prepare_snp6: Prepare SNP6 data for haplotype construction
In shaghayeghsoudi/Battenberg_customized: Battenberg subclonal copy number caller

This function performs part of the Battenberg SNP6 pipeline: Extract BAF and logR from the CEL files and performing GC content correction.

prepare_snp6(
  tumour_cel_file,
  normal_cel_file,
  tumourname,
  chrom_names,
  snp6_reference_info_file,
  apt.probeset.genotype.exe = "apt-probeset-genotype",
  apt.probeset.summarize.exe = "apt-probeset-summarize",
  norm.geno.clust.exe = "normalize_affy_geno_cluster.pl",
  birdseed_report_file = "birdseed.report.txt"
)

`tumour_cel_file`	Full path to a CEL file containing the tumour raw data
`normal_cel_file`	Full path to a CEL file containing the normal raw data
`tumourname`	Identifier to be used for tumour output files
`chrom_names`	A vector containing the names of chromosomes to be included
`snp6_reference_info_file`	Full path to the SNP6 reference info file
`apt.probeset.genotype.exe`	Full path to the apt.probeset.genotype executable (Default: expected in $PATH)
`apt.probeset.summarize.exe`	Full path to the apt.probeset.summarize executable (Default: expected in $PATH)
`norm.geno.clust.exe`	Full path to the norm.geno.clust.exe executable (Default: expected in $PATH)
`birdseed_report_file`	Name of the birdseed output file. This is a temp output file of one of the internally called functions of which the name cannot be defined. Don't change this parameter. (Default: birdseed.report.txt)