From 8f9f93f3936772301b327c8466f2e3a155e05575 Mon Sep 17 00:00:00 2001
From: Florian <45581601+TheGreatJack@users.noreply.github.com>
Date: Thu, 28 Nov 2024 18:06:52 -0500
Subject: [PATCH 1/2] Update __init__.py softclip handling

Adding softclip and hardclip hadling to output correct reads with these kind of alignments
---
 BioExt/misc/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BioExt/misc/__init__.py b/BioExt/misc/__init__.py
index 00260b8..17cba64 100644
--- a/BioExt/misc/__init__.py
+++ b/BioExt/misc/__init__.py
@@ -345,7 +345,7 @@ def gapless(seq):
     raise ValueError('seq must have type SeqRecord, Seq, or str')
 
 
-_cigar_regexp = re_compile(r'([0-9]+)([M=XID])')
+_cigar_regexp = re_compile(r'([0-9]+)([M=XIDSH])')
 
 
 def gapful(record, insertions=True):

From 7878316794ff18e59001359e98917b7c35ba4384 Mon Sep 17 00:00:00 2001
From: Florian <45581601+TheGreatJack@users.noreply.github.com>
Date: Fri, 29 Nov 2024 23:13:31 -0500
Subject: [PATCH 2/2] Update __init__.py

Hard clipping removed. Hard clipping doesn't include the "clipped" sequence for a bam record. So no need to skip over the query sequence. Adding "H" it in the match would clip things that it shouldn't in hardclipped alignments.
---
 BioExt/misc/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BioExt/misc/__init__.py b/BioExt/misc/__init__.py
index 17cba64..c22c9df 100644
--- a/BioExt/misc/__init__.py
+++ b/BioExt/misc/__init__.py
@@ -345,7 +345,7 @@ def gapless(seq):
     raise ValueError('seq must have type SeqRecord, Seq, or str')
 
 
-_cigar_regexp = re_compile(r'([0-9]+)([M=XIDSH])')
+_cigar_regexp = re_compile(r'([0-9]+)([M=XIDS])')
 
 
 def gapful(record, insertions=True):