remove gz argument in assign_read

shimlab · Jul 1, 2024 · 543184f · 543184f
1 parent 6565e56
commit 543184f
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/blaze/read_assignment.py b/blaze/read_assignment.py
@@ -247,7 +247,7 @@ def _assign_read_batches(r_batch, whitelist, max_ed, gz, minQ=0):
     # logger.info(helper.green_msg(f"Successfully demultiplexed reads / Total reads: {sum(df.BC_corrected!='')} / {len(df.BC_corrected)}. ", printit = False))
 
 def assign_read(fastq_fns=None, fastq_out=None, putative_bc_csv=None, 
-                    whitelsit_csv=None, max_ed=None, n_process=None, gz=None,
+                    whitelsit_csv=None, max_ed=None, n_process=None,
                     batchsize=None, minQ=0, args=None):
     """Main function: Demultiplex fastq files using putative barcode csv and whitelist csv
         Input:
@@ -269,9 +269,10 @@ def assign_read(fastq_fns=None, fastq_out=None, putative_bc_csv=None,
         whitelsit_csv = args.out_whitelist_fn
         max_ed = args.max_edit_distance
         n_process = args.threads
-        gz = args.output_fastq.endswith('.gz')
         batchsize = args.batch_size
 
+    gz = fastq_out.endswith('.gz')
+
     # greating generator for read and putative barcode batches
     r_batches = \
         _read_and_bc_batch_generator_with_idx(fastq_fns, putative_bc_csv, batchsize)