From 572430dd7b19be1c0d2d9e7a1aee0d4b0665c576 Mon Sep 17 00:00:00 2001
From: Andrew Lonsdale <andrew.lonsdale@petermac.org>
Date: Sun, 14 Aug 2022 21:32:11 +1000
Subject: [PATCH] Fix mismatchsize paramter being ignored

---
 src/pseudoaligner.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pseudoaligner.rs b/src/pseudoaligner.rs
index 6e2f0f8..3eb7f63 100644
--- a/src/pseudoaligner.rs
+++ b/src/pseudoaligner.rs
@@ -517,7 +517,7 @@ pub fn match_read<K: Kmer + Sync + Send>(optional: Option<(Vec<u32>, usize, usiz
 
 	match optional {
         	Some((eq_class,coverage,mismatches,readlen)) => {
-                                    if coverage >= seq.len() && mismatches == 0 &&  eq_class.len() == 1 {
+                                    if coverage >= seq.len() && mismatches <= mismatchsize &&  eq_class.len() == 1 {
                                     //if coverage >= READ_COVERAGE_THRESHOLD && eq_class.len() == 1 {
                                         debug!("{:?}",&seq);
                                       if trim { // trim check