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1 # cython: language_level=3
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2 from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
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3 from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
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4 from libc.stdlib cimport malloc, calloc, realloc, free
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5 from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup
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6 from libc.stdio cimport FILE, printf
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7 cimport cython
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8
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9 from cpython cimport array
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10 from pysam.libchtslib cimport faidx_t, kstring_t, BGZF
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11
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12 # These functions are put here and not in chtslib.pxd in order
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13 # to avoid warnings for unused functions.
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14 cdef extern from "pysam_stream.h" nogil:
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15
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16 ctypedef struct kstream_t:
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17 pass
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18
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19 ctypedef struct kseq_t:
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20 kstring_t name
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21 kstring_t comment
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22 kstring_t seq
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23 kstring_t qual
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24
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25 kseq_t *kseq_init(BGZF *)
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26 int kseq_read(kseq_t *)
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27 void kseq_destroy(kseq_t *)
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28 kstream_t *ks_init(BGZF *)
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29 void ks_destroy(kstream_t *)
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30
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31 # Retrieve characters from stream until delimiter
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32 # is reached placing results in str.
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33 int ks_getuntil(kstream_t *,
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34 int delimiter,
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35 kstring_t * str,
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36 int * dret)
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37
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38 cdef class FastaFile:
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39 cdef bint is_remote
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40 cdef object _filename, _references, _lengths, reference2length
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41 cdef faidx_t* fastafile
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42 cdef char* _fetch(self, char* reference,
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43 int start, int end, int* length) except? NULL
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44
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45
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46 cdef class FastqProxy:
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47 cdef kseq_t * _delegate
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48 cdef cython.str to_string(self)
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49 cdef cython.str tostring(self)
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50 cpdef array.array get_quality_array(self, int offset=*)
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51
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52
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53 cdef class FastxRecord:
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54 """
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55 Python container for pysam.libcfaidx.FastqProxy with persistence.
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56 """
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57 cdef public str comment, quality, sequence, name
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58 cdef cython.str to_string(self)
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59 cdef cython.str tostring(self)
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60 cpdef array.array get_quality_array(self, int offset=*)
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61
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62 cdef class FastxFile:
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63 cdef object _filename
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64 cdef BGZF * fastqfile
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65 cdef kseq_t * entry
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66 cdef bint persist
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67 cdef bint is_remote
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68
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69 cdef kseq_t * getCurrent(self)
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70 cdef int cnext(self)
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71
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72
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73 # Compatibility Layer for pysam 0.8.1
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74 cdef class FastqFile(FastxFile):
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75 pass
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76
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77
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78 # Compatibility Layer for pysam < 0.8
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79 cdef class Fastafile(FastaFile):
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80 pass
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81
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