careful output storage based on compression

closes #29
merenlab · Jul 29, 2021 · cd87a73 · cd87a73
1 parent a6fcb58
commit cd87a73
Showing 1 changed file with 10 additions and 4 deletions.
diff --git a/IlluminaUtils/lib/fastqlib.py b/IlluminaUtils/lib/fastqlib.py
@@ -188,10 +188,16 @@ def __init__(self, file_path, compressed = False):
         super(FastQOutput, self).__init__(file_path, compressed)
 
     def store_entry(self, e):
-        self.file_pointer.write('@' + e.header_line + '\n')
-        self.file_pointer.write(e.sequence + '\n')
-        self.file_pointer.write('+' + e.optional + '\n')
-        self.file_pointer.write(e.qual_scores + '\n')
+        if self.compressed_output:
+            self.file_pointer.write(('@' + e.header_line + '\n').encode())
+            self.file_pointer.write((e.sequence + '\n').encode())
+            self.file_pointer.write(('+' + e.optional + '\n').encode())
+            self.file_pointer.write((e.qual_scores + '\n').encode())
+        else:
+            self.file_pointer.write('@' + e.header_line + '\n')
+            self.file_pointer.write(e.sequence + '\n')
+            self.file_pointer.write('+' + e.optional + '\n')
+            self.file_pointer.write(e.qual_scores + '\n')
 
 
 class FastQSource: