config-comik.txt

## CoMIK CONFIG FILE

## Required Input
POSITIVE_FASTA_FILE=./sample_data/simulated_dataset1/pos.fasta
NEGATIVE_FASTA_FILE=./sample_data/simulated_dataset1/neg.fasta
NUMBER_OF_POSITIVES=600
NUMBER_OF_NEGATIVES=600
TEST_INDICES=[501:600 1101:1200]
OUTPUT_FOLDER=comik_run_simulated_dataset1

##  ODH requirements
OLIGO_LEN=[2 3]
MAX_DIST=10

##  For CoMIK
SEGMENT_SIZE_IN_BPS=10
NUMBER_OF_CLUSTERS=[2 5 7]
SIGMA_VALUES=10.^[1:1:2]
COST_VALUES=10.^[-3:1:3]
## Above are params which are required
## Further, params with otherwise default values
MKL_NORM=2.0
NUMBER_OF_INNER_FOLDS=10
NUMBER_OF_OUTER_FOLDS=5
WHETHER_TO_PLOT_HEATMAP=No
WHETHER_TO_VISUALIZE_WEIGHT_VECTOR=Yes
DEBUG_LEVEL=0
DEBUG_MSG_LOCATION=runLog.txt
COMPUTATION_VERSION=Looping