From c4d45900d0a03f1bcdd37f43433a748781d22760 Mon Sep 17 00:00:00 2001
From: "A. Murat Eren (Meren)" <a.murat.eren@gmail.com>
Date: Mon, 4 Dec 2023 16:28:35 +0100
Subject: [PATCH] pysam import can take a long time.

only do it when necessary?
---
 anvio/filesnpaths.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/anvio/filesnpaths.py b/anvio/filesnpaths.py
index a9d7939cbc..2940d7a372 100644
--- a/anvio/filesnpaths.py
+++ b/anvio/filesnpaths.py
@@ -5,7 +5,6 @@
 import os
 import json
 import time
-import pysam
 import shutil
 import tarfile
 import tempfile
@@ -305,8 +304,10 @@ def is_file_bam_file(file_path, dont_raise=False, ok_if_not_indexed=False):
 
     is_file_exists(file_path)
 
+    from pysam import AlignmentFile
+
     try:
-        bam_file = pysam.AlignmentFile(file_path, "rb")
+        bam_file = AlignmentFile(file_path, "rb")
     except Exception as e:
         if dont_raise:
             return False