fix getting read length issue for single index

mskcc · Mar 29, 2024 · d3e6ad0 · d3e6ad0
1 parent 26484bf
commit d3e6ad0
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Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/demux_run_dag.py b/demux_run_dag.py
@@ -171,6 +171,7 @@ def stats(ds, **kwargs):
 
         # check if the run is 10X by read length
         atac, use_bases_mask = scripts.get_sequencing_read_data.main(sequencer_path)
+        print("read length: {}".format(use_bases_mask))
         if use_bases_mask == [29, 89] or atac:
             # if is atac run, demux is using cellranger mkfastq
             if atac:

diff --git a/scripts/get_sequencing_read_data.py b/scripts/get_sequencing_read_data.py
@@ -36,7 +36,7 @@ def get_sequencing_read_data(sequencer_path):
 		use_bases_mask = "Y" + str(reads_tag[0][1]) + ",I" + str(reads_tag[1][1]) + ",Y" + str(reads_tag[2][1]) + ",Y" + str(reads_tag[3][1])
 	else:
 		atac = False
-		use_bases_mask = [reads_tag[0][1], reads_tag[3][1]]
+		use_bases_mask = [reads_tag[0][1], reads_tag[-1][1]]
 
 	return(atac, use_bases_mask)