From b9b61256bdb14ba8f1bba38de358796b721939bd Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Tue, 20 Feb 2018 10:55:01 +0100
Subject: [PATCH] Optimize no_match function
---
src/dgenies/lib/paf.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/src/dgenies/lib/paf.py b/src/dgenies/lib/paf.py
index 7eb4e7f..c8ca29b 100644
--- a/src/dgenies/lib/paf.py
+++ b/src/dgenies/lib/paf.py
@@ -542,6 +542,7 @@ class Paf:
"""
index = self.idx_q if to == "query" else self.idx_t
name, contigs_list, contigs, reversed, abs_start, c_len = Index.load(index)
+ contigs_list = set(contigs_list)
with open(self.paf, "r") as paf:
for line in paf:
c_name = line.strip("\n").split("\t")[0 if to == "query" else 5]
--
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