BLUPPP_parameters.par

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##### 								BLUPPP parameter file							#####
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## WORKING DIRECTORY:
WDIR=

## DIRECTORY FOR BLUPF90 PREPARATION:
# If specified, phenotypes, relationships and processed genotypes will be relocated inside (genotypes will be symlinked).
BF90D=BLUPF90

## LOCATION AND NAME OF FILES (genotypes, phenotypes, relationships and SNP .map):
# Note: smap will only be necessary if '-l' flag (plink filter) is used.
genotypes=
phenot=
parent=
smap=

## PROCESSING OPTIONS: These options will only work if '-p' flag is used.
# appendg: If specified, add new genotypes to the previous file. Otherwise, leave blank.
# headers: How do you want to treat headers in your genotypes file? values -> 0=absent; 1=present,remove; 2=present,keep.
# duplicates: Are there duplicated samples to process? y/n.
# NAto5: Do you want to convert NAs/-1 to numeric value (5)? y/n.
# modif: Values: 'join' (all number-coded SNPs all together) or 'separate' (number-coded SNPs separated by spaces). Leave blank if not required.
appendg=
headers=
duplicates=
NAto5=
modif=

## EXTRA PROCESSING FUNCTION: This function will only work with '-p' flag.
# Sometimes, extra processing might be needed for some genotypes files. Here, a custom function can be created for applying it before joining or separating.
# If this function is not necessary, remove it.
# The function will be passed as: EXTRA_PROC "$gname.tmp". Function's output file must be $gname.tmp as well. So, input and output files inside the function 
# must be referred as $1. Note: $gname.tmp is a temporary file created from $genotypes at the beginning (or after adding new genotypes if specified). 
EXTRA_PROC(){
	#Example: Remove an extra non-SNP column:
  cut -d ' ' -f1 $1 > ids.tmp
	cut -f3- -d ' ' $1 > snps.tmp
	paste -d ' ' ids.tmp snps.tmp > $1
	rm ids.tmp snps.tmp
}