BANDWIDTH=3
CONVERSION=T>C
MINIMUM_READ_COUNT_PER_GROUP=5
MINIMUM_READ_COUNT_PER_CLUSTER=5
MINIMUM_READ_COUNT_FOR_KDE=5
MINIMUM_CLUSTER_SIZE=10
MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=1
MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=1
MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=5
MINIMUM_READ_LENGTH=13
MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=0

ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL=5

BOWTIE_FILE=./Pumilio2_aligned/Pumilio2.bowtie=COLLAPSED
GENOME_2BIT_FILE=hg19.2bit

FILTER_FILE=./RepeatMasker/DNA.txt=DNA
FILTER_FILE=./RepeatMasker/LINE.txt=LINE
FILTER_FILE=./RepeatMasker/Low_complexity.txt=Low_complexity
FILTER_FILE=./RepeatMasker/LTR.txt=LTR
FILTER_FILE=./RepeatMasker/Other.txt=Other
FILTER_FILE=./RepeatMasker/RC.txt=RC
FILTER_FILE=./RepeatMasker/RNA.txt=RNA
FILTER_FILE=./RepeatMasker/Satellite.txt=Satallite
FILTER_FILE=./RepeatMasker/SINE.txt=SINE
FILTER_FILE=./RepeatMasker/Unknown.txt=Unknown

OUTPUT_DISTRIBUTIONS_FILE=Pumilio2_5deep_distribution.csv
OUTPUT_GROUPS_FILE=Pumilio2_5deep_groups.csv
OUTPUT_CLUSTERS_FILE=Pumilio2_kde_plus3_5deep