From 12dce7887a62338852f87c5b163346c0d20a7994 Mon Sep 17 00:00:00 2001
From: Jacob Morrison <Jacob.Morrison@vai.org>
Date: Thu, 2 May 2024 13:31:55 -0400
Subject: [PATCH] fix snp beg/end flank for longer reads

---
 src/epiread.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/epiread.c b/src/epiread.c
index 3c4302b..e675be0 100644
--- a/src/epiread.c
+++ b/src/epiread.c
@@ -544,8 +544,8 @@ static void *process_func(void *data) {
         rec.tid = w.tid;
         char *chrm = header->target_name[w.tid];
 
-        uint32_t snp_beg = w.beg>1000 ? w.beg-1000 : 1; // start location of snps
-        uint32_t snp_end = w.end+1000;
+        uint32_t snp_beg = w.beg > flank ? w.beg-flank : 1; // start location of snps
+        uint32_t snp_end = w.end+flank;
 
         // Make snp lookup table (if supplied)
         uint8_t *snps = NULL;