From 6549f1f879781f66ef378f9f9950d61afca0eb87 Mon Sep 17 00:00:00 2001
From: Dylan Costo <99520325+DylanCosto@users.noreply.github.com>
Date: Sat, 10 Oct 2026 23:43:01 -0400
Subject: [PATCH 1/2] Remove all-gap alignment columns without repeated list
 deletion

---
 lib/bx/align/core.py      | 41 +++++++++++----------------------------
 lib/bx/align/maf_tests.py |  9 ++++++++-
 2 files changed, 19 insertions(+), 31 deletions(-)

diff --git a/lib/bx/align/core.py b/lib/bx/align/core.py
index 379736e..6864525 100644
--- a/lib/bx/align/core.py
+++ b/lib/bx/align/core.py
@@ -166,36 +166,17 @@ def remove_all_gap_columns(self):
         Remove any columns containing only gaps from alignment components,
         text of components is modified IN PLACE.
         """
-        seqs = []
-        for c in self.components:
-            if c.empty:
-                seqs.append(None)
-            try:
-                seqs.append(list(c.text))
-            except TypeError:
-                seqs.append(None)
-        i = 0
-        text_size = self.text_size
-        while i < text_size:
-            all_gap = True
-            for seq in seqs:
-                if seq is None:
-                    continue
-                if seq[i] != "-":
-                    all_gap = False
-            if all_gap:
-                for seq in seqs:
-                    if seq is None:
-                        continue
-                    del seq[i]
-                text_size -= 1
-            else:
-                i += 1
-        for i in range(len(self.components)):
-            if seqs[i] is None:
-                continue
-            self.components[i].text = "".join(seqs[i])
-        self.text_size = text_size
+        components = [c for c in self.components if not c.empty and c.text is not None]
+        if any("-" not in c.text for c in components):
+            return
+        # Decide which columns to retain before modifying any component. Deleting
+        # individual gaps from lists repeatedly shifts the remaining alignment.
+        keep = [i for i in range(self.text_size) if any(c.text[i] != "-" for c in components)]
+        if len(keep) == self.text_size:
+            return
+        for component in components:
+            component.text = "".join(component.text[i] for i in keep)
+        self.text_size = len(keep)
 
     def __eq__(self, other):
         if other is None or not isinstance(other, type(self)):
diff --git a/lib/bx/align/maf_tests.py b/lib/bx/align/maf_tests.py
index d343f0f..d82b1e1 100644
--- a/lib/bx/align/maf_tests.py
+++ b/lib/bx/align/maf_tests.py
@@ -4,6 +4,8 @@
 
 from io import StringIO
 
+import pytest
+
 from bx import align
 from bx.align import maf
 
@@ -211,7 +213,8 @@ def test_column_iter():
         assert c == expected[i]
 
 
-def test_remove_all_gap_column():
+@pytest.mark.parametrize("empty_index", [0, 1, 3])
+def test_remove_all_gap_column(empty_index):
     complex_maf_gap = align.Alignment()
     complex_maf_gap.score = "7009"
     complex_maf_gap.components.append(
@@ -231,7 +234,11 @@ def test_remove_all_gap_column():
     complex_maf_gap.components[-1].empty = True
     complex_maf_gap.components[-1].synteny_empty = maf.MAF_INSERT_STATUS
     complex_maf_gap.text_size = 11
+    empty = complex_maf_gap.components.pop()
+    complex_maf_gap.components.insert(empty_index, empty)
     complex_maf_gap.remove_all_gap_columns()
+    # Return the empty row to its fixture position for the equality check.
+    complex_maf_gap.components.append(complex_maf_gap.components.pop(empty_index))
     assert complex_maf_gap == complex_maf
 
 

From 5637291dd37a2842785d834dae4c31912ac687a7 Mon Sep 17 00:00:00 2001
From: Dylan Costo <99520325+DylanCosto@users.noreply.github.com>
Date: Sun, 11 Oct 2026 00:05:19 -0400
Subject: [PATCH 2/2] Compact shared alignment components only once

---
 lib/bx/align/core.py      | 2 ++
 lib/bx/align/maf_tests.py | 7 ++++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/lib/bx/align/core.py b/lib/bx/align/core.py
index 6864525..3772191 100644
--- a/lib/bx/align/core.py
+++ b/lib/bx/align/core.py
@@ -167,6 +167,8 @@ def remove_all_gap_columns(self):
         text of components is modified IN PLACE.
         """
         components = [c for c in self.components if not c.empty and c.text is not None]
+        # A component can occur more than once; rebuild each object only once.
+        components = list({id(c): c for c in components}.values())
         if any("-" not in c.text for c in components):
             return
         # Decide which columns to retain before modifying any component. Deleting
diff --git a/lib/bx/align/maf_tests.py b/lib/bx/align/maf_tests.py
index d82b1e1..cf0710c 100644
--- a/lib/bx/align/maf_tests.py
+++ b/lib/bx/align/maf_tests.py
@@ -214,7 +214,8 @@ def test_column_iter():
 
 
 @pytest.mark.parametrize("empty_index", [0, 1, 3])
-def test_remove_all_gap_column(empty_index):
+@pytest.mark.parametrize("repeat_component", [False, True])
+def test_remove_all_gap_column(empty_index, repeat_component):
     complex_maf_gap = align.Alignment()
     complex_maf_gap.score = "7009"
     complex_maf_gap.components.append(
@@ -236,7 +237,11 @@ def test_remove_all_gap_column(empty_index):
     complex_maf_gap.text_size = 11
     empty = complex_maf_gap.components.pop()
     complex_maf_gap.components.insert(empty_index, empty)
+    if repeat_component:
+        complex_maf_gap.add_component(next(c for c in complex_maf_gap.components if not c.empty))
     complex_maf_gap.remove_all_gap_columns()
+    if repeat_component:
+        complex_maf_gap.components.pop()
     # Return the empty row to its fixture position for the equality check.
     complex_maf_gap.components.append(complex_maf_gap.components.pop(empty_index))
     assert complex_maf_gap == complex_maf