idat_to_gtc: Convert raw itensity IDAT files to GTC using IAAP-cli
In Meiomap/SureTypeSCR: Library for (single-cell) SNP array processing

The raw itensity data (red and green channel) are processed into GTC using Illumina's IAAP-cli. Function runs configure_iaap() before instantiating IAAP-cli to make sure IAAP-cli is properly configured.

1	idat_to_gtc(idat_inputfolder,gtc_output,manifest,cluster)

`idat_inputfolder`	input folder with stored idat files
`gtc_output`	output folder for the GTC files
`manifest`	path to manifest file
`cluster`	path to cluster file

#library(GEOquery)
#gse <- getGEO("GSE19247",GSEMatrix = TRUE)

#samplelist_sperm=as.data.frame(gse$`GSE19247-GPL6985_series_matrix.txt.gz`) %>% 
#  filter((str_detect(cell.type.ch1,'sperm')) & str_detect(cell.amplication.ch1,'MDA')) %>%
#  rownames()  

#metadf_sperm=map_if(samplelist_sperm,function(x) !is.null(x),
#                    function(x) getGEO_and_folder_in(x,download=TRUE))
#metadf_sperm_merged = Reduce(function(...) merge(..., all=T), metadf_sperm)

#manifest=system.file("files/HumanCytoSNP-12v2_H.bpm",package="SureTypeSCR")
#cluster=system.file("files/HumanCytoSNP-12v2_H.egt",package="SureTypeSCR")

#for (ar in unique(metadf_sperm_merged$arrayid))
#{
#  idat_to_gtc(ar,'GTC',manifest,cluster)
#}