[BioC] readChp in affxparser

[Gábor Csárdi]

OK, it seems that this was a bug in affxparser, here is a tiny patch
that seems to be good according to my test and my rather incomplete
knowledge about these files:

--- affxparser-1.15.orig/src/R_affx_chp_parser.cpp   2008-10-22
01:33:12.000000000 +0200
+++ affxparser-1.15/src/R_affx_chp_parser.cpp   2008-10-31
14:54:31.000000000 +0100
@@ -778,7 +778,7 @@
   if(nGeno > 0) nDataTypes++;
   if(nGenoC > 0) nDataTypes++;

-  lstNbr = nDataTypes + 6;
+  lstNbr = nDataTypes + 7;
   PROTECT(lst = NEW_LIST(lstNbr));
   PROTECT(nms = NEW_CHARACTER(lstNbr));
   nprotect+=2;

Best,
Gabor

On Fri, Oct 31, 2008 at 12:39 PM, Gábor Csárdi <csardi.gabor at gmail.com> wrote:
> Hmmm, I am sorry for not including these in the original post:
>
> R version 2.8.0 (2008-10-20)
> i486-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] affxparser_1.15.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.8.0
>
> On Fri, Oct 31, 2008 at 12:34 PM, Gábor Csárdi <Gabor.Csardi at unil.ch> wrote:
>> Dear All, I'm trying to read a CHP file produced by Affymetrix
>> Genotyping Console software. It seems that readChp can only read the
>> summary information from the file, is that correct, or am I doing
>> something wrong? Is there another package or piece of software that
>> can read these files?
>>
>> Thanks, Gabor
>> --
>> Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM
>>
>
> --
> Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM
>



-- 
Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM