# Paths and system Settings
JOB_NAME=AutoHiC
AutoHiC_DIR=/home/ubuntu/AutoHiC
RESULT_DIR=/home/ubuntu/result
N_CPU=40

# Data options
SPECIES_NAME=At
REFERENCE_GENOME=/home/ubuntu/at/references/at.fa

# Juicer options
JUICER_DIR=/home/ubuntu/HiC/juicer
FASTQ_DIR=/home/ubuntu/at/rawdata
ENZYME=DpnII


# 3D-DNA options
TD_DNA_DIR=/home/ubuntu/3d-dna
NUMBER_OF_EDIT_ROUNDS=2

# AutoHiC options
ERROR_PRETRAINED_MODEL=/home/ubuntu/downloads/error_model.pth
CHR_PRETRAINED_MODEL=/home/ubuntu/downloads/chr_model.pth

TRANSLOCATION_ADJUST=True
INVERSION_ADJUST=True
DEBRIS_ADJUST=False

ERROR_MAX_EPOCH=5
ERROR_MIN_LEN=15000
ERROR_MAX_LEN=20000000
ERROR_FILTER_SCORE=0.9
ERROR_FILTER_IOU_SCORE=0.8