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- # cython: language_level=3
- ###############################################################################
- ###############################################################################
- ## Cython wrapper for htslib VCF/BCF reader/writer
- ###############################################################################
- #
- # The MIT License
- #
- # Copyright (c) 2015, 2016 Kevin Jacobs (jacobs@bioinformed.com)
- #
- # Permission is hereby granted, free of charge, to any person obtaining a
- # copy of this software and associated documentation files (the "Software"),
- # to deal in the Software without restriction, including without limitation
- # the rights to use, copy, modify, merge, publish, distribute, sublicense,
- # and/or sell copies of the Software, and to permit persons to whom the
- # Software is furnished to do so, subject to the following conditions:
- #
- # The above copyright notice and this permission notice shall be included in
- # all copies or substantial portions of the Software.
- #
- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
- # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- #
- ###############################################################################
-
- from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
- from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
- from libc.stdlib cimport malloc, calloc, realloc, free
- from libc.string cimport memcpy, memcmp, memmove, strncpy, strlen, strdup
-
- from pysam.libchtslib cimport *
-
-
- cdef class VariantHeader(object):
- cdef bcf_hdr_t *ptr
-
- cdef _add_sample(self, name)
- cdef _hdr_sync(self)
- cdef _subset_samples(self, include_samples)
-
-
- cdef class VariantHeaderRecord(object):
- cdef readonly VariantHeader header
- cdef bcf_hrec_t *ptr
-
-
- cdef class VariantHeaderRecords(object):
- cdef readonly VariantHeader header
-
-
- cdef class VariantHeaderContigs(object):
- cdef readonly VariantHeader header
-
-
- cdef class VariantHeaderSamples(object):
- cdef readonly VariantHeader header
-
-
- cdef class VariantContig(object):
- cdef readonly VariantHeader header
- cdef int id
-
-
- cdef class VariantMetadata(object):
- cdef readonly VariantHeader header
- cdef int type
- cdef int id
-
-
- cdef class VariantHeaderMetadata(object):
- cdef readonly VariantHeader header
- cdef int32_t type
-
-
- cdef class VariantRecord(object):
- cdef readonly VariantHeader header
- cdef bcf1_t *ptr
-
-
- cdef class VariantRecordFilter(object):
- cdef VariantRecord record
-
-
- cdef class VariantRecordFormat(object):
- cdef VariantRecord record
-
-
- cdef class VariantRecordInfo(object):
- cdef VariantRecord record
-
-
- cdef class VariantRecordSamples(object):
- cdef VariantRecord record
-
-
- cdef class VariantRecordSample(object):
- cdef VariantRecord record
- cdef readonly int32_t index
-
-
- cdef class BaseIndex(object):
- cdef tuple refs
- cdef dict refmap
-
-
- cdef class BCFIndex(BaseIndex):
- cdef readonly VariantHeader header
- cdef hts_idx_t *ptr
-
-
- cdef class TabixIndex(BaseIndex):
- cdef tbx_t *ptr
-
-
- cdef class BaseIterator(object):
- cdef VariantFile bcf
- cdef hts_itr_t *iter
-
-
- cdef class BCFIterator(BaseIterator):
- cdef BCFIndex index
-
-
- cdef class TabixIterator(BaseIterator):
- cdef TabixIndex index
- cdef kstring_t line_buffer
-
-
- cdef class VariantFile(HTSFile):
- cdef readonly VariantHeader header
- cdef readonly BaseIndex index
-
- cdef readonly bint drop_samples # true if sample information is to be ignored
-
- # FIXME: Temporary, use htsFormat when it is available
- cdef readonly bint is_reading # true if file has begun reading records
- cdef readonly bint header_written # true if header has already been written
-
- cpdef int write(self, VariantRecord record) except -1
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