note that SummaryTables.Rnw vignette is designed for small number of markers

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GeneticsBase
Add as.geneSet.R source file to Collate
Add as.geneSet methods to NAMESPACE
Fix check and warning for alleles argument to makeCCodesAndTTables()
Fix typos
Fix typos
Add as.geneSet() function and documentation
Set pedigree-specific argument founderOnly to be FALSE by default, since it FAILS when pedigree information is not present. TODO: This should be changed to *detech* if pedigree information is present, then act appropriately. Also, correct he default value for confidence interval quantiles to be 2.5% and 97.5% rather than (usually incorrect) 95%.
Minor code reformatting
Fix handling when missing codes are specified by a single 'ALL' entry for all markers
Implement code for remove.spaces=TRUE, convert empty alleles to NA, correct behavior when only one column of genotypes is provided

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GeneticsBase
Add packed unsigned array/vector accessors
Add initial work on bitArrayVector C++ clas to provide a space-efficient variable-bit-width array class

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GeneticsBase
More changes to bitArrayVector.cpp

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GeneticsBase
More work on bitArrayVector class

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GeneticsBase
Correct description of power calculation example code
Remove unrelated material from HOWTO
The power.casectl function was performing and invalid calculation.
Replaced it with correct functions "GeneticsPower.Quantitative.Factor"
and "GeneticsPower.Quantitative.Numeric", and modified the
GeneticsBase Tutorial vignette to use the new functions. The old
function is only present as a stub, which raises a depreciated error

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GeneticsBase
removed whitespace from \item{object} {geneSet object}

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GeneticsBase
fix Rd errors

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GeneticsBase
fixed Rd version 2 parser warnings

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GeneticsBase
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

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GeneticsBase
Remove commented-out code

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GeneticsBase
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.

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GeneticsBase
make it compile on openSUSE 11.0/gcc 4.3.1

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GeneticsBase
Reneame the 'tutorial' vignette to 'Tutorial' to be consistent with capitalization of the other vignettes.
Update HWE.exact doc to include proper attribution and literature reference
Update TODO list based on telecon 2007-01-25

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GeneticsBase
Update TODO from old changes

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