From 08aaf77e6af471b85a467ee6fe2a90b6fd72b374 Mon Sep 17 00:00:00 2001
From: "nloyfer@gmail.com" <nloyfer@gmail.com>
Date: Mon, 15 Jul 2024 11:30:09 +0300
Subject: [PATCH] fixed strip bug

---
 src/pat2beta/mask_pat.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/pat2beta/mask_pat.cpp b/src/pat2beta/mask_pat.cpp
index 054b885..f7fce00 100644
--- a/src/pat2beta/mask_pat.cpp
+++ b/src/pat2beta/mask_pat.cpp
@@ -95,8 +95,10 @@ int proc_line(std::vector<std::string> tokens, std::set<int> &sites_to_hide) {
     }
     tokens[2] = pattern;
     // strip pat and ignore this read if it's all dots
-    if (strip_pat(tokens[2]) < 0) { return 0; }
+    int pos = strip_pat(tokens[2]);
+    if (pos < 0) { return 0; }
 
+    tokens[1] = std::to_string(pos + std::stoi(tokens[1]));
     output_vec(tokens);
     return 0;
 }