"""
Truvari main parameters
"""
# pylint: disable=too-few-public-methods
[docs]
class VariantParams():
"""
Holds variant parsing and matching parameters.
Attributes
----------
.. list-table::
:header-rows: 1
* - Attribute
- Description
* - `refdist`
- Distance threshold for comparing positions in the reference genome. Default: 500.
* - `pctseq`
- Minimum percentage of sequence similarity required for a match. Default: 0.70 (70%).
* - `pctsize`
- Minimum percentage of size similarity required for a match. Default: 0.70 (70%).
* - `pctovl`
- Minimum percentage of reciprocal overlap required for comparing variants. Default: 0.0 (disabled).
* - `typeignore`
- Whether to ignore variant type mismatches during comparison. Default: `False`.
* - `no_roll`
- Disable rolling of sequences for comparisons. Default: `False`.
* - `chunksize`
- Number of entries to process in each chunk. Default: 1000.
* - `bSample`
- Sample name or index for the "base" (a.k.a. self) variants during comparisons. Default: 0.
* - `cSample`
- Sample name or index for the "comparison" (a.k.a. other) variants during comparisons. Default: 0.
* - `dup_to_ins`
- Whether to treat duplications as insertions for some operations. Default: `False`.
* - `bnddist`
- Maximum allowed distance for breakend (BND) comparisons. Default: 100.
* - `sizemin`
- Minimum variant size to consider. Default: 50.
* - `sizefilt`
- Minimum size filter for comparison in the "comparison" dataset. Default: 30.
* - `sizemax`
- Maximum variant size to consider. Default: 50,000; -1, off.
* - `passonly`
- Whether to only consider variants with a "PASS" filter status. Default: `False`.
* - `no_ref`
- Whether to ignore reference homozygous variants in (a)ll, (b)ase, or (c)omp VCF Default: `False` (off)`.
* - `pick`
- Strategy for picking matches by Bench (single, ac, multi).
* - `ignore_monref`
- Whether to ignore monoallelic reference calls. Default: `True`.
* - `check_multi`
- Whether to check for and handle multi-allelic records. Default: `True`.
* - `check_monref`
- Whether to check for monoallelic reference calls. Default: `True`.
* - `no_single_bnd`
- Whether to exclude single-end breakends (BNDs) from comparisons. Default: `True`.
* - `write_resolved`
- Whether to write resolved REF/ALT sequences to output. Default: `False`.
* - `decompose`
- Decompose symbolic variants (e.g. <DEL>) into BNDs when comparing with BNDs. Default: `True`
* - `short_circuit`
- Whether to enable short-circuit logic for early exits in comparisons. Default: `False`.
* - `skip_gt`
- Whether to skip genotype comparisons. Default: `False`.
* - `max_resolve`
- Maximum size of a variant to attempt sequence resolving. Default: 25000.
"""
DEFAULTS = {
"reference": None,
"refdist": 500,
"pctseq": 0.70,
"pctsize": 0.70,
"pctovl": 0.0,
"typeignore": False,
"no_roll": False,
"chunksize": 1000,
"bSample": 0,
"cSample": 0,
"dup_to_ins": False,
"bnddist": 100,
"sizemin": 50,
"sizefilt": 30,
"sizemax": 50000,
"passonly": False,
"no_ref": False,
"pick": "single",
"ignore_monref": True,
"check_multi": True,
"check_monref": True,
"no_single_bnd": True,
"write_resolved": False,
"decompose": True,
"short_circuit": False,
"skip_gt": False,
"max_resolve": 25000,
}
def __init__(self, args=None, **kwargs):
"""
Initialize VariantParams with defaults, args, and kwargs.
Parameters
----------
args : Namespace (optional)
An argparse.Namespace object to initialize parameters.
kwargs : dict
Additional parameters to override defaults.
"""
# Start with defaults
params = self.DEFAULTS.copy()
# Override with args if provided
if args:
for key in vars(args):
if key in params:
params[key] = getattr(args, key)
# Override with kwargs
for key, value in kwargs.items():
if key in params:
params[key] = value
else:
raise ValueError(f"Invalid parameter: {key}")
# Set attributes
self.__dict__.update(params)