revert min_mapq

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

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