diff --git a/python/obitools3/dms/obiseq.pyx b/python/obitools3/dms/obiseq.pyx index beed690..655f100 100644 --- a/python/obitools3/dms/obiseq.pyx +++ b/python/obitools3/dms/obiseq.pyx @@ -26,6 +26,7 @@ SEQUENCE_COLUMN = b"SEQ" SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN] +QUALITY_ASCII_BASE = 33 cdef class Seq(dict) : @@ -127,7 +128,7 @@ cdef class Seq(dict) : 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 bytes k_b cdef int q @@ -183,7 +184,7 @@ cdef class Nuc_Seq(Seq) : else: 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 if type(new_quality) == list: quality_int = new_quality @@ -290,7 +291,7 @@ cdef class Nuc_Seq_Stored(Seq_Stored) : # if column_name_b in SPECIAL_COLUMNS: # 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 bytes k_b cdef int q @@ -336,7 +337,7 @@ cdef class Nuc_Seq_Stored(Seq_Stored) : Column.new_column(self._view, QUALITY_COLUMN, OBI_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: 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)