@@ -110,30 +110,30 @@ is decoded and scanned

 * added cdfName as argument to computeCopynumber

-2009-04-07 B Carvalho - committed versioni 1.0.74

+2009-04-07 B Carvalho - committed version 1.0.74

 * Added documentation for snprma.

 * Removed 'svn:executable' property of readIdatFiles.Rd

-2009-04-07 Rob Scharpf - committed versioni 1.0.75

+2009-04-07 Rob Scharpf - committed version 1.0.75

 * modifications to chromosome X copy number estimation

-2009-04-07 Rob Scharpf - committed versioni 1.0.76

+2009-04-07 Rob Scharpf - committed version 1.0.76

 * fixed bug in cnrma

-2009-04-07 Rob Scharpf - committed versioni 1.0.77

+2009-04-07 Rob Scharpf - committed version 1.0.77

 * cnrma accepts other cdfNames

 * fixed bug in cnrma

-2009-04-07 Rob Scharpf - committed versioni 1.0.78

+2009-04-07 Rob Scharpf - committed version 1.0.78

 * added conf as argument to instantiateObjects

+2009-04-08 Matt Ritchie - committed version 1.0.79

-

-

+* fixed bug in readIDAT and readIdatFiles from reading in RunInfo header information

@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays.

-Version: 1.0.78

+Version: 1.0.79

 Date: 2008-12-30

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -53,9 +53,7 @@ readIdatFiles = function(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".",

                          Position = rep(NA, narrays)) # this may also vary a bit

        dates = list(decode=rep(NA, narrays),

-                    scan=rep(NA, narrays),

-                    register=rep(NA, narrays),

-                    extract=rep(NA, narrays))

+                    scan=rep(NA, narrays))

        # read in the data

        for(i in seq(along=arrayNames)) {

@@ -90,8 +88,6 @@ readIdatFiles = function(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".",

          dates$decode[i] = G$RunInfo[1, 1]

          dates$scan[i] = G$RunInfo[2, 1]

-         dates$register[i] = G$RunInfo[3, 1]

-         dates$extract[i] = G$RunInfo[4, 1]

          if(i==1) {

            if(is.null(ids) && !is.null(G))

@@ -245,7 +241,7 @@ readIDAT <- function(idatFile){

   RunInfo <- matrix(NA, nRunInfoBlocks, 5)

   colnames(RunInfo) <- c("RunTime", "BlockType", "BlockPars", 

                          "BlockCode", "CodeVersion")

-  for(i1 in 1:nRunInfoBlocks){

+  for(i1 in 1:2) { #nRunInfoBlocks){  ## MR edit

     for(i2 in 1:5){

       nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

       RunInfo[i1,i2] <- readChar(tempCon, nChars)