jpayne@68: # cython: language_level=3
jpayne@68: ###############################################################################
jpayne@68: ###############################################################################
jpayne@68: ## Cython wrapper for htslib VCF/BCF reader/writer
jpayne@68: ###############################################################################
jpayne@68: #
jpayne@68: # The MIT License
jpayne@68: #
jpayne@68: # Copyright (c) 2015, 2016 Kevin Jacobs (jacobs@bioinformed.com)
jpayne@68: #
jpayne@68: # Permission is hereby granted, free of charge, to any person obtaining a
jpayne@68: # copy of this software and associated documentation files (the "Software"),
jpayne@68: # to deal in the Software without restriction, including without limitation
jpayne@68: # the rights to use, copy, modify, merge, publish, distribute, sublicense,
jpayne@68: # and/or sell copies of the Software, and to permit persons to whom the
jpayne@68: # Software is furnished to do so, subject to the following conditions:
jpayne@68: #
jpayne@68: # The above copyright notice and this permission notice shall be included in
jpayne@68: # all copies or substantial portions of the Software.
jpayne@68: #
jpayne@68: # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
jpayne@68: # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
jpayne@68: # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL
jpayne@68: # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
jpayne@68: # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
jpayne@68: # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
jpayne@68: # DEALINGS IN THE SOFTWARE.
jpayne@68: #
jpayne@68: ###############################################################################
jpayne@68: 
jpayne@68: from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
jpayne@68: from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
jpayne@68: from libc.stdlib cimport malloc, calloc, realloc, free
jpayne@68: from libc.string cimport memcpy, memcmp, memmove, strncpy, strlen, strdup
jpayne@68: 
jpayne@68: from pysam.libchtslib cimport *
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantHeader(object):
jpayne@68:     cdef bcf_hdr_t *ptr
jpayne@68: 
jpayne@68:     cdef _add_sample(self, name)
jpayne@68:     cdef _hdr_sync(self)
jpayne@68:     cdef _subset_samples(self, include_samples)
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantHeaderRecord(object):
jpayne@68:     cdef readonly VariantHeader header
jpayne@68:     cdef bcf_hrec_t *ptr
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantHeaderRecords(object):
jpayne@68:     cdef readonly VariantHeader header
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantHeaderContigs(object):
jpayne@68:     cdef readonly VariantHeader header
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantHeaderSamples(object):
jpayne@68:     cdef readonly VariantHeader header
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantContig(object):
jpayne@68:     cdef readonly VariantHeader header
jpayne@68:     cdef int id
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantMetadata(object):
jpayne@68:     cdef readonly VariantHeader header
jpayne@68:     cdef int type
jpayne@68:     cdef int id
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantHeaderMetadata(object):
jpayne@68:     cdef readonly VariantHeader header
jpayne@68:     cdef int32_t type
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantRecord(object):
jpayne@68:     cdef readonly VariantHeader header
jpayne@68:     cdef bcf1_t *ptr
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantRecordFilter(object):
jpayne@68:     cdef VariantRecord record
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantRecordFormat(object):
jpayne@68:     cdef VariantRecord record
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantRecordInfo(object):
jpayne@68:     cdef VariantRecord record
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantRecordSamples(object):
jpayne@68:     cdef VariantRecord record
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantRecordSample(object):
jpayne@68:     cdef VariantRecord record
jpayne@68:     cdef readonly int32_t index
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class BaseIndex(object):
jpayne@68:     cdef tuple refs
jpayne@68:     cdef dict refmap
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class BCFIndex(BaseIndex):
jpayne@68:     cdef readonly VariantHeader header
jpayne@68:     cdef hts_idx_t *ptr
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class TabixIndex(BaseIndex):
jpayne@68:     cdef tbx_t *ptr
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class BaseIterator(object):
jpayne@68:     cdef VariantFile bcf
jpayne@68:     cdef hts_itr_t  *iter
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class BCFIterator(BaseIterator):
jpayne@68:     cdef BCFIndex index
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class TabixIterator(BaseIterator):
jpayne@68:     cdef TabixIndex index
jpayne@68:     cdef kstring_t line_buffer
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class VariantFile(HTSFile):
jpayne@68:     cdef readonly VariantHeader  header
jpayne@68:     cdef readonly BaseIndex      index
jpayne@68: 
jpayne@68:     cdef readonly bint           drop_samples  # true if sample information is to be ignored
jpayne@68: 
jpayne@68:     # FIXME: Temporary, use htsFormat when it is available
jpayne@68:     cdef readonly bint       is_reading     # true if file has begun reading records
jpayne@68:     cdef readonly bint       header_written # true if header has already been written
jpayne@68: 
jpayne@68:     cpdef int write(self, VariantRecord record) except -1