Do not write out blank seq

PennChopMicrobiomeProgram · Apr 27, 2021 · 44d0352 · 44d0352
1 parent 0093a0f
commit 44d0352
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/primertrim/command.py b/primertrim/command.py
@@ -94,7 +94,8 @@ def main(argv=None):
                 trimmable_reads.register_match(read_id, matchobj)
 
     for desc, seq, qual in trimmable_reads.get_trimmed_reads():
-        args.output_fastq.write("@{0}\n{1}\n+\n{2}\n".format(desc, seq, qual))
+        if seq != "":
+            args.output_fastq.write("@{0}\n{1}\n+\n{2}\n".format(desc, seq, qual))
 
     if args.log:
         for read_id, matchobj in trimmable_reads.matches.items():