Cython: fasta and fastq parsers now return bytes and take NA string

argument

python/obitools3/format/fastq.pyx

@@ -5,28 +5,25 @@ from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN
 from obitools3.utils cimport bytes2str, str2bytes, tobytes
 
 
-# TODO quality offset option
+# TODO quality offset option?
 cdef class FastqFormat:
 	
-	def __init__(self, list tags=[], bint printNAKeys=False):
+	def __init__(self, list tags=[], bint printNAKeys=False, bytes NAString=b"NA"):
 		self.headerFormatter = HeaderFormat("fastq",
-										    tags,
-										    printNAKeys)
+										    tags=tags,
+										    printNAKeys=printNAKeys,
+										    NAString=NAString)
 		
 	@cython.boundscheck(False)	
 	def __call__(self, object data):
 		
-		cdef bytes quality
+		cdef bytes quality	
 		
-		if hasattr(data, "quality_str"):
-			quality = str2bytes(data.quality_str)    # TODO quality_bytes property
+		if hasattr(data, "quality_bytes"):
+			quality = data.quality_bytes
 		elif hasattr(data, "quality"):
 			quality = tobytes(data.quality)
 		else:
 			raise AttributeError("No quality when exporting to fastq")  # TODO discuss
 		
-		return bytes2str(self.headerFormatter(data) + 
-						b"\n" + 
-						data[NUC_SEQUENCE_COLUMN] +
-						b"\n+\n" + 
-						quality)   
+		return self.headerFormatter(data) + b"\n" + data[NUC_SEQUENCE_COLUMN] + b"\n+\n" + quality