From 75eb684569b9718bd837eb13d873adbf04b6e11a Mon Sep 17 00:00:00 2001
From: cmaceves <christineaceves22@gmail.com>
Date: Tue, 24 Jan 2023 15:54:42 -0800
Subject: [PATCH] revert to the original way isize_flag is calculated

---
 src/trim_primer_quality.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/trim_primer_quality.cpp b/src/trim_primer_quality.cpp
index 339c694e..df13fbd3 100755
--- a/src/trim_primer_quality.cpp
+++ b/src/trim_primer_quality.cpp
@@ -584,7 +584,6 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,
     //isize is insert size
     //l_qseq is the query length 
     isize_flag = (abs(aln->core.isize) - max_primer_len) > abs(aln->core.l_qseq);
-    isize_flag = (abs(aln->core.isize) - max_primer_len) > 0;
     // if reverse strand
     if((aln->core.flag&BAM_FPAIRED) != 0 && isize_flag){ // If paired
     get_overlapping_primers(aln, primers, overlapping_primers);