Improve fastq file type guessing Fixes #284

lib/util.py

@@ -112,12 +112,13 @@ def fasta_file_is_empty(fasta_path):
 def is_fastq_file(args, file_name):
     """Check if this a FASTQ file."""
     if args.get('fasta'):
-        is_fastq = False
-    elif args.get('fastq'):
-        is_fastq = True
-    else:
-        is_fastq = file_name.lower().endswith('q')
-    return is_fastq
+        return False
+    if args.get('fastq'):
+        return True
+
+    parts = file_name.lower().split('.')
+    index = -2 if re.search(r'[zp2]$', parts[-1]) and len(parts) > 2 else -1
+    return parts[index].startswith('f') and parts[index].endswith('q')
 
 
 def shard_file_size(args, file_name):