view CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libctabixproxies.pxd @ 69:33d812a61356

planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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# cython: language_level=3

from libc.stdint cimport uint8_t, int32_t, uint32_t, int64_t, uint64_t

cdef class TupleProxy:

    cdef:
        char * data
        char ** fields
        int nfields
        int nbytes
        int offset
        bint is_modified

    cdef encoding

    cpdef int getMaxFields(self)
    cpdef int getMinFields(self)
#    cdef char * _getindex(self, int idx)

    cdef take(self, char * buffer, size_t nbytes)
    cdef present(self, char * buffer, size_t nbytes)
    cdef copy(self, char * buffer, size_t nbytes, bint reset=*)
    cdef update(self, char * buffer, size_t nbytes)


cdef class TupleProxyIterator:
    cdef TupleProxy proxy
    cdef int index


cdef class NamedTupleProxy(TupleProxy):
    pass


cdef class GTFProxy(NamedTupleProxy):
    cdef object attribute_dict
    cpdef int getMaxFields(self)
    cpdef int getMinFields(self)


cdef class GFF3Proxy(GTFProxy):
    pass


cdef class BedProxy(NamedTupleProxy):

    cdef:
        char * contig
        uint32_t start
        uint32_t end
        int bedfields

    cpdef int getMaxFields(self)
    cpdef int getMinFields(self)
    cdef update(self, char * buffer, size_t nbytes)

cdef class VCFProxy(NamedTupleProxy) :

    cdef:
        char * contig
        uint32_t pos

    cdef update(self, char * buffer, size_t nbytes)