black

bin/mapped_2hic_dnase.py

@@ -362,7 +362,6 @@ if __name__ == "__main__":
 
             if cur_handler is not None:
                 if not r1.is_unmapped and not r2.is_unmapped:
-
                     ##reorient reads to ease duplicates removal
                     or1, or2 = get_ordered_reads(r1, r2)
                     or1_chrom = samfile.get_reference_name(or1.reference_id)

bin/mapped_2hic_fragments.py

@@ -619,7 +619,6 @@ if __name__ == "__main__":
                 r2_chrom = None
 
             if r1_resfrag is not None or r2_resfrag is not None:
-
                 interactionType = get_interaction_type(r1, r1_chrom, r1_resfrag, r2, r2_chrom, r2_resfrag, verbose)
                 dist = get_PE_fragment_size(r1, r2, r1_resfrag, r2_resfrag, interactionType)
                 cdist = get_cis_dist(r1, r2)

bin/mergeSAM.py

@@ -71,7 +71,6 @@ def get_read_name(read):
 
 
 def sam_flag(read1, read2, hr1, hr2):
-
     f1 = read1.flag
     f2 = read2.flag