small bug fix and add note about streaming k-mers through instead of …

…reads through. #15

CMash/Query.py

@@ -288,6 +288,9 @@ def intersect(self):
 		if self.verbose:
 			print("dumping intersection to FASTA file")
 		if self.verbose:
+			# replacing out_path with in_path would mean we stream all the read k-mers through, instead of all the reads through
+			# this may speed things up in real-world applications, and it returns (basically) the same results
+			# so might be worth considering...
 			res = subprocess.run(f"{self.kmc_dump} -ci0 {out_path} {dump_path}", shell=True)
 		else:
 			res = subprocess.run(f"{self.kmc_dump} -ci0 {out_path} {dump_path}", shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)

scripts/StreamingQueryDNADatabase.py

@@ -192,7 +192,7 @@ def map_func(sequence):
 		intersecter.compute_intersection()
 		#print("intersection located at: {}".format(intersecter.out_file))
 		# change query file to the intersection file
-		query_file = intersecter.out_file
+		query_file = intersecter.final_out_file
 	# Open the file to prepare for processing
 	fid = khmer.ReadParser(query_file)  # This is faster than screed
 	match_tuples = []