Updating gitignore

Author: joshfactorial

.gitignore

@@ -29,9 +29,3 @@ dist/
 build/
 *.egg-info/
 *.egg
-
-# gitnexus stuff
-/.gitnexus/
-/.claude/
-AGENTS.md
-CLAUDE.md

AGENTS.md

@@ -1,7 +1,7 @@
 <!-- gitnexus:start -->
 # GitNexus — Code Intelligence
 
-This project is indexed by GitNexus as **NEAT** (2742 symbols, 5450 relationships, 62 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
+This project is indexed by GitNexus as **NEAT** (3389 symbols, 6682 relationships, 71 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
 
 > If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.
 

CLAUDE.md

@@ -1,7 +1,7 @@
 <!-- gitnexus:start -->
 # GitNexus — Code Intelligence
 
-This project is indexed by GitNexus as **NEAT** (2742 symbols, 5450 relationships, 62 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
+This project is indexed by GitNexus as **NEAT** (3389 symbols, 6682 relationships, 71 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
 
 > If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.
 

neat/read_simulator/utils/vcf_func.py

@@ -244,8 +244,11 @@ def parse_input_vcf(
                         )
                     elif len(ref) > len(alt) and ref.startswith(alt):
                         # type = deletion
+                        # length is the full reference span (number of bases the deletion
+                        # covers, including the shared anchor base), matching how deletions
+                        # are reconstructed on output and generated by the mutation model.
                         temp_variant = Deletion(
-                            location, len(alt), temp_genotype, record[5], is_input=True, kwargs=data
+                            location, len(ref), temp_genotype, record[5], is_input=True, kwargs=data
                         )
                     elif len(alt) > len(ref) and alt.startswith(ref):
                         # type = insertion

tests/test_read_simulator/test_vcf_func.py

@@ -167,6 +167,10 @@ def test_parse_deletion(tmp_path, ref_fasta, empty_input_dict, opts):
     variants = empty_input_dict["chr1"].contig_variants.get(4, [])
     assert len(variants) == 1
     assert isinstance(variants[0], Deletion)
+    # length is the full reference span (len(ref)), not len(alt). For ACGT -> A
+    # that is 4, so the deletion is reconstructed as ACGT -> A on output rather
+    # than being truncated to a single base. Regression test for issue #305.
+    assert variants[0].length == 4
 
 
 def test_parse_insertion(tmp_path, ref_fasta, empty_input_dict, opts):