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python/obitools3/parsers/universal.pyx

@@ -1,7 +1,10 @@
+#cython: language_level=3
+
 import re 
 from obitools3.parsers.fasta import fastaNucIterator
 from obitools3.parsers.fastq import fastqIterator
 
+
 oligore = re.compile("^[ACGTRYSWKMBDHVN]+$",re.I)
 tagre   = re.compile("^([ACGTRYSWKMBDHVN]+|-)(:([ACGTRYSWKMBDHVN]+)|-)?$",re.I)
 
@@ -21,14 +24,14 @@ def entryIteratorFactory(lineiterator,
                   only=None,
                   bytes seqtype=b'nuc',
                   int qualityoffset=32,
-                  bool noquality=False,
+                  bint noquality=False,
-                  bool skiperror=True,
+                  bint skiperror=True,
-                  bool header=False,
+                  bint header=False,
                   bytes sep=None,
                   bytes dec=b'.',
                   bytes nastring=b"NA",
-                  bool stripwhite=True,
+                  bint stripwhite=True,
-                  bool blanklineskip=True,
+                  bint blanklineskip=True,
                   bytes commentchar=b"#",
                   int buffersize=100000000):
 
@@ -70,7 +73,7 @@ def entryIteratorFactory(lineiterator,
                     Nuc_Seq)
         else:
             raise NotImplementedError()
-    elif format=b'fastq':
+    elif format==b'fastq':
             return (fastqIterator(lineiterator,
                                  skip,only,
                                  qualityoffset,