#config file for imputation, small seq test
#!!! Required Parameters !!!
#--- Database ---
host=localHost
user=sqlite
password=sqlite
DB=/phg/phgSmallSeq.db
DBtype=sqlite

#--- Used for writing and indexing a pangenome ---
pangenomeHaplotypeMethod=CONSENSUS
pangenomeDir=/phg/pangenome/
indexKmerLength=21
indexWindowSize=11
indexNumberBases=90G

#--- Used for mapping reads
inputType=fastq
readMethod=READS_FASTQ
keyFile=/phg/genotypingKeyFile.txt
fastqDir=/phg/data/
samDir=**UNASSIGNED**
lowMemMode=true
maxRefRangeErr=0.25
outputSecondaryStats=false
maxSecondary=20
minimapLocation=minimap2

#--- Used for path finding
pathHaplotypeMethod=CONSENSUS
pathMethod=PATH_METHOD
maxNodes=1000
maxReads=10000
minReads=0
minTaxa=2
minTransitionProb=0.0001
numThreads=3
probCorrect=0.99
removeEqual=true
splitNodes=true
splitProb=0.99
usebf=false
#   used by haploid path finding only
usebf=false
minP=0.8
#   used by diploid path finding only
maxHap=11
maxReadsKB=100
algorithmType=classic
outVcfFile=/phg/outputDir/output.vcf