From 71d2d2465255885acdf84186ef7f2d49f5b5d3f1 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 6 Nov 2023 09:05:09 -0800
Subject: [PATCH] Improve concordance calculation by scanning in both
 directions

The updated function now creates a list with the same length as the
input strings, initialized with zeros. The function then performs a
moving window average comparison on the strings in both forward and
reverse directions. This enhancement is designed to provide a more
thorough and robust analysis of the sequence comparisons.

Also add a docstring to it.
---
 micall/core/contig_stitcher.py | 42 +++++++++++++++++++++++++---------
 1 file changed, 31 insertions(+), 11 deletions(-)

diff --git a/micall/core/contig_stitcher.py b/micall/core/contig_stitcher.py
index f36234304..f4a057ec6 100644
--- a/micall/core/contig_stitcher.py
+++ b/micall/core/contig_stitcher.py
@@ -133,20 +133,40 @@ def find_overlapping_contig(self, aligned_contigs):
                default=None)
 
 
-def calculate_concordance(left: str, right: str) -> Iterable[float]:
-    window_size = 10
-    scores = deque([0] * window_size, maxlen=window_size)
-    scores_sum = 0
-    result = []
+def calculate_concordance(left: str, right: str) -> List[float]:
+    """
+    Calculate concordance for two given sequences using a sliding window method.
+
+    The function compares the two strings from both left to right and then right to left,
+    calculating for each position the ratio of matching characters in a window around the
+    current position (10 characters to the left and right).
+
+    It's required that the input strings are of the same length.
+
+    :param left: string representing first sequence
+    :param right: string representing second sequence
+    :return: list representing concordance ratio for each position
+    """
+
+    result = [0] * len(left)
 
     assert len(left) == len(right), "Can only calculate concordance for same sized sequences"
 
-    for (a, b) in zip(left, right):
-        current = a == b
-        scores_sum -= scores.popleft()
-        scores_sum += (a == b)
-        scores.append(current)
-        result.append(scores_sum / window_size)
+    def slide(left, right):
+        window_size = 10
+        scores = deque([0] * window_size, maxlen=window_size)
+        scores_sum = 0
+
+        for i, (a, b) in enumerate(zip(left, right)):
+            current = a == b
+            scores_sum -= scores.popleft()
+            scores_sum += current
+            scores.append(current)
+            result[i] += scores_sum / window_size
+
+    # Slide forward, then in reverse, adding the scores at each position.
+    slide(left, right)
+    slide(reversed(left), reversed(right))
 
     return result