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affxparser
moved the updates from release to devel

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affxparser
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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affxparser
Really updated to Fusion 1.10b. Fixed an error in the help page for readCel.R

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affxparser
more updates for CHP files, MultiData files begun

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affxparser
added code for legacy genotyping arrays
mostly working on the Resequencing arrays
fixed a couple of bugs in the CHP parsing code
more mods for CHP files

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affxparser
more mods for CHP files

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affxparser
more changes to the CHP parsing

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affxparser
CPP code for parsing CHP tiling arrays
code of the parsing chp files

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affxparser
Robert adding in the necessary files to Makevars for reading CHP files

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affxparser
Added a check to make sure that the indices are sorted for now. The larger fix requires reading the file in a different way because of the linked list type setup. Or it requires a little bit of fixing up on the way out, which might be the appropriate way.

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affxparser
Moved readPgf, readClf to *Env, added readPgf,readClf,readClfHeader,readPgfHeader. These now return lists and use an indices argument to specify which probesets should be read. The value of these over the environment function is questionable.
updated to Fusion 1.0.10b

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affxparser
updated to Fusion 1.0.10b

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affxparser
o (unexposed) function .pgfProbeIndexFromProbesetIndex failed to
handle last probe correctly

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affxparser
Version; 1.11.6 [2008-03-04]
o Add ability to parse PGF and CLF files

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affxparser
Version: 1.11.5 [2008-02-29]
o Updated cdfMergeStrands() to merge any even number of groups,
not only units with two or four group pairs.
o BUG FIX: The code in findFiles() for testing if R.utils is loaded
or not in v1.11.4 was not correct making it fail to detect R.utils.
Version: 1.11.4 [2008-02-20]
o Now findFiles() and hence findCdf() is only utilizing the R.utils
package if it is already loaded. It will no longer try to load R.utils.
o Added argument 'allFiles=TRUE' to findFiles().
o Updated readCcg() according to the newer file format specifications.
Now it is possible to do low-level reading of copy-number CNCHP
files generated by the Affymetrix Genotype Console v2.

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affxparser
Last commit contained an embarrassing bug. Fixed
Fixed the loading of R.utils in findFiles. This loading had bad consequences for R CMD check - unfortunately. A better fix would be to take care of the problem at its root.

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affxparser
Fixed the loading of R.utils in findFiles. This loading had bad consequences for R CMD check - unfortunately. A better fix would be to take care of the problem at its root.

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affxparser
Version: 1.11.3 [2007-12-01]
o Removed argument 'reorder' from readCel() and readCelUnits()
since its name was misleading (the returned value was identical
regardless of 'reorder', but the reading speed was faster when
'reorder' was TRUE, which is how it is now hardwired).

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affxparser
Bugfix in .initializeCdf thanks to bug report from E. Purdum

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affxparser
Added a Makefile, bumped version
Fixed small as.integer() bug in tpmap2bpmap

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