vg_anchors/config.ini at main · shlokanegi/vg_anchors · GitHub

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[debug]
DEBUG = False
PRINT_RUNTIME_LOGS = True
OUTPUT_LOGGING_FILES = False

[anchor_params]
MIN_ANCHOR_LENGTH = 16
MIN_NODES_IN_ANCHOR = 2

[anchor_dict]
FORWARD_DICTIONARY = 0
REVERSE_DICTIONARY = 1
END_NODE_POS = 0
SNARL_ID_POS = 1

[gaf_parsing]
EXPECTED_GAF_TAGS = 16
EXPECTED_MAP_Q = 1
MIN_CS_LEN = 6
READ_NAME_ID = 0
READ_LEN = 1
READ_START_ID = 2
RELATIVE_STRAND_ID = 4
PATH_ID = 5
PATH_START_ID = 7
PATH_END_ID = 8
DIV_ID = 15
MAP_Q_ID = 11
CS_TAG_ID = 14

[alignment_list]
READ_POSITION = 0
R_LEN_POSITION = 1
READ_START_POS = 2
STRAND_POSITION = 3
START_POSITION = 4
END_POSITION = 5
NODE_POSITION = 6
ORIENTATION_POSITION = 7
CIGAR_POSITION = 8

[bp_matched_read_list]
READ_ID = 0
READ_STRAND = 1
ANCHOR_START = 2
ANCHOR_END = 3
MATCH_LIMIT = 4
CS_LEFT_AVAIL = 5
CS_RIGHT_AVAIL = 6

[extension_merging]
MIN_ANCHOR_READS = 2
HET_FRACTION_READS_RETAINED_THRESHOLD_FOR_MERGING = 0.9
HOMO_FRACTION_READS_RETAINED_THRESHOLD_FOR_MERGING = 0.4
MIN_READS_REQUIRED_FOR_MERGING_R0 = 9
MIN_READS_REQUIRED_FOR_MERGING_R1 = 3
MIN_ANCHOR_READCOV = 9
MIN_ANCHOR_READCOV_FOR_INDEPENDENT_ANCHOR_EXTENSION = 3
FRACTION_READS_FOR_SNARL_BOUNDARY_EXTENTION = 0.9
MIN_READS_REQUIRED_FOR_BOUNDARY_EXTENSION = 0
DROP_FRACTION = 0.1

[reliability]
MIN_SNARL_LINKAGE_THRESHOLD = 3
ADD_BACK_HOMO_SNARLS = True
RELIABLE_SNARL_FRACTION_THRESHOLD = 0.1
ERROR_TOLERANCE_IN_COMPATIBILITY_CHECK = 0
ENABLE_UNEQUAL_SET_COMPATIBILITY = False
MIN_READS_FOR_PARTITION_COMPATIBILITY = 1

[gtest]
USE_GTEST_FOR_PARTITION_COMPATIBILITY = False
DETANGLE_MAX_LOG_P = 30
DETANGLE_MIN_LOG_P_DELTA = 10
DETANGLE_GTEST_EPSILON = 0.1