# Benchmarking Config File for FTSearch
# Path to the input Query File
queryFile = "path_query.txt"
# size of kmer to search for
kmerSize = 30
# read length
readLength = 150
# Path to the index Props ini
indexPropsFile = "Index_MixedVirus_100_index.ini"
# Directory to save the results file
outputFolder = ""
# Query File has Ref or Ref&Alt sequences
refOnly = true
# Search type: CENTERED or SLIDING
searchType = SLIDING
# search for the reverse complement of each kmer
revCompSearch = true
# Count only once for paired reads
countAsPairs = false
# Search using multiple threads
multithread = true
# Create a fastq file for each query that contains reads
# which match to that query
matchingReads = false
# overlap between kmers
overlap = 0
# return only those queries that have read matches
return_only_positive_matches = false
# stride of the sequence taken
stride = 5
# max occurences is the upper bound number of occurences for a sequence
maxOccurences = 100
# thread number is the number of threads to run the algorithm with
numOfThreads = 20
# ignore Kmers
ignoreNonUniqueKmers = true
ignoreOverCountedKmers = true
#output flagged kmers
outputNonUniqueKmers = true;
outputOverCountedKmers = true;
# crossover
crossover = false
#print search time
printSearchTime = false
#max Kmers Per Query
maxKmersPerQuery = 100000000
#max total kmers
maxTotalKmers = 1000000
