From b591b12c22539948782704446989893bde826a29 Mon Sep 17 00:00:00 2001
From: rvaser <robert.vaser@gmail.com>
Date: Fri, 2 Jul 2021 07:52:14 -0400
Subject: [PATCH] Fix overlap parsing bug

---
 src/polisher.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/polisher.cpp b/src/polisher.cpp
index fb2bfcf..46c4d02 100644
--- a/src/polisher.cpp
+++ b/src/polisher.cpp
@@ -311,7 +311,6 @@ void Polisher::initialize() {
     oparser_->Reset();
     uint64_t c = 0;
     while (true) {
-        uint64_t l = overlaps.size();
         auto overlaps_chunk = oparser_->Parse(kChunkSize);
         if (overlaps_chunk.empty()) {
           break;
@@ -321,6 +320,7 @@ void Polisher::initialize() {
             std::make_move_iterator(overlaps_chunk.begin()),
             std::make_move_iterator(overlaps_chunk.end()));
 
+        uint64_t l = c;
         for (uint64_t i = l; i < overlaps.size(); ++i) {
             overlaps[i]->transmute(sequences_, name_to_id, id_to_id);