Doc & code clean

Got the context manager working
ACEnglish · Jan 7, 2025 · 6db6e8e · 6db6e8e
1 parent 5995137
commit 6db6e8e
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Showing 4 changed files with 103 additions and 63 deletions.
diff --git a/docs/api/truvari.package.rst b/docs/api/truvari.package.rst
@@ -22,54 +22,46 @@ Variant Handling
 .. autoclass:: VariantParams
    :members:
 
-Extra Methods
--------------
-.. autofunction:: bed_ranges
-
-.. autofunction:: best_seqsim
-
-.. autofunction:: read_bed_tree
-
-.. autofunction:: check_vcf_index
-
-.. autofunction:: compress_index_vcf
-
-.. autofunction:: get_gt
-
-.. autofunction:: get_scalebin
-
-.. autofunction:: get_sizebin
-
-.. autofunction:: get_svtype
+Objects
+-------
 
-.. autofunction:: msa2vcf
+.. autoclass:: MatchResult
+   :members:
 
-.. autofunction:: overlap_percent
+.. autoclass:: GT
+   :members:
 
-.. autofunction:: overlaps
+.. autoclass:: SV
+   :members:
 
-.. autofunction:: phab
+.. autoclass:: Bench
+   :members:
 
-.. autofunction:: reciprocal_overlap
+.. autoclass:: BenchOutput
+   :members:
 
-.. autofunction:: ref_ranges
+.. autoclass:: StatsBox
+   :members:
 
-.. autofunction:: roll_seqsim
+.. autoclass:: LogFileStderr
+   :members:
 
-.. autofunction:: seqsim
+Extra Methods
+-------------
+.. autofunction:: bed_ranges
 
-.. autofunction:: sizesim
+.. autofunction:: benchdir_count_entries
 
-.. autofunction:: unroll_seqsim
+.. autofunction:: best_seqsim
 
-.. autofunction:: vcf_ranges
+.. autofunction:: read_bed_tree
 
-Dev Methods
------------
-.. autofunction:: benchdir_count_entries
+.. autofunction:: check_vcf_index
 
 .. autofunction:: chunker
 
+.. autofunction:: compress_index_vcf
+
 .. autofunction:: cmd_exe
 
 .. autofunction:: coords_within
@@ -80,45 +72,51 @@ Dev Methods
 
 .. autofunction:: help_unknown_cmd
 
+.. autofunction:: get_gt
+
+.. autofunction:: get_scalebin
+
+.. autofunction:: get_sizebin
+
+.. autofunction:: get_svtype
+
 .. autofunction:: make_temp_filename
 
+.. autofunction:: msa2vcf
+
 .. autofunction:: opt_gz_open
 
 .. autofunction:: optimize_df_memory
 
+.. autofunction:: overlap_percent
+
+.. autofunction:: overlaps
+
 .. autofunction:: performance_metrics
 
-.. autofunction:: restricted_float
+.. autofunction:: phab
 
-.. autofunction:: restricted_int
+.. autofunction:: reciprocal_overlap
 
-.. autofunction:: setup_logging
+.. autofunction:: restricted_float
 
-.. autofunction:: vcf_to_df
+.. autofunction:: restricted_int
 
-Objects
--------
+.. autofunction:: ref_ranges
 
-.. autoclass:: Bench
-   :members:
+.. autofunction:: roll_seqsim
 
-.. autoclass:: BenchOutput
-   :members:
+.. autofunction:: seqsim
 
-.. autoclass:: StatsBox
-   :members:
+.. autofunction:: setup_logging
 
-.. autoclass:: GT
-   :members:
+.. autofunction:: sizesim
 
-.. autoclass:: LogFileStderr
-   :members:
+.. autofunction:: unroll_seqsim
 
-.. autoclass:: MatchResult
-   :members:
+.. autofunction:: vcf_ranges
 
-.. autoclass:: SV
-   :members:
+.. autofunction:: vcf_to_df
 
 Data
 ----

diff --git a/truvari/annotations/svinfo.py b/truvari/annotations/svinfo.py
@@ -59,8 +59,8 @@ def svinfo_main(cmdargs):
     args = parse_args(cmdargs)
     vcf = truvari.VariantFile(args.input)
     n_header = edit_header(vcf.header.copy())
-    out = truvari.VariantFile(args.output, 'w', header=n_header)
-    for entry in vcf:
-        add_svinfo(entry, args.minsize, n_header)
-        out.write(entry)
+    with truvari.VariantFile(args.output, 'w', header=n_header) as out:
+        for entry in vcf:
+            add_svinfo(entry, args.minsize, n_header)
+            out.write(entry)
     logging.info("Finished svinfo")
diff --git a/truvari/matching.py b/truvari/matching.py
@@ -10,7 +10,40 @@
 @total_ordering
 class MatchResult():  # pylint: disable=too-many-instance-attributes
     """
-    A base/comp match holder
+    Holds results from a matching operation
+
+    Attributes
+    ----------
+    .. list-table::
+       :header-rows: 1
+
+       * - Attribute
+         - Description
+       * - `base`
+         - The base (a.k.a. self) variant
+       * - `comp`
+         - The comp (a.k.a. other) variant
+       * - `state`
+         - Boolean of if variants match
+       * - `seqsim`
+         - Sequence similarity of variants
+       * - `sizesim`
+         - Size similarity of variants
+       * - `ovlpct`
+         - Reciprocal overlap ov variants
+       * - `sizediff`
+         - Base variant var_size minus comp variant var_size
+       * - `st_dist`
+         - Base variant start position minus comp variant start position
+       * - `ed_dist`
+         - Base variant end position minus comp variant end position
+       * - `gt_match`
+         -  Boolean of if genotypes match
+       * - `score`
+         - TruScore of matches
+       * - `matid`
+         - Place to put MatchIds, not populated by `truvari.VariantRecord.match`
+
     """
     __slots__ = ["base", "comp", "base_gt", "base_gt_count", "comp_gt", "comp_gt_count",
                  "state", "seqsim", "sizesim", "ovlpct", "sizediff", "st_dist", "ed_dist",

diff --git a/truvari/variant_file.py b/truvari/variant_file.py
@@ -9,10 +9,7 @@
 
 class VariantFile:
     """
-    Wrapper around pysam.VariantFile with helper functions for iteration.
-
-    .. note::
-        The context manager functionality of pysam.VariantFile is not available with truvari.VariantFile.
+    Wrapper around `pysam.VariantFile` with helper functions for iteration.
     """
 
     def __init__(self, filename, *args, params=None, **kwargs):
@@ -29,6 +26,19 @@ def __init__(self, filename, *args, params=None, **kwargs):
         self.params = params
         self._vcf = pysam.VariantFile(filename, *args, **kwargs)
 
+    def __enter__(self):
+        """
+        Enter the context of the wrapped `pysam.VariantFile` object
+        """
+        self._vcf.__enter__()
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        """
+        Exit the context of the wrapped `pysam.VariantFile` object
+        """
+        return self._vcf.__exit__(exc_type, exc_value, traceback)
+
     def __getattr__(self, name):
         """
         Delegate attribute access to the original VariantFile.
@@ -88,7 +98,6 @@ def fetch_bed(self, bed_fn, inside=True, with_region=False):
         tree = truvari.read_bed_tree(bed_fn)
         return self.fetch_regions(tree, inside, with_region)
 
-
     def fetch_regions(self, tree, inside=True, with_region=False):
         """
         Fetch variants from the VCF based on regions defined in a tree of chrom:IntervalTree.