expanding VariantParams documentation

And cleaning it up

docs/api/truvari.examples.rst

@@ -37,7 +37,7 @@ This returns a `truvari.MatchResult`. You can customize matching thresholds by p
 .. code-block:: python
 
     # Disable sequence and size similarity; enable reciprocal overlap
-    matcher = truvari.VariantParams(seqsim=0, sizesim=0, recovl=0.5)
+    matcher = truvari.VariantParams(seqsim=0, sizesim=0, pctovl=0.5)
     vcf = truvari.VariantFile("input.vcf.gz", matcher=matcher)
     entry1 = next(vcf)
     entry2 = next(vcf)

repo_utils/sub_tests/unittest.sh → repo_utils/sub_tests/unittests.sh

@@ -1,7 +1,7 @@
 # ------------------------------------------------------------
-#                                 unittest
+#                                 unittests
 # ------------------------------------------------------------
-run unittest coverage run --concurrency=multiprocessing -p repo_utils/run_unittest.py
+run unittests coverage run --concurrency=multiprocessing -p repo_utils/run_unittest.py
 if [ $unittest ]; then
     assert_exit_code 0 
 fi

repo_utils/truvari_ssshtests.sh

@@ -24,7 +24,7 @@ source $TESTSRC/sub_tests/phab.sh
 source $TESTSRC/sub_tests/refine.sh
 source $TESTSRC/sub_tests/segment.sh
 source $TESTSRC/sub_tests/stratify.sh
-source $TESTSRC/sub_tests/unittest.sh
+source $TESTSRC/sub_tests/unittests.sh
 source $TESTSRC/sub_tests/vcf2df.sh
 source $TESTSRC/sub_tests/version.sh
 

truvari/bench.py

@@ -25,7 +25,7 @@ def parse_args(args):
     """
     Pull the command line parameters
     """
-    defaults = truvari.VariantParams.make_params()
+    defaults = truvari.VariantParams()
     parser = argparse.ArgumentParser(prog="bench", description=__doc__,
                                      formatter_class=argparse.RawDescriptionHelpFormatter)
     parser.add_argument("-b", "--base", type=str, required=True,

truvari/variant_params.py

@@ -1,86 +1,123 @@
 """
 Truvari main parameters
 """
-import types
-
-
+#pylint: disable=too-few-public-methods
 class VariantParams():
     """
     Holds variant parsing and matching parameters.
 
-    Example
-        >>> import truvari
-        >>> p = truvari.VariantParams(pctseq=0)
-        >>> v = truvari.VariantFile('repo_utils/test_files/variants/input1.vcf.gz', params=p)
-        >>> one = next(v); two = next(v)
-        >>> one.match(two)
-        <truvari.bench.MatchResult (False 2.381)>
+    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`
+         - Whether to disable rolling of sequences for comparisons. Default: `False`.
+       * - `chunksize`
+         - Number of entries to process in each chunk. Default: 1000.
+       * - `bSample`
+         - Sample index for the "base" (a.k.a. self) variants during comparisons. Default: 0.
+       * - `cSample`
+         - Sample 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: 50000.
+       * - `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`.
+       * - `short_circuit`
+         - Whether to enable short-circuit logic for early exits in comparisons. Default: `False`.
+       * - `skip_gt`
+         - Whether to skip genotype comparisons. Default: `False`.
 
-    Look at `VariantParams.make_params()` for a list of all params and their defaults
     """
 
+    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,
+        "short_circuit": False,
+        "skip_gt": False,
+    }
+
     def __init__(self, args=None, **kwargs):
         """
-        Initalize. args is a Namespace from argparse
+        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.
         """
-        if args is not None:
-            params = self.make_params_from_args(args)
-        else:
-            params = self.make_params()
+        # 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 parameters with those provided in kwargs
+        # Override with kwargs
         for key, value in kwargs.items():
-            if hasattr(params, key):
-                setattr(params, key, value)
+            if key in params:
+                params[key] = value
             else:
                 raise ValueError(f"Invalid parameter: {key}")
 
-        for key, value in params.__dict__.items():
-            setattr(self, key, value)
-
-    @staticmethod
-    def make_params():
-        """
-        Makes a simple namespace of matching parameters. Holds defaults
-        """
-        params = types.SimpleNamespace()
-        params.reference = None
-        params.refdist = 500
-        params.pctseq = 0.70
-        params.pctsize = 0.70
-        params.pctovl = 0.0
-        params.typeignore = False
-        params.no_roll = False
-        params.chunksize = 1000
-        params.bSample = 0
-        params.cSample = 0
-        params.dup_to_ins = False
-        params.bnddist = 100
-        params.sizemin = 50
-        params.sizefilt = 30
-        params.sizemax = 50000
-        params.passonly = False
-        params.no_ref = False
-        params.pick = 'single'
-        params.ignore_monref = True
-        params.check_multi = True
-        params.check_monref = True
-        params.no_single_bnd = True
-        params.write_resolved = False
-        params.short_circuit = False
-        params.skip_gt = False
-        return params
-
-    @staticmethod
-    def make_params_from_args(args):
-        """
-        Makes a simple namespace of matching parameters.
-        Populates defaults from make_params, then updates with values from args.
-        """
-        ret = VariantParams.make_params()
-
-        for key in vars(ret):
-            if hasattr(args, key):
-                setattr(ret, key, getattr(args, key))
-
-        return ret
+        # Set attributes
+        self.__dict__.update(params)