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Cython API: better handling of default quality offset value

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Celine Mercier
2018-05-17 15:01:25 +02:00
parent b91b3176b0
commit ffebc6acfb
1 changed files with 5 additions and 4 deletions
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9
python/obitools3/dms/obiseq.pyx
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@ -26,6 +26,7 @@ SEQUENCE_COLUMN = b"SEQ"
SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN] SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
QUALITY_ASCII_BASE = 33
cdef class Seq(dict) : cdef class Seq(dict) :
@ -127,7 +128,7 @@ cdef class Seq(dict) :
cdef class Nuc_Seq(Seq) : cdef class Nuc_Seq(Seq) :
def __init__(self, object id, object seq, object definition=None, object quality=None, int offset=-1, object tags=None) : def __init__(self, object id, object seq, object definition=None, object quality=None, int offset=QUALITY_ASCII_BASE, object tags=None) :
cdef object k cdef object k
cdef bytes k_b cdef bytes k_b
cdef int q cdef int q
@ -183,7 +184,7 @@ cdef class Nuc_Seq(Seq) :
else: else:
return None return None
cpdef set_quality(self, object new_quality, int offset=-1): cpdef set_quality(self, object new_quality, int offset=QUALITY_ASCII_BASE):
cdef list quality_int cdef list quality_int
if type(new_quality) == list: if type(new_quality) == list:
quality_int = new_quality quality_int = new_quality
@ -290,7 +291,7 @@ cdef class Nuc_Seq_Stored(Seq_Stored) :
# if column_name_b in SPECIAL_COLUMNS: # if column_name_b in SPECIAL_COLUMNS:
# self[column_name_b] = tags[column_name] # self[column_name_b] = tags[column_name]
cpdef set(self, object id, object seq, object definition=None, object quality=None, int offset=-1, object tags=None): cpdef set(self, object id, object seq, object definition=None, object quality=None, int offset=QUALITY_ASCII_BASE, object tags=None):
cdef object k cdef object k
cdef bytes k_b cdef bytes k_b
cdef int q cdef int q
@ -336,7 +337,7 @@ cdef class Nuc_Seq_Stored(Seq_Stored) :
Column.new_column(self._view, QUALITY_COLUMN, OBI_QUAL) Column.new_column(self._view, QUALITY_COLUMN, OBI_QUAL)
self._view.get_column(QUALITY_COLUMN).set_line(self.index, new_qual) self._view.get_column(QUALITY_COLUMN).set_line(self.index, new_qual)
cpdef set_quality_char(self, object new_qual, int offset=-1): cpdef set_quality_char(self, object new_qual, int offset=QUALITY_ASCII_BASE):
if QUALITY_COLUMN not in self: if QUALITY_COLUMN not in self:
Column.new_column(self._view, QUALITY_COLUMN, OBI_QUAL) Column.new_column(self._view, QUALITY_COLUMN, OBI_QUAL)
self._view.get_column(QUALITY_COLUMN).set_str_line(self.index, tobytes(new_qual), offset=offset) self._view.get_column(QUALITY_COLUMN).set_str_line(self.index, tobytes(new_qual), offset=offset)