Merge pull request #30 from jodyphelan/dev

updates and bug fixes
jodyphelan · Jul 12, 2023 · d65a0ba · d65a0ba
2 parents 6d913de + 8083cae
commit d65a0ba
Showing 1 changed file with 3 additions and 1 deletion.
diff --git 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":[],