From 0732d1fe81d48761d25ba8f1082fa96ffc59d427 Mon Sep 17 00:00:00 2001
From: Akshay Avvaru <avvaruakshay@gmail.com>
Date: Thu, 16 Apr 2026 13:14:02 -0600
Subject: [PATCH] not skip internal repeats

---
 data/STRchive-loci.json | 2 +-
 scripts/make-catalog.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json
index 908f69e2..6732e8e5 100644
--- a/data/STRchive-loci.json
+++ b/data/STRchive-loci.json
@@ -1354,7 +1354,7 @@
   "locus_structure": [
   {
     "motif": "AAAAT",
-    "count": 7,
+    "count": 15,
     "type": "internal_repeat"
   },
   {
diff --git a/scripts/make-catalog.py b/scripts/make-catalog.py
index a07077bc..e0b1ce60 100644
--- a/scripts/make-catalog.py
+++ b/scripts/make-catalog.py
@@ -313,7 +313,7 @@ def atarva_catalog(row, genome = 'hg38'):
                 bed_string += f"{row['chrom']}\t{start}\t{stop}\t{motif}\t{motif_len}\t{this_id}\n"
             elif struct_dict['type'] == 'interruption' or struct_dict['type'] == 'internal_repeat':
                 # interruptions and internal repeats are not included in the structure
-                continue
+                bed_string += f"{row['chrom']}\t{start}\t{stop}\t{motif}\t{motif_len}\t{this_id}\n"
             else:
                 # this is a flank repeat
                 bed_string += f"{row['chrom']}\t{start}\t{stop}\t{motif}\t{motif_len}\t{this_id}_flank\n"