--- a/trips_bam_to_sqlite/bam_to_sqlite.py	Sun Apr 17 08:44:20 2022 +0000
+++ b/trips_bam_to_sqlite/bam_to_sqlite.py	Wed Apr 20 15:18:00 2022 +0000
@@ -228,8 +228,8 @@
     return (pos_modifier, readlen_modifier, mismatches)
 
 
-def process_bam(bam_filepath, transcriptome_info_dict_path, outputfile):
-    desc = "NULL"
+def process_bam(bam_filepath, transcriptome_info_dict_path, outputfile, desc):
+    desc = desc
     start_time = time.time()
     study_dict = {}
     nuc_count_dict = {"mapped": {}, "unmapped": {}}
@@ -289,6 +289,7 @@
     master_metagene_stop_dict = {"fiveprime": {}, "threeprime": {}}
 
     os.system(f'samtools sort -n {bam_filepath} -o {bam_filepath}_n_sorted.bam')
+    pysam.set_verbosity(0)
     infile = pysam.Samfile(f"{bam_filepath}_n_sorted.bam", "rb")
     header = infile.header["HD"]
     unsorted = False
@@ -721,9 +722,10 @@
         sys.exit()
     bam_filepath = sys.argv[1]
     annotation_sqlite_filepath = sys.argv[2]
-    # try:
-    # 	desc = sys.argv[3]
-    # except:
-    # 	desc = bam_filepath.split("/")[-1]
-    outputfile = bam_filepath + "v2.sqlite"
-    process_bam(bam_filepath, annotation_sqlite_filepath, outputfile)
+    try:
+        desc = sys.argv[3]
+    except:
+        desc = bam_filepath.split("/")[-1]
+
+    outputfile = sys.argv[4]
+    process_bam(bam_filepath, annotation_sqlite_filepath, outputfile, desc)