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1 # cython: language_level=3
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2 #########################################################################
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3 # Utility functions used across pysam
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4 #########################################################################
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5 cimport cython
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6 from cpython cimport array as c_array
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7
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8 cpdef parse_region(contig=*, start=*, stop=*, region=*, reference=*, end=*)
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9
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10 cdef int libc_whence_from_io(int whence)
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11
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12 #########################################################################
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13 # Utility functions for quality string conversions
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14
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15 cpdef c_array.array qualitystring_to_array(input_str, int offset=*)
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16 cpdef array_to_qualitystring(c_array.array arr, int offset=*)
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17 cpdef qualities_to_qualitystring(qualities, int offset=*)
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18
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19 ########################################################################
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20 ## String encoding configuration facilities
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21 ########################################################################
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22
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23 cpdef get_encoding_error_handler()
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24 cpdef set_encoding_error_handler(name)
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25
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26 ########################################################################
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27 ## Python 3 compatibility functions
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28 ########################################################################
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29 cdef charptr_to_str(const char *s, encoding=*, errors=*)
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30 cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*)
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31 cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
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32 cdef force_str(object s, encoding=*, errors=*)
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33 cdef bytes force_bytes(object s, encoding=*, errors=*)
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34 cdef decode_bytes(bytes s, encoding=*, errors=*)
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35 cdef bytes encode_filename(object filename)
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36 cdef from_string_and_size(const char *s, size_t length)
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37
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