# HG changeset patch
# User jackcurragh
# Date 1667400737 0
# Node ID 3d2b1532a1b0e3423c73265a1a244d9051e9e9c4
# Parent  78afd30c0cbf53e71585effff78848e991ce3538
Uploaded

diff -r 78afd30c0cbf -r 3d2b1532a1b0 trips_bam_to_sqlite/bam_to_sqlite.py
--- a/trips_bam_to_sqlite/bam_to_sqlite.py	Tue Oct 25 08:19:05 2022 +0000
+++ b/trips_bam_to_sqlite/bam_to_sqlite.py	Wed Nov 02 14:52:17 2022 +0000
@@ -250,13 +250,18 @@
 	master_offset_dict = {"fiveprime":{}, "threeprime":{}}
 	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(bam_filepath, "rb")
+	infile = pysam.Samfile(f"{bam_filepath}_n_sorted.bam", "rb")
+	header = infile.header["HD"]
 
-	header = infile.header["HD"]
 	unsorted = False
 	if "SO" in header:
+		print("Sorting order: "+header["SO"])
 		if header["SO"] != "queryname":
+			print("Sorting order is not queryname")
 			unsorted = True
 	else:
 		unsorted = True
@@ -575,9 +580,6 @@
 		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"
+	desc = sys.argv[3]
+	outputfile = sys.argv[4]
 	process_bam(bam_filepath,annotation_sqlite_filepath,outputfile)