From 8083caea3324d1f42d45bae7c050b1fc2db819ba Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshtm.ac.uk>
Date: Wed, 12 Jul 2023 18:35:28 +0100
Subject: [PATCH] updates and bug fixes

---
 ntm_profiler/utils.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/ntm_profiler/utils.py b/ntm_profiler/utils.py
index 701da26..12ba4e1 100644
--- a/ntm_profiler/utils.py
+++ b/ntm_profiler/utils.py
@@ -49,7 +49,9 @@ def get_mash_hit(args):
         pp.run_cmd(f"mash dist -m 2 {args.species_conf['mash_db']} {reads} | sort -gk3 | head > {args.files_prefix}.mash_dist.txt")
     elif args.fasta:
         pp.run_cmd(f"mash dist {args.species_conf['mash_db']} {args.fasta} | sort -gk3 | head > {args.files_prefix}.mash_dist.txt")
-
+    elif args.bam:
+        pp.run_cmd(f"samtools fastq {args.bam} | mash dist -m 2 {args.species_conf['mash_db']} - | sort -gk3 | head > {args.files_prefix}.mash_dist.txt")
+        
     result =  {
         "prediction_method":"mash",
         "prediction":[],