From 4e75514bade8a0bfb37f09f3e4373579be71b57a Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Thu, 29 Aug 2019 18:26:09 +0200
Subject: [PATCH] obi import: fixed entry count

---
 python/obitools3/utils.pyx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/python/obitools3/utils.pyx b/python/obitools3/utils.pyx
index 45fafdb..28ef89a 100755
--- a/python/obitools3/utils.pyx
+++ b/python/obitools3/utils.pyx
@@ -72,6 +72,8 @@ cpdef int count_entries(file, bytes format):
                 return -1
             mmapped_file = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)
             total_count += len(re.findall(sep, mmapped_file))
+            if format != b"ngsfilter" and format != b"tabular":
+                total_count += 1 # adding +1 for 1st entry because separators include \n (ngsfilter and tabular already count one more because of last \n)
             
     except:
         if len(files) > 1: