| # 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 | |