From 91784a334bd5d96258e930ed6f750b0ad39fc988 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 22 May 2023 18:04:00 +0100
Subject: [PATCH] black
---
bin/mapped_2hic_dnase.py | 1 -
bin/mapped_2hic_fragments.py | 1 -
bin/mergeSAM.py | 1 -
3 files changed, 3 deletions(-)
diff --git a/bin/mapped_2hic_dnase.py b/bin/mapped_2hic_dnase.py
index ff59366..c417907 100755
--- a/bin/mapped_2hic_dnase.py
+++ b/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)
diff --git a/bin/mapped_2hic_fragments.py b/bin/mapped_2hic_fragments.py
index cc0e40b..a129871 100755
--- a/bin/mapped_2hic_fragments.py
+++ b/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)
diff --git a/bin/mergeSAM.py b/bin/mergeSAM.py
index 82ab8c3..d670ec2 100755
--- a/bin/mergeSAM.py
+++ b/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
--
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