### CHANGE log for package pdInfoBuilder ###
BC: 12/12/08
Updates featureSet table from POS file (NGS)

Changes made by Matt Settles 12-8-08
moved closeDb function from many instances in XinitDb.R to one instance in utils.R
added connectDb function in utils.R
changed getGeometry to return a list with nrow and ncols instead of character nrows;ncols
updated man pages 
more work on Affy Tiling and ST arrays

Changes made by Matt Settles 12-4-2008

** All changes should generally have effect on only Affy Tiling, ST and expression arrays.
Changes made that effect, but not break, all objects
	moved url from PkgSeed to PDInfoPkgSeed
	added organism and species to PDINfoPkgSeed, default provided
Changes currently isolated to Affy tiling and ST and expression arrays
	added new generic function getGeometry
	added utils file, contains some general functions
	modifed chipName function for affy tiling and affy st arrays
	moved affy tiling cif file to cel file, may change back, in general the cif file appears to contain no relevant information
	added new pdInfo.PKG.template folde inst, I'm trying something out
	modified package building proceedures for tiling, st and expression arrays
	
Changes by BC in Feb-Mar 2009

** Added new builders for NGS Tiling and Affy Exon. These builders use the minimum of "gene-centric" annotation and should be able to link to org pkgs to extract more info.

03-08-09 - Benilton Carvalho

** In the new builder (v2) for Exon arrays, added a statement to remove probes that are not in the probeset.csv file.

03-09-09 - BC

** Added support to Gene ST arrays. Because these share *much* of the Exon arrays structure, I reused most of the code by adding the 'geneArray' argument to the relevant functions (parsers/builder)

03-17-09 - BC - Committed version  1.7.13

** Added support to HT Expression arrays. The same structure is expected to serve to regular Affymetrix Expression arrays as well

** Several unused functions and structures were removed.

03-19-09 - BC - Committed version 1.7.14

** Added diagnostic messages.

** Added vignette explaining how to build packages for several array types. (v 1.7.15)

03-24-09 - BC - Committed version 1.7.19

** Removed dbImport.AffyHuExArrayAnnCSV.R

** Moved contents of affy*R and ngs*R to toBeRemoved.R. The revamped versions of the builders are more robust and minimize the use of gene-centric annotation.

** Exported only classes that are used to build packages

03-25-2009 - B Carvalho

** Implemented changes mainly to templates, so pacakges pass R CMD check.

** Added slot annotation to PDInfo, so we can easily find any information about the object.

03-26-2009 - B Carvalho

** Added indices

04-02-2009 - B Carvalho

** Added SNP/CNV array

** Added increaseDbPerformance(conn)

04-07-2009 - B Carvalho

** Added warnings in case the user builds a package for a Human SNP Chip. These are available from BioConductor and do support CRLMM, the ones built here do *NOT* support CRLMM.

** Updated vignette

04-16-2009 - B Carvalho

** Fixed the builder for non human tiling arrays

04-24-2009 - B Carvalho

** Sorted *Sequence.rda files by 'fid'

04-29-2009 - B Carvalho

** Fixed merging of NDF and POS files (NimbleGen Tiling Arrays)

05-14-2009 - B Carvalho

** Fixed problem with chipName for NimbleGen arrays. Improved the regular expression to find specifically "\\.ndf$"

** Removed requirement of ALLELE in probe sequence file for Affy SNP chips

10-13-2009 - B Carvalho

** Updated loaders, because the annotation files' format changed, once more (all SNP platforms)

** Updated dependencies on both pdInfoBuilder and template

** Updated NAMESPACE - template

02-08-2010 - B Carvalho

(1.11.3) added if (length(controls)>0) in builder for NGS Expression

03-01-2010 - B Carvalho

(1.11.5) removed unused C code
(1.11.4) moved probes from bg to pmfeature table on exon/gene arrays

03-04-2010 - B Carvalho

(1.11.6) fixed format of NEWS
         fixed docs for sequence on template
         fixed affy expression ht

03-26-2010 - B Carvalho

(1.11.7) Added C code back (used old SNP chips)

04-06-2010 - B Carvalho

(1.11.8) Parser for tab seq file (Affymetrix) has a converter for IUPAC codes
         for the case [X/Y] -> Z (SNPs)

(1.11.9) Replaced cat() by message()/simpleMessage()

(1.11.10) Added checkFields function

(1.11.11) changed way to read NDF

(1.11.12) moved CONTAINER in NimbleGen Tiling from featureSet to (pm/bg)feature table
