From b97877cb9f869e2861e0515327c4f663b9df322d Mon Sep 17 00:00:00 2001
From: hiruna534 <hiruna@unsw.edu.au>
Date: Fri, 27 Dec 2024 14:47:28 +1100
Subject: [PATCH] use pi aux tag too to filter split reads

---
 src/reform.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/reform.py b/src/reform.py
index a9f18db..7841b8f 100644
--- a/src/reform.py
+++ b/src/reform.py
@@ -85,7 +85,7 @@ def run(args):
     with pysam.AlignmentFile(args.bam, "rb", check_sq=False) as bam:
         for sam_record in bam:
             len_seq = len(sam_record.get_forward_sequence()) - kmer_length + 1 # to get the number of kmers
-            if sam_record.has_tag("sp"):
+            if sam_record.has_tag("sp") or sam_record.has_tag("pi"):
                 count_split_reads += 1
                 continue
             if sam_record.has_tag("dx") and int(sam_record.get_tag("dx")) == 1: