refactoring bwa options

bwapy/libbwaaln.pyx

@@ -28,9 +28,8 @@ cdef class BwaAlnOptions:
 
     def __init__(self):
         self._max_hits = 3
-        self._cinit()
 
-    cdef _cinit(self):
+    def __cinit__(self):
         self._delegate = gap_init_opt()
 
     def __dealloc__(self):

bwapy/libbwaindex.pxd

@@ -45,7 +45,7 @@ cdef class BwaIndex:
     """Contains the index and nucleotide sequence for Bwa"""
     cdef bwaidx_t *_delegate
     cdef public object header
-    cdef _cinit(self, prefix, mode)
     cdef bwt_t *bwt(self)
     cdef bntseq_t *bns(self)
-    cdef uint8_t *pac(self)
+    cdef uint8_t *pac(self)
+    cdef _load_index(self, prefix, mode)

bwapy/libbwaindex.pyx

@@ -48,18 +48,17 @@ cdef class BwaIndex:
                  random base)
         """
         cdef int mode
+
         mode = 0
         if bwt:
             mode |= BWA_IDX_BWT
         if bns:
             mode |= BWA_IDX_BNS
         if pac:
             mode |= BWA_IDX_PAC
-        self._cinit(f"{prefix}", mode)
-
-    cdef _cinit(self, prefix, mode):
-        cdef char *local_prefix
+        self._load_index(f"{prefix}", mode)
 
+    cdef _load_index(self, prefix, mode):
         prefix = bwa_idx_infer_prefix(force_bytes(prefix))
         if not prefix:
             # FIXME: better error message

bwapy/libbwamem.pyi

@@ -1,7 +1,6 @@
 import enum
 from pathlib import Path
 from typing import List
-from typing import Self
 
 from pysam import AlignedSegment
 from pysam import FastxRecord
@@ -18,9 +17,8 @@ class BwaMemMode(enum.Enum):
     INTRACTG = enum.auto()
 
 class BwaMemOptions:
-    _ignore_alt: bool
     def __init__(self, finalize: bool = False) -> None: ...
-    def finalize(self) -> Self: ...
+    _ignore_alt: bool
     min_seed_len: int
     mode: BwaMemMode
     band_width: int
@@ -52,6 +50,10 @@ class BwaMemOptions:
     gap_extension_penalty: int | tuple[int, int]
     clipping_penalty: int | tuple[int, int]
 
+class BwaMemOptionsBuilder(BwaMemOptions):
+    def __init__(self, options: BwaMemOptions | None = None) -> None: ...
+    def build(self) -> BwaMemOptions: ...
+
 class BwaMem:
     _index: BwaIndex
     def __init__(self, prefix: str | Path | None = None, index: BwaIndex | None = None) -> None: ...