# Imputation Pipeline parameters for fastq or SAM files

#!!! Required Parameters !!!
#--- Database ---
host=localHost
user=sqlite
password=sqlite
DB=**UNASSIGNED**
DBtype=sqlite

#--- Used by liquibase to check DB version ---
liquibaseOutdir=/phg/outputDir

#--- Used for writing a pangenome reference fasta(not needed when inputType=vcf) ---
pangenomeHaplotypeMethod=**UNASSIGNED**
pangenomeDir=/phg/outputDir/pangenome
indexKmerLength=21
indexWindowSize=11
indexNumberBases=90G

#--- Used for mapping reads
inputType=fastq
readMethod=**UNASSIGNED**
keyFile=/phg/readMapping_key_file.txt
fastqDir=/phg/inputDir/imputation/fastq/
samDir=/phg/inputDir/imputation/sam/
lowMemMode=true
maxRefRangeErr=0.25
outputSecondaryStats=false
maxSecondary=20
fParameter=f1000,5000
minimapLocation=minimap2

#--- Used for path finding
pathHaplotypeMethod=**UNASSIGNED*
pathMethod=**UNASSIGNED*
maxNodes=1000
maxReads=10000
minReads=1
minTaxa=20
minTransitionProb=0.001
numThreads=3
probCorrect=0.99
removeEqual=true
splitNodes=true
splitProb=0.99
usebf=false
maxParents = 1000000
minCoverage = 1.0
#parentOutputFile = **OPTIONAL**

#   used by haploid path finding only
usebf=false
minP=0.8

#   used by diploid path finding only
maxHap=11
maxReadsKB=100
algorithmType=efficient

#--- Used to output a vcf file for pathMethod
outVcfFile=**UNASSIGNED**
#~~~ Optional Parameters ~~~
#pangenomeIndexName=**OPTIONAL**
#readMethodDescription=**OPTIONAL**
#pathMethodDescription=**OPTIONAL**
#debugDir=**OPTIONAL**
#bfInfoFile=**OPTIONAL**