From eca3bac1e67c7177b9c8dfe23d709f3ca094e2a5 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 1 Feb 2021 18:40:40 +0100
Subject: [PATCH] revert min_mapq
---
CHANGELOG.md | 1 -
bin/mergeSAM.py | 2 +-
2 files changed, 1 insertion(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2b11e76..27746ee 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## v1.3.0dev
-* Change min_mapq behavior by removing pairs only when the two mates have a mapq<min_mapq
* Add HiCExplorer distance decay quality control
* Add HiCExplorer TADs calling
* Add insulation score TADs calling
diff --git a/bin/mergeSAM.py b/bin/mergeSAM.py
index b40fd23..a907fd7 100755
--- a/bin/mergeSAM.py
+++ b/bin/mergeSAM.py
@@ -234,7 +234,7 @@ if __name__ == "__main__":
## both mapped
elif r1.is_unmapped == False and r2.is_unmapped == False:
## quality
- if mapq != None and (r1.mapping_quality < int(mapq) and r2.mapping_quality < int(mapq)):
+ if mapq != None and (r1.mapping_quality < int(mapq) or r2.mapping_quality < int(mapq)):
lowq_pairs_counter += 1
continue
--
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