From 8b053ea998c7c6d645f404d5963003ac1b0a23b3 Mon Sep 17 00:00:00 2001
From: Adam English <ACEnglish@gmail.com>
Date: Tue, 7 Jan 2025 13:26:09 -0500
Subject: [PATCH] Fix pysam.VariantFile attribute setting

Minor code cleaning and docs
---
 truvari/bench.py          | 12 ++++++++----
 truvari/matching.py       | 24 ++++++++++++++++++------
 truvari/variant_record.py | 19 ++++++++++++++++---
 3 files changed, 42 insertions(+), 13 deletions(-)

diff --git a/truvari/bench.py b/truvari/bench.py
index 93306d54..08a0e1d6 100644
--- a/truvari/bench.py
+++ b/truvari/bench.py
@@ -333,8 +333,10 @@ def __init__(self, bench, params):
         with open(os.path.join(self.m_bench.outdir, 'params.json'), 'w') as fout:
             json.dump(param_dict, fout)
 
-        b_vcf = truvari.VariantFile(self.m_bench.base_vcf, params=self.m_params)
-        c_vcf = truvari.VariantFile(self.m_bench.comp_vcf, params=self.m_params)
+        b_vcf = truvari.VariantFile(
+            self.m_bench.base_vcf, params=self.m_params)
+        c_vcf = truvari.VariantFile(
+            self.m_bench.comp_vcf, params=self.m_params)
         self.n_headers = {'b': edit_header(b_vcf),
                           'c': edit_header(c_vcf)}
 
@@ -407,6 +409,7 @@ def close_outputs(self):
         self.stats_box.write_json(os.path.join(
             self.m_bench.outdir, "summary.json"))
 
+
 class Bench():
     """
     Object to perform operations of truvari bench
@@ -524,6 +527,7 @@ def compare_chunk(self, chunk):
         logging.debug("Comparing chunk %s", chunk_id)
         result = self.compare_calls(
             chunk_dict["base"], chunk_dict["comp"], chunk_id)
+        # Not checking BNDs as part of refine_candidates because they can't be refined.
         self.check_refine_candidate(result)
         # Check BNDs separately
         if self.params.bnddist != -1 and (chunk_dict['base_BND'] or chunk_dict['comp_BND']):
@@ -619,8 +623,8 @@ def check_refine_candidate(self, result):
             # min(10, self.matcher.chunksize) need to make sure the refine covers the region
             buf = 10
             start = max(0, min(*pos) - buf)
-            self.refine_candidates.append(
-                f"{chrom}\t{start}\t{max(*pos) + buf}")
+            end = max(*pos) + buf
+            self.refine_candidates.append(f"{chrom}\t{start}\t{end}")
 
 #################
 # Match Pickers #
diff --git a/truvari/matching.py b/truvari/matching.py
index 5978dc6a..fcf1c8ef 100644
--- a/truvari/matching.py
+++ b/truvari/matching.py
@@ -101,13 +101,25 @@ def __repr__(self):
 
 def file_zipper(*start_files):
     """
-    Zip files to yield the entries in order.
-    Each file must be sorted in the same order.
-    start_files is a tuple of ('key', iterable)
-    where key is the identifier (so we know which file the yielded entry came from)
-    and iterable is usually a truvari.VariantFile
+    Zip multiple files to yield their entries in order.
 
-    yields key, truvari.VariantRecord
+    The function takes as input tuples of (`key`, `iterable`), where:
+
+    - `key` is an identifier (used to track which file the yielded entry comes from).
+    - `iterable` is an iterable object, typically a `truvari.VariantFile`.
+
+    The function iterates through all input files in a coordinated manner, yielding the entries in order.
+
+    :param start_files: A variable-length argument list of tuples (`key`, `iterable`).
+    :type start_files: tuple
+
+    :yields: A tuple of (`key`, `truvari.VariantRecord`), where `key` is the file identifier and the second element is the next record from the corresponding file.
+    :rtype: tuple
+
+    :raises StopIteration: Raised when all input files have been exhausted.
+
+    **Logs**:
+        - Logs a summary of the zipping process after all files have been processed.
     """
     markers = []  # list of lists: [name, file_handler, top_entry]
     file_counts = Counter()
diff --git a/truvari/variant_record.py b/truvari/variant_record.py
index c07eeab5..730309a0 100644
--- a/truvari/variant_record.py
+++ b/truvari/variant_record.py
@@ -10,7 +10,6 @@
 
 RC = str.maketrans("ATCG", "TAGC")
 
-
 class VariantRecord:
     """
     Wrapper around pysam.VariantRecords with helper functions of variant properties and basic comparisons
@@ -35,6 +34,21 @@ def __getattr__(self, name):
         """
         return getattr(self._record, name)
 
+    def __setattr__(self, name, value):
+        """
+        Attempt to delegate attribute setting to the original VariantRecord first
+        """
+        if name.startswith("_") or not hasattr(self, "_record"):
+            # Directly set internal attributes or during __init__ before _record is set
+            super().__setattr__(name, value)
+        else:
+            try:
+                # Try to set the attribute on the wrapped _record
+                setattr(self._record, name, value)
+            except AttributeError:
+                # If the wrapped object does not have the attribute, set it on self
+                super().__setattr__(name, value)
+
     def __str__(self):
         return str(self._record)
 
@@ -348,8 +362,7 @@ def is_present(self, sample=0, allow_missing=True):
         gt = self.gt(sample)
         if allow_missing:
             return 1 in gt
-        # Hemi...
-        return truvari.get_gt(gt)[truvari.GT.HET, truvari.GT.HOM]
+        return truvari.get_gt(gt) in [truvari.GT.HET, truvari.GT.HOM]
 
     def is_single_bnd(self):
         """