csp2: CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libchtslib.pxd comparison

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libchtslib.pxd @ 69:33d812a61356

planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d

author	jpayne
date	Tue, 18 Mar 2025 17:55:14 -0400
parents
children

comparison

equal deleted inserted replaced

-:0e9998148a16
+:33d812a61356
+# cython: language_level=3
+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, strncpy, strlen, strdup
+from libc.stdio cimport FILE, printf
+from posix.types cimport off_t
+cdef extern from "Python.h":
+FILE* PyFile_AsFile(object)
+# cython does not wrap stdarg
+cdef extern from "stdarg.h":
+ctypedef struct va_list:
+pass
+cdef extern from "htslib/kstring.h" nogil:
+ctypedef struct kstring_t:
+size_t l, m
+char *s
+int kputc(int c, kstring_t *s)
+int kputw(int c, kstring_t *s)
+int kputl(long c, kstring_t *s)
+int ksprintf(kstring_t *s, const char *fmt, ...)
+cdef extern from "htslib_util.h" nogil:
+int hts_set_verbosity(int verbosity)
+int hts_get_verbosity()
+ctypedef uint32_t khint32_t
+ctypedef uint32_t khint_t
+ctypedef khint_t  khiter_t
+# Used to manage BCF Header info
+ctypedef struct vdict_t:
+khint_t n_buckets, size, n_occupied, upper_bound
+khint32_t *flags
+const char *keys
+bcf_idinfo_t *vals
+# Used to manage indexed contigs in Tabix
+ctypedef struct s2i_t:
+khint_t n_buckets, size, n_occupied, upper_bound
+khint32_t *flags
+const char *keys
+int64_t *vals
+# Generic khash methods
+khint_t kh_size(void *d)
+khint_t kh_begin(void *d)
+khint_t kh_end(void *d)
+int kh_exist(void *d, khiter_t i)
+# Specialized khash methods for vdict
+khint_t kh_get_vdict(vdict_t *d, const char *key)
+const char *kh_key_vdict "kh_key" (vdict_t *d, khint_t i)
+bcf_idinfo_t kh_val_vdict "kh_val" (vdict_t *d, khint_t i)
+cdef extern from "htslib/hfile.h" nogil:
+ctypedef struct hFILE
+# @abstract  Open the named file or URL as a stream
+# @return    An hFILE pointer, or NULL (with errno set) if an error occurred.
+hFILE *hopen(const char *filename, const char *mode, ...)
+# @abstract  Associate a stream with an existing open file descriptor
+# @return    An hFILE pointer, or NULL (with errno set) if an error occurred.
+# @notes     For socket descriptors (on Windows), mode should contain 's'.
+hFILE *hdopen(int fd, const char *mode)
+# @abstract  Report whether the file name or URL denotes remote storage
+# @return    0 if local, 1 if remote.
+# @notes     "Remote" means involving e.g. explicit network access, with the
+#   implication that callers may wish to cache such files' contents locally.
+int hisremote(const char *filename)
+# @abstract  Flush (for output streams) and close the stream
+# @return    0 if successful, or EOF (with errno set) if an error occurred.
+int hclose(hFILE *fp)
+# @abstract  Close the stream, without flushing or propagating errors
+# @notes     For use while cleaning up after an error only.  Preserves errno.
+void hclose_abruptly(hFILE *fp)
+# @abstract  Return the stream's error indicator
+# @return    Non-zero (in fact, an errno value) if an error has occurred.
+# @notes     This would be called herror() and return true/false to parallel
+#   ferror(3), but a networking-related herror(3) function already exists.  */
+int herrno(hFILE *fp)
+# @abstract  Clear the stream's error indicator
+void hclearerr(hFILE *fp)
+# @abstract  Reposition the read/write stream offset
+# @return    The resulting offset within the stream (as per lseek(2)),
+#   or negative if an error occurred.
+off_t hseek(hFILE *fp, off_t offset, int whence)
+# @abstract  Report the current stream offset
+# @return    The offset within the stream, starting from zero.
+off_t htell(hFILE *fp)
+# @abstract  Read one character from the stream
+# @return    The character read, or EOF on end-of-file or error
+int hgetc(hFILE *fp)
+# Read from the stream until the delimiter, up to a maximum length
+#    @param buffer  The buffer into which bytes will be written
+#    @param size    The size of the buffer
+#    @param delim   The delimiter (interpreted as an `unsigned char`)
+#    @param fp      The file stream
+#    @return  The number of bytes read, or negative on error.
+#    @since   1.4
+#
+# Bytes will be read into the buffer up to and including a delimiter, until
+# EOF is reached, or _size-1_ bytes have been written, whichever comes first.
+# The string will then be terminated with a NUL byte (`\0`).
+ssize_t hgetdelim(char *buffer, size_t size, int delim, hFILE *fp)
+# Read a line from the stream, up to a maximum length
+#    @param buffer  The buffer into which bytes will be written
+#    @param size    The size of the buffer
+#    @param fp      The file stream
+#    @return  The number of bytes read, or negative on error.
+#    @since   1.4
+#
+# Specialization of hgetdelim() for a `\n` delimiter.
+ssize_t hgetln(char *buffer, size_t size, hFILE *fp)
+# Read a line from the stream, up to a maximum length
+#    @param buffer  The buffer into which bytes will be written
+#    @param size    The size of the buffer (must be > 1 to be useful)
+#    @param fp      The file stream
+#    @return  _buffer_ on success, or `NULL` if an error occurred.
+#    @since   1.4
+#
+# This function can be used as a replacement for `fgets(3)`, or together with
+# kstring's `kgetline()` to read arbitrarily-long lines into a _kstring_t_.
+char *hgets(char *buffer, int size, hFILE *fp)
+# @abstract  Peek at characters to be read without removing them from buffers
+# @param fp      The file stream
+# @param buffer  The buffer to which the peeked bytes will be written
+# @param nbytes  The number of bytes to peek at; limited by the size of the
+#   internal buffer, which could be as small as 4K.
+# @return    The number of bytes peeked, which may be less than nbytes if EOF
+#   is encountered; or negative, if there was an I/O error.
+# @notes  The characters peeked at remain in the stream's internal buffer,
+#   and will be returned by later hread() etc calls.
+ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes)
+# @abstract  Read a block of characters from the file
+# @return    The number of bytes read, or negative if an error occurred.
+# @notes     The full nbytes requested will be returned, except as limited
+#   by EOF or I/O errors.
+ssize_t hread(hFILE *fp, void *buffer, size_t nbytes)
+# @abstract  Write a character to the stream
+# @return    The character written, or EOF if an error occurred.
+int hputc(int c, hFILE *fp)
+# @abstract  Write a string to the stream
+# @return    0 if successful, or EOF if an error occurred.
+int hputs(const char *text, hFILE *fp)
+# @abstract  Write a block of characters to the file
+# @return    Either nbytes, or negative if an error occurred.
+# @notes     In the absence of I/O errors, the full nbytes will be written.
+ssize_t hwrite(hFILE *fp, const void *buffer, size_t nbytes)
+# @abstract  For writing streams, flush buffered output to the underlying stream
+# @return    0 if successful, or EOF if an error occurred.
+int hflush(hFILE *fp)
+cdef extern from "htslib/bgzf.h" nogil:
+ctypedef struct bgzf_mtaux_t
+ctypedef struct bgzidx_t
+ctypedef struct z_stream
+ctypedef struct BGZF:
+unsigned           errcode
+unsigned           is_write
+int           is_be
+int           compress_level
+int           is_compressed
+int           is_gzip
+int           cache_size
+int64_t       block_address
+int64_t       uncompressed_address
+void         *uncompressed_block
+void         *compressed_block
+void         *cache
+hFILE        *fp
+bgzf_mtaux_t *mt
+bgzidx_t     *idx
+int           idx_build_otf
+z_stream     *gz_stream
+#*****************
+#  Basic routines *
+# *****************/
+#  Open an existing file descriptor for reading or writing.
+#
+#  @param fd    file descriptor
+#  @param mode  mode matching /[rwag][u0-9]+/: 'r' for reading, 'w' for
+#               writing, 'a' for appending, 'g' for gzip rather than BGZF
+#               compression (with 'w' only), and digit specifies the zlib
+#               compression level.
+#               Note that there is a distinction between 'u' and '0': the
+#               first yields plain uncompressed output whereas the latter
+#               outputs uncompressed data wrapped in the zlib format.
+#  @return      BGZF file handler; 0 on error
+BGZF* bgzf_dopen(int fd, const char *mode)
+BGZF* bgzf_fdopen(int fd, const char *mode) # for backward compatibility
+#  Open the specified file for reading or writing.
+BGZF* bgzf_open(const char* path, const char *mode)
+#  Open an existing hFILE stream for reading or writing.
+BGZF* bgzf_hopen(hFILE *fp, const char *mode)
+#  Close the BGZF and free all associated resources.
+#
+#  @param fp    BGZF file handler
+#  @return      0 on success and -1 on error
+int bgzf_close(BGZF *fp)
+#  Read up to _length_ bytes from the file storing into _data_.
+#
+#  @param fp     BGZF file handler
+#  @param data   data array to read into
+#  @param length size of data to read
+#  @return       number of bytes actually read; 0 on end-of-file and -1 on error
+ssize_t bgzf_read(BGZF *fp, void *data, size_t length)
+#  Write _length_ bytes from _data_ to the file.  If no I/O errors occur,
+#  the complete _length_ bytes will be written (or queued for writing).
+#
+#  @param fp     BGZF file handler
+#  @param data   data array to write
+#  @param length size of data to write
+#  @return       number of bytes written (i.e., _length_); negative on error
+ssize_t bgzf_write(BGZF *fp, const void *data, size_t length)
+#  Read up to _length_ bytes directly from the underlying stream without
+#  decompressing.  Bypasses BGZF blocking, so must be used with care in
+#  specialised circumstances only.
+#
+#  @param fp     BGZF file handler
+#  @param data   data array to read into
+#  @param length number of raw bytes to read
+#  @return       number of bytes actually read; 0 on end-of-file and -1 on error
+ssize_t bgzf_raw_read(BGZF *fp, void *data, size_t length)
+#  Write _length_ bytes directly to the underlying stream without
+#  compressing.  Bypasses BGZF blocking, so must be used with care
+#  in specialised circumstances only.
+#
+#  @param fp     BGZF file handler
+#  @param data   data array to write
+#  @param length number of raw bytes to write
+#  @return       number of bytes actually written; -1 on error
+ssize_t bgzf_raw_write(BGZF *fp, const void *data, size_t length)
+#  Write the data in the buffer to the file.
+int bgzf_flush(BGZF *fp)
+#  Return a virtual file pointer to the current location in the file.
+#  No interpretation of the value should be made, other than a subsequent
+#  call to bgzf_seek can be used to position the file at the same point.
+#  Return value is non-negative on success.
+int64_t bgzf_tell(BGZF *fp)
+#  Set the file to read from the location specified by _pos_.
+#
+#  @param fp     BGZF file handler
+#  @param pos    virtual file offset returned by bgzf_tell()
+#  @param whence must be SEEK_SET (cimported from libc.stdio / posix.unistd)
+#  @return       0 on success and -1 on error
+# /
+int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence)
+#  Check if the BGZF end-of-file (EOF) marker is present
+#
+#  @param fp    BGZF file handler opened for reading
+#  @return      1 if the EOF marker is present and correct
+#               2 if it can't be checked, e.g., because fp isn't seekable
+#               0 if the EOF marker is absent
+#               -1 (with errno set) on error
+int bgzf_check_EOF(BGZF *fp)
+#  Check if a file is in the BGZF format
+#
+#  @param fn    file name
+#  @return      1 if _fn_ is BGZF; 0 if not or on I/O error
+int bgzf_is_bgzf(const char *fn)
+#*********************
+#  Advanced routines *
+#*********************
+#  Set the cache size. Only effective when compiled with -DBGZF_CACHE.
+#
+#  @param fp    BGZF file handler
+#  @param size  size of cache in bytes; 0 to disable caching (default)
+void bgzf_set_cache_size(BGZF *fp, int size)
+#  Flush the file if the remaining buffer size is smaller than _size_
+#  @return      0 if flushing succeeded or was not needed; negative on error
+int bgzf_flush_try(BGZF *fp, ssize_t size)
+#  Read one byte from a BGZF file. It is faster than bgzf_read()
+#  @param fp     BGZF file handler
+#  @return       byte read; -1 on end-of-file or error
+int bgzf_getc(BGZF *fp)
+#  Read one line from a BGZF file. It is faster than bgzf_getc()
+#
+#  @param fp     BGZF file handler
+#  @param delim  delimiter
+#  @param str    string to write to; must be initialized
+#  @return       length of the string; 0 on end-of-file; negative on error
+int bgzf_getline(BGZF *fp, int delim, kstring_t *str)
+#  Read the next BGZF block.
+int bgzf_read_block(BGZF *fp)
+#  Enable multi-threading (only effective on writing and when the
+#  library was compiled with -DBGZF_MT)
+#
+#  @param fp          BGZF file handler; must be opened for writing
+#  @param n_threads   #threads used for writing
+#  @param n_sub_blks  #blocks processed by each thread; a value 64-256 is recommended
+int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks)
+# Compress a single BGZF block.
+#
+# @param dst    output buffer (must have size >= BGZF_MAX_BLOCK_SIZE)
+# @param dlen   size of output buffer; updated on return to the number
+#               of bytes actually written to dst
+# @param src    buffer to be compressed
+# @param slen   size of data to compress (must be <= BGZF_BLOCK_SIZE)
+# @param level  compression level
+# @return       0 on success and negative on error
+#
+int bgzf_compress(void *dst, size_t *dlen, const void *src, size_t slen, int level)
+#*******************
+#  bgzidx routines *
+#   BGZF at the uncompressed offset
+#
+#   @param fp           BGZF file handler; must be opened for reading
+#   @param uoffset      file offset in the uncompressed data
+#   @param where        SEEK_SET (cimported from libc.stdio) supported atm
+#
+#   Returns 0 on success and -1 on error.
+int bgzf_useek(BGZF *fp, long uoffset, int where)
+#   Position in uncompressed BGZF
+#
+#   @param fp           BGZF file handler; must be opened for reading
+#
+#   Returns the current offset on success and -1 on error.
+long bgzf_utell(BGZF *fp)
+#  Tell BGZF to build index while compressing.
+#
+#  @param fp          BGZF file handler; can be opened for reading or writing.
+#
+#  Returns 0 on success and -1 on error.
+int bgzf_index_build_init(BGZF *fp)
+#  Load BGZF index
+#
+#  @param fp          BGZF file handler
+#  @param bname       base name
+#  @param suffix      suffix to add to bname (can be NULL)
+#
+#  Returns 0 on success and -1 on error.
+int bgzf_index_load(BGZF *fp, const char *bname, const char *suffix)
+#  Save BGZF index
+#
+#  @param fp          BGZF file handler
+#  @param bname       base name
+#  @param suffix      suffix to add to bname (can be NULL)
+#
+#  Returns 0 on success and -1 on error.
+int bgzf_index_dump(BGZF *fp, const char *bname, const char *suffix)
+cdef extern from "htslib/hts.h" nogil:
+uint32_t kroundup32(uint32_t x)
+ctypedef struct cram_fd
+union FilePointerUnion:
+BGZF    *bgzf
+cram_fd *cram
+hFILE   *hfile
+void    *voidp
+enum htsFormatCategory:
+unknown_category
+sequence_data    # Sequence data -- SAM, BAM, CRAM, etc
+variant_data     # Variant calling data -- VCF, BCF, etc
+index_file       # Index file associated with some data file
+region_list      # Coordinate intervals or regions -- BED, etc
+category_maximum
+enum htsExactFormat:
+unknown_format
+binary_format
+text_format
+sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed
+format_maximum
+enum htsCompression:
+no_compression, gzip, bgzf, custom
+compression_maximum
+cdef enum hts_fmt_option:
+CRAM_OPT_DECODE_MD,
+CRAM_OPT_PREFIX,
+CRAM_OPT_VERBOSITY,
+CRAM_OPT_SEQS_PER_SLICE,
+CRAM_OPT_SLICES_PER_CONTAINER,
+CRAM_OPT_RANGE,
+CRAM_OPT_VERSION,
+CRAM_OPT_EMBED_REF,
+CRAM_OPT_IGNORE_MD5,
+CRAM_OPT_REFERENCE,
+CRAM_OPT_MULTI_SEQ_PER_SLICE,
+CRAM_OPT_NO_REF,
+CRAM_OPT_USE_BZIP2,
+CRAM_OPT_SHARED_REF,
+CRAM_OPT_NTHREADS,
+CRAM_OPT_THREAD_POOL,
+CRAM_OPT_USE_LZMA,
+CRAM_OPT_USE_RANS,
+CRAM_OPT_REQUIRED_FIELDS,
+HTS_OPT_COMPRESSION_LEVEL,
+HTS_OPT_NTHREADS,
+ctypedef struct htsVersion:
+short major, minor
+ctypedef struct htsFormat:
+htsFormatCategory category
+htsExactFormat    format
+htsVersion        version
+htsCompression    compression
+short             compression_level
+void              *specific
+ctypedef struct htsFile:
+uint8_t  is_bin
+uint8_t  is_write
+uint8_t  is_be
+uint8_t  is_cram
+int64_t lineno
+kstring_t line
+char *fn
+char *fn_aux
+FilePointerUnion fp
+htsFormat format
+int hts_verbose
+cdef union hts_opt_val_union:
+int i
+char *s
+ctypedef struct hts_opt:
+char *arg
+hts_fmt_option opt
+hts_opt_val_union val
+void *next
+# @abstract Parses arg and appends it to the option list.
+# @return   0 on success and -1 on failure
+int hts_opt_add(hts_opt **opts, const char *c_arg)
+# @abstract Applies an hts_opt option list to a given htsFile.
+# @return   0 on success and -1 on failure
+int hts_opt_apply(htsFile *fp, hts_opt *opts)
+# @abstract Frees an hts_opt list.
+void hts_opt_free(hts_opt *opts)
+# @abstract Table for converting a nucleotide character to 4-bit encoding.
+# The input character may be either an IUPAC ambiguity code, '=' for 0, or
+# '0'/'1'/'2'/'3' for a result of 1/2/4/8.  The result is encoded as 1/2/4/8
+# for A/C/G/T or combinations of these bits for ambiguous bases.
+const unsigned char *seq_nt16_table
+# @abstract Table for converting a 4-bit encoded nucleotide to an IUPAC
+# ambiguity code letter (or '=' when given 0).
+const char *seq_nt16_str
+# @abstract Table for converting a 4-bit encoded nucleotide to about 2 bits.
+# Returns 0/1/2/3 for 1/2/4/8 (i.e., A/C/G/T), or 4 otherwise (0 or ambiguous).
+const int *seq_nt16_int
+# @abstract  Get the htslib version number
+# @return    For released versions, a string like "N.N[.N]"; or git describe
+# output if using a library built within a Git repository.
+const char *hts_version()
+# @abstract    Determine format by peeking at the start of a file
+# @param fp    File opened for reading, positioned at the beginning
+# @param fmt   Format structure that will be filled out on return
+# @return      0 for success, or negative if an error occurred.
+int hts_detect_format(hFILE *fp, htsFormat *fmt)
+# @abstract    Get a human-readable description of the file format
+# @return      Description string, to be freed by the caller after use.
+char *hts_format_description(const htsFormat *format)
+# @abstract       Open a SAM/BAM/CRAM/VCF/BCF/etc file
+# @param fn       The file name or "-" for stdin/stdout
+# @param mode     Mode matching / [rwa][bceguxz0-9]* /
+# @discussion
+#     With 'r' opens for reading; any further format mode letters are ignored
+#     as the format is detected by checking the first few bytes or BGZF blocks
+#     of the file.  With 'w' or 'a' opens for writing or appending, with format
+#     specifier letters:
+#       b  binary format (BAM, BCF, etc) rather than text (SAM, VCF, etc)
+#       c  CRAM format
+#       g  gzip compressed
+#       u  uncompressed
+#       z  bgzf compressed
+#       [0-9]  zlib compression level
+#     and with non-format option letters (for any of 'r'/'w'/'a'):
+#       e  close the file on exec(2) (opens with O_CLOEXEC, where supported)
+#       x  create the file exclusively (opens with O_EXCL, where supported)
+#     Note that there is a distinction between 'u' and '0': the first yields
+#     plain uncompressed output whereas the latter outputs uncompressed data
+#     wrapped in the zlib format.
+# @example
+#     [rw]b  .. compressed BCF, BAM, FAI
+#     [rw]bu .. uncompressed BCF
+#     [rw]z  .. compressed VCF
+#     [rw]   .. uncompressed VCF
+htsFile *hts_open(const char *fn, const char *mode)
+# @abstract       Open a SAM/BAM/CRAM/VCF/BCF/etc file
+# @param fn       The file name or "-" for stdin/stdout
+# @param mode     Open mode, as per hts_open()
+# @param fmt      Optional format specific parameters
+# @discussion
+#     See hts_open() for description of fn and mode.
+#     // TODO Update documentation for s/opts/fmt/
+#     Opts contains a format string (sam, bam, cram, vcf, bcf) which will,
+#     if defined, override mode.  Opts also contains a linked list of hts_opt
+#     structures to apply to the open file handle.  These can contain things
+#     like pointers to the reference or information on compression levels,
+#     block sizes, etc.
+htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt)
+# @abstract       Open an existing stream as a SAM/BAM/CRAM/VCF/BCF/etc file
+# @param fp       The already-open file handle
+# @param fn       The file name or "-" for stdin/stdout
+# @param mode     Open mode, as per hts_open()
+htsFile *hts_hopen(hFILE *fp, const char *fn, const char *mode)
+# @abstract  For output streams, flush any buffered data
+# @param fp  The file handle to be flushed
+# @return    0 for success, or negative if an error occurred.
+# @since     1.14
+int hts_flush(htsFile *fp)
+# @abstract  Close a file handle, flushing buffered data for output streams
+# @param fp  The file handle to be closed
+# @return    0 for success, or negative if an error occurred.
+int hts_close(htsFile *fp)
+# @abstract  Returns the file's format information
+# @param fp  The file handle
+# @return    Read-only pointer to the file's htsFormat.
+const htsFormat *hts_get_format(htsFile *fp)
+# @ abstract      Returns a string containing the file format extension.
+# @ param format  Format structure containing the file type.
+# @ return        A string ("sam", "bam", etc) or "?" for unknown formats.
+const char *hts_format_file_extension(const htsFormat *format)
+# @abstract  Sets a specified CRAM option on the open file handle.
+# @param fp  The file handle open the open file.
+# @param opt The CRAM_OPT_* option.
+# @param ... Optional arguments, dependent on the option used.
+# @return    0 for success, or negative if an error occurred.
+int hts_set_opt(htsFile *fp, hts_fmt_option opt, ...)
+int hts_getline(htsFile *fp, int delimiter, kstring_t *str)
+char **hts_readlines(const char *fn, int *_n)
+#   @abstract       Parse comma-separated list or read list from a file
+#   @param list     File name or comma-separated list
+#   @param is_file
+#   @param _n       Size of the output array (number of items read)
+#   @return         NULL on failure or pointer to newly allocated array of
+#                   strings
+char **hts_readlist(const char *fn, int is_file, int *_n)
+# @abstract  Create extra threads to aid compress/decompression for this file
+# @param fp  The file handle
+# @param n   The number of worker threads to create
+# @return    0 for success, or negative if an error occurred.
+# @notes     THIS THREADING API IS LIKELY TO CHANGE IN FUTURE.
+int hts_set_threads(htsFile *fp, int n)
+# @abstract  Set .fai filename for a file opened for reading
+# @return    0 for success, negative on failure
+# @discussion
+#     Called before *_hdr_read(), this provides the name of a .fai file
+#     used to provide a reference list if the htsFile contains no @SQ headers.
+int hts_set_fai_filename(htsFile *fp, const char *fn_aux)
+int8_t HTS_IDX_NOCOOR
+int8_t HTS_IDX_START
+int8_t HTS_IDX_REST
+int8_t HTS_IDX_NONE
+int8_t HTS_FMT_CSI
+int8_t HTS_FMT_BAI
+int8_t HTS_FMT_TBI
+int8_t HTS_FMT_CRAI
+BGZF *hts_get_bgzfp(htsFile *fp)
+ctypedef struct hts_idx_t
+ctypedef struct hts_pair64_t:
+uint64_t u, v
+ctypedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, int *beg, int *end)
+ctypedef struct hts_bins_t:
+int n, m
+int *a
+ctypedef struct hts_itr_t:
+uint32_t read_rest
+uint32_t finished
+int tid, bed, end, n_off, i
+int curr_tid, curr_beg, curr_end
+uint64_t curr_off
+hts_pair64_t *off
+hts_readrec_func *readfunc
+hts_bins_t bins
+hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls)
+void hts_idx_destroy(hts_idx_t *idx)
+int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int is_mapped)
+void hts_idx_finish(hts_idx_t *idx, uint64_t final_offset)
+#### Save an index to a file
+#    @param idx  Index to be written
+#    @param fn   Input BAM/BCF/etc filename, to which .bai/.csi/etc will be added
+#    @param fmt  One of the HTS_FMT_* index formats
+#    @return  0 if successful, or negative if an error occurred.
+int hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt)
+#### Save an index to a specific file
+#    @param idx    Index to be written
+#    @param fn     Input BAM/BCF/etc filename
+#    @param fnidx  Output filename, or NULL to add .bai/.csi/etc to @a fn
+#    @param fmt    One of the HTS_FMT_* index formats
+#    @return  0 if successful, or negative if an error occurred.
+int hts_idx_save_as(const hts_idx_t *idx, const char *fn, const char *fnidx, int fmt)
+#### Load an index file
+#    @param fn   BAM/BCF/etc filename, to which .bai/.csi/etc will be added or
+#                the extension substituted, to search for an existing index file
+#    @param fmt  One of the HTS_FMT_* index formats
+#    @return  The index, or NULL if an error occurred.
+hts_idx_t *hts_idx_load(const char *fn, int fmt)
+#### Load a specific index file
+#    @param fn     Input BAM/BCF/etc filename
+#    @param fnidx  The input index filename
+#    @return  The index, or NULL if an error occurred.
+hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx)
+#### Load a specific index file
+#    @param fn     Input BAM/BCF/etc filename
+#     @param fnidx  The input index filename
+#     @param fmt    One of the HTS_FMT_* index formats
+#     @param flags  Flags to alter behaviour (see description)
+#     @return  The index, or NULL if an error occurred.
+hts_idx_t *hts_idx_load3(const char *fn, const char *fnidx, int fmt, int flags)
+int HTS_IDX_SAVE_REMOTE
+int HTS_IDX_SILENT_FAIL
+uint8_t *hts_idx_get_meta(hts_idx_t *idx, uint32_t *l_meta)
+void hts_idx_set_meta(hts_idx_t *idx, int l_meta, uint8_t *meta, int is_copy)
+int hts_idx_get_stat(const hts_idx_t* idx, int tid,
+uint64_t* mapped, uint64_t* unmapped)
+uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx)
+int HTS_PARSE_THOUSANDS_SEP  # Ignore ',' separators within numbers
+# Parse a numeric string
+#    The number may be expressed in scientific notation, and optionally may
+#    contain commas in the integer part (before any decimal point or E notation).
+#    @param str     String to be parsed
+#    @param strend  If non-NULL, set on return to point to the first character
+#                   in @a str after those forming the parsed number
+#    @param flags   Or'ed-together combination of HTS_PARSE_* flags
+#    @return  Converted value of the parsed number.
+#
+#    When @a strend is NULL, a warning will be printed (if hts_verbose is 2
+#    or more) if there are any trailing characters after the number.
+long long hts_parse_decimal(const char *str, char **strend, int flags)
+# Parse a "CHR:START-END"-style region string
+#    @param str  String to be parsed
+#    @param beg  Set on return to the 0-based start of the region
+#    @param end  Set on return to the 1-based end of the region
+#    @return  Pointer to the colon or '\0' after the reference sequence name,
+#             or NULL if @a str could not be parsed.
+const char *hts_parse_reg(const char *str, int *beg, int *end)
+hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec)
+void hts_itr_destroy(hts_itr_t *iter)
+ctypedef int (*hts_name2id_f)(void*, const char*)
+ctypedef const char *(*hts_id2name_f)(void*, int)
+ctypedef hts_itr_t *hts_itr_query_func(
+const hts_idx_t *idx,
+int tid,
+int beg,
+int end,
+hts_readrec_func *readrec)
+hts_itr_t *hts_itr_querys(
+const hts_idx_t *idx,
+const char *reg,
+hts_name2id_f getid,
+void *hdr,
+hts_itr_query_func *itr_query,
+hts_readrec_func *readrec)
+int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data)
+const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr)  # free only the array, not the values
+# hts_file_type() - Convenience function to determine file type
+# @fname: the file name
+#
+# Returns one of the FT_* defines.
+#
+# DEPRECATED:  This function has been replaced by hts_detect_format().
+# It and these FT_* macros will be removed in a future HTSlib release.
+int FT_UNKN
+int FT_GZ
+int FT_VCF
+int FT_VCF_GZ
+int FT_BCF
+int FT_BCF_GZ
+int FT_STDIN
+int hts_file_type(const char *fname)
+# /***************************
+#  * Revised MAQ error model *
+#  ***************************/
+ctypedef struct errmod_t
+errmod_t *errmod_init(double depcorr)
+void errmod_destroy(errmod_t *em)
+# /*
+#     n: number of bases
+#     m: maximum base
+#     bases[i]: qual:6, strand:1, base:4
+#     q[i*m+j]: phred-scaled likelihood of (i,j)
+#  */
+int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *Probabilistic)
+# /*****************************************
+#  * q banded glocal alignment *
+#  *****************************************/
+ctypedef struct probaln_par_t:
+float d, e
+int bw
+int probaln_glocal(const uint8_t *ref,
+int l_ref,
+const uint8_t *query,
+int l_query, const uint8_t *iqual,
+const probaln_par_t *c,
+int *state, uint8_t *q)
+# /**********************
+#  * MD5 implementation *
+#  **********************/
+ctypedef struct hts_md5_context
+# /*! @abstract   Initialises an MD5 context.
+#  *  @discussion
+#  *    The expected use is to allocate an hts_md5_context using
+#  *    hts_md5_init().  This pointer is then passed into one or more calls
+#  *    of hts_md5_update() to compute successive internal portions of the
+#  *    MD5 sum, which can then be externalised as a full 16-byte MD5sum
+#  *    calculation by calling hts_md5_final().  This can then be turned
+#  *    into ASCII via hts_md5_hex().
+#  *
+#  *    To dealloate any resources created by hts_md5_init() call the
+#  *    hts_md5_destroy() function.
+#  *
+#  *  @return     hts_md5_context pointer on success, NULL otherwise.
+#  */
+hts_md5_context *hts_md5_init()
+# /*! @abstract Updates the context with the MD5 of the data. */
+void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long size)
+# /*! @abstract Computes the final 128-bit MD5 hash from the given context */
+void hts_md5_final(unsigned char *digest, hts_md5_context *ctx)
+# /*! @abstract Resets an md5_context to the initial state, as returned
+#  *            by hts_md5_init().
+#  */
+void hts_md5_reset(hts_md5_context *ctx)
+# /*! @abstract Converts a 128-bit MD5 hash into a 33-byte nul-termninated
+#  *            hex string.
+#  */
+void hts_md5_hex(char *hex, const unsigned char *digest)
+# /*! @abstract Deallocates any memory allocated by hts_md5_init. */
+void hts_md5_destroy(hts_md5_context *ctx)
+int hts_reg2bin(int64_t beg, int64_t end, int min_shift, int n_lvls)
+int hts_bin_bot(int bin, int n_lvls)
+# * Endianness *
+int ed_is_big()
+uint16_t ed_swap_2(uint16_t v)
+void *ed_swap_2p(void *x)
+uint32_t ed_swap_4(uint32_t v)
+void *ed_swap_4p(void *x)
+uint64_t ed_swap_8(uint64_t v)
+void *ed_swap_8p(void *x)
+cdef extern from "htslib/sam.h" nogil:
+#**********************
+#*** SAM/BAM header ***
+#**********************
+# @abstract Structure for the alignment header.
+# @field n_targets   number of reference sequences
+# @field l_text      length of the plain text in the header
+# @field target_len  lengths of the reference sequences
+# @field target_name names of the reference sequences
+# @field text        plain text
+# @field sdict       header dictionary
+ctypedef struct bam_hdr_t:
+int32_t n_targets, ignore_sam_err
+uint32_t l_text
+uint32_t *target_len
+uint8_t *cigar_tab
+char **target_name
+char *text
+void *sdict
+#****************************
+#*** CIGAR related macros ***
+#****************************
+int BAM_CMATCH
+int BAM_CINS
+int BAM_CDEL
+int BAM_CREF_SKIP
+int BAM_CSOFT_CLIP
+int BAM_CHARD_CLIP
+int BAM_CPAD
+int BAM_CEQUAL
+int BAM_CDIFF
+int BAM_CBACK
+char    *BAM_CIGAR_STR
+int      BAM_CIGAR_SHIFT
+uint32_t BAM_CIGAR_MASK
+uint32_t BAM_CIGAR_TYPE
+char bam_cigar_op(uint32_t c)
+uint32_t bam_cigar_oplen(uint32_t c)
+char bam_cigar_opchr(uint32_t)
+uint32_t bam_cigar_gen(char, uint32_t)
+int bam_cigar_type(char o)
+# @abstract the read is paired in sequencing, no matter whether it is mapped in a pair
+int BAM_FPAIRED
+# @abstract the read is mapped in a proper pair
+int BAM_FPROPER_PAIR
+# @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
+int BAM_FUNMAP
+# @abstract the mate is unmapped
+int BAM_FMUNMAP
+# @abstract the read is mapped to the reverse strand
+int BAM_FREVERSE
+# @abstract the mate is mapped to the reverse strand
+int BAM_FMREVERSE
+# @abstract this is read1
+int BAM_FREAD1
+# @abstract this is read2
+int BAM_FREAD2
+# @abstract not primary alignment
+int BAM_FSECONDARY
+# @abstract QC failure
+int BAM_FQCFAIL
+# @abstract optical or PCR duplicate
+int BAM_FDUP
+# @abstract supplementary alignment
+int BAM_FSUPPLEMENTARY
+#*************************
+#*** Alignment records ***
+#*************************
+# @abstract Structure for core alignment information.
+# @field  tid     chromosome ID, defined by bam_hdr_t
+# @field  pos     0-based leftmost coordinate
+# @field  bin     bin calculated by bam_reg2bin()
+# @field  qual    mapping quality
+# @field  l_qname length of the query name
+# @field  flag    bitwise flag
+# @field  n_cigar number of CIGAR operations
+# @field  l_qseq  length of the query sequence (read)
+# @field  mtid    chromosome ID of next read in template, defined by bam_hdr_t
+# @field  mpos    0-based leftmost coordinate of next read in template
+ctypedef struct bam1_core_t:
+int32_t tid
+int32_t pos
+uint16_t bin
+uint8_t qual
+uint8_t l_qname
+uint16_t flag
+uint8_t unused1
+uint8_t l_extranul
+uint32_t n_cigar
+int32_t l_qseq
+int32_t mtid
+int32_t mpos
+int32_t isize
+# @abstract Structure for one alignment.
+# @field  core       core information about the alignment
+# @field  l_data     current length of bam1_t::data
+# @field  m_data     maximum length of bam1_t::data
+# @field  data       all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux
+#
+# @discussion Notes:
+#
+# 1. qname is zero tailing and core.l_qname includes the tailing '\0'.
+# 2. l_qseq is calculated from the total length of an alignment block
+# on reading or from CIGAR.
+# 3. cigar data is encoded 4 bytes per CIGAR operation.
+# 4. seq is nybble-encoded according to seq_nt16_table.
+ctypedef struct bam1_t:
+bam1_core_t core
+int l_data
+uint32_t m_data
+uint8_t *data
+uint64_t id
+# @abstract  Get whether the query is on the reverse strand
+# @param  b  pointer to an alignment
+# @return    boolean true if query is on the reverse strand
+int bam_is_rev(bam1_t *b)
+# @abstract  Get whether the query's mate is on the reverse strand
+# @param  b  pointer to an alignment
+# @return    boolean true if query's mate on the reverse strand
+int bam_is_mrev(bam1_t *b)
+# @abstract  Get the name of the query
+# @param  b  pointer to an alignment
+# @return    pointer to the name string, null terminated
+char *bam_get_qname(bam1_t *b)
+# @abstract  Get the CIGAR array
+# @param  b  pointer to an alignment
+# @return    pointer to the CIGAR array
+#
+# @discussion In the CIGAR array, each element is a 32-bit integer. The
+# lower 4 bits gives a CIGAR operation and the higher 28 bits keep the
+# length of a CIGAR.
+uint32_t *bam_get_cigar(bam1_t *b)
+# @abstract  Get query sequence
+# @param  b  pointer to an alignment
+# @return    pointer to sequence
+#
+# @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G,
+# 8 for T and 15 for N. Two bases are packed in one byte with the base
+# at the higher 4 bits having smaller coordinate on the read. It is
+# recommended to use bam_seqi() macro to get the base.
+char *bam_get_seq(bam1_t *b)
+# @abstract  Get query quality
+# @param  b  pointer to an alignment
+# @return    pointer to quality string
+uint8_t *bam_get_qual(bam1_t *b)
+# @abstract  Get auxiliary data
+# @param  b  pointer to an alignment
+# @return    pointer to the concatenated auxiliary data
+uint8_t *bam_get_aux(bam1_t *b)
+# @abstract  Get length of auxiliary data
+# @param  b  pointer to an alignment
+# @return    length of the concatenated auxiliary data
+int bam_get_l_aux(bam1_t *b)
+# @abstract  Get a base on read
+# @param  s  Query sequence returned by bam1_seq()
+# @param  i  The i-th position, 0-based
+# @return    4-bit integer representing the base.
+char bam_seqi(char *s, int i)
+#**************************
+#*** Exported functions ***
+#**************************
+#***************
+#*** BAM I/O ***
+#***************
+bam_hdr_t *bam_hdr_init()
+bam_hdr_t *bam_hdr_read(BGZF *fp)
+int bam_hdr_write(BGZF *fp, const bam_hdr_t *h)
+void bam_hdr_destroy(bam_hdr_t *h)
+int bam_name2id(bam_hdr_t *h, const char *ref)
+bam_hdr_t* bam_hdr_dup(const bam_hdr_t *h0)
+bam1_t *bam_init1()
+void bam_destroy1(bam1_t *b)
+int bam_read1(BGZF *fp, bam1_t *b)
+int bam_write1(BGZF *fp, const bam1_t *b)
+bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
+bam1_t *bam_dup1(const bam1_t *bsrc)
+int bam_cigar2qlen(int n_cigar, const uint32_t *cigar)
+int bam_cigar2rlen(int n_cigar, const uint32_t *cigar)
+# @abstract Calculate the rightmost base position of an alignment on the
+# reference genome.
+# @param  b  pointer to an alignment
+# @return    the coordinate of the first base after the alignment, 0-based
+# @discussion For a mapped read, this is just b->core.pos + bam_cigar2rlen.
+# For an unmapped read (either according to its flags or if it has no cigar
+# string), we return b->core.pos + 1 by convention.
+int32_t bam_endpos(const bam1_t *b)
+int   bam_str2flag(const char *str)  # returns negative value on error
+char *bam_flag2str(int flag)         # The string must be freed by the user
+#*************************
+#*** BAM/CRAM indexing ***
+#*************************
+# These BAM iterator functions work only on BAM files.  To work with either
+# BAM or CRAM files use the sam_index_load() & sam_itr_*() functions.
+void bam_itr_destroy(hts_itr_t *iter)
+hts_itr_t *bam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end)
+hts_itr_t *bam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region)
+int bam_itr_next(htsFile *htsfp, hts_itr_t *itr, void *r)
+# Load/build .csi or .bai BAM index file.  Does not work with CRAM.
+# It is recommended to use the sam_index_* functions below instead.
+hts_idx_t *bam_index_load(const char *fn)
+int bam_index_build(const char *fn, int min_shift)
+# Load a BAM (.csi or .bai) or CRAM (.crai) index file
+# @param fp  File handle of the data file whose index is being opened
+# @param fn  BAM/CRAM/etc filename to search alongside for the index file
+# @return  The index, or NULL if an error occurred.
+hts_idx_t *sam_index_load(htsFile *fp, const char *fn)
+# Load a specific BAM (.csi or .bai) or CRAM (.crai) index file
+# @param fp     File handle of the data file whose index is being opened
+# @param fn     BAM/CRAM/etc data file filename
+# @param fnidx  Index filename, or NULL to search alongside @a fn
+# @return  The index, or NULL if an error occurred.
+hts_idx_t *sam_index_load2(htsFile *fp, const char *fn, const char *fnidx)
+# Load or stream a BAM (.csi or .bai) or CRAM (.crai) index file
+# @param fp     File handle of the data file whose index is being opened
+# @param fn     BAM/CRAM/etc data file filename
+# @param fnidx  Index filename, or NULL to search alongside @a fn
+# @param flags  Flags to alter behaviour
+# @return  The index, or NULL if an error occurred.
+hts_idx_t *sam_index_load3(htsFile *fp, const char *fn, const char *fnidx, int flags)
+# Generate and save an index file
+# @param fn        Input BAM/etc filename, to which .csi/etc will be added
+# @param min_shift Positive to generate CSI, or 0 to generate BAI
+# @return  0 if successful, or negative if an error occurred (usually -1; or
+#         -2: opening fn failed; -3: format not indexable)
+int sam_index_build(const char *fn, int min_shift)
+# Generate and save an index to a specific file
+# @param fn        Input BAM/CRAM/etc filename
+# @param fnidx     Output filename, or NULL to add .bai/.csi/etc to @a fn
+# @param min_shift Positive to generate CSI, or 0 to generate BAI
+# @return  0 if successful, or negative if an error occurred.
+int sam_index_build2(const char *fn, const char *fnidx, int min_shift)
+void sam_itr_destroy(hts_itr_t *iter)
+hts_itr_t *sam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end)
+hts_itr_t *sam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region)
+int sam_itr_next(htsFile *htsfp, hts_itr_t *itr, void *r)
+#***************
+#*** SAM I/O ***
+#***************
+htsFile *sam_open(const char *fn, const char *mode)
+htsFile *sam_open_format(const char *fn, const char *mode, const htsFormat *fmt)
+int sam_close(htsFile *fp)
+int sam_open_mode(char *mode, const char *fn, const char *format)
+# A version of sam_open_mode that can handle ,key=value options.
+# The format string is allocated and returned, to be freed by the caller.
+# Prefix should be "r" or "w",
+char *sam_open_mode_opts(const char *fn, const char *mode, const char *format)
+bam_hdr_t *sam_hdr_parse(int l_text, const char *text)
+bam_hdr_t *sam_hdr_read(htsFile *fp)
+int sam_hdr_write(htsFile *fp, const bam_hdr_t *h)
+int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b)
+int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
+int sam_read1(htsFile *fp, bam_hdr_t *h, bam1_t *b)
+int sam_write1(htsFile *fp, const bam_hdr_t *h, const bam1_t *b)
+#*************************************
+#*** Manipulating auxiliary fields ***
+#*************************************
+uint8_t *bam_aux_get(const bam1_t *b, const char *tag)
+int64_t  bam_aux2i(const uint8_t *s)
+double   bam_aux2f(const uint8_t *s)
+char     bam_aux2A(const uint8_t *s)
+char    *bam_aux2Z(const uint8_t *s)
+void bam_aux_append(bam1_t *b, const char *tag, char type, int len, uint8_t *data)
+int bam_aux_del(bam1_t *b, uint8_t *s)
+#**************************
+#*** Pileup and Mpileup ***
+#**************************
+#  @abstract Generic pileup 'client data'.
+#  @discussion The pileup iterator allows setting a constructor and
+#  destructor function, which will be called every time a sequence is
+#  fetched and discarded.  This permits caching of per-sequence data in
+#  a tidy manner during the pileup process.  This union is the cached
+#  data to be manipulated by the "client" (the caller of pileup).
+#
+union bam_pileup_cd:
+void *p
+int64_t i
+double f
+# @abstract Structure for one alignment covering the pileup position.
+# @field  b          pointer to the alignment
+# @field  qpos       position of the read base at the pileup site, 0-based
+# @field  indel      indel length; 0 for no indel, positive for ins and negative for del
+# @field  level      the level of the read in the "viewer" mode
+# @field  is_del     1 iff the base on the padded read is a deletion
+# @field  is_head    ???
+# @field  is_tail    ???
+# @field  is_refskip ???
+# @field  aux        ???
+#
+# @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
+# difference between the two functions is that the former does not
+# set bam_pileup1_t::level, while the later does. Level helps the
+# implementation of alignment viewers, but calculating this has some
+# overhead.
+#
+# is_del, is_head, etc are a bit field, declaring as below should
+# work as expected, see
+# https://groups.google.com/forum/#!msg/cython-users/24tD1kwRY7A/pmoPuSmanM0J
+ctypedef struct bam_pileup1_t:
+bam1_t *b
+int32_t qpos
+int indel, level
+uint32_t is_del
+uint32_t is_head
+uint32_t is_tail
+uint32_t is_refskip
+uint32_t aux
+bam_pileup_cd cd
+ctypedef int (*bam_plp_auto_f)(void *data, bam1_t *b)
+ctypedef int (*bam_test_f)()
+ctypedef struct __bam_plp_t
+ctypedef __bam_plp_t *bam_plp_t
+ctypedef struct __bam_mplp_t
+ctypedef __bam_mplp_t *bam_mplp_t
+# bam_plp_init() - sets an iterator over multiple
+# @func:      see mplp_func in bam_plcmd.c in samtools for an example. Expected return
+#             status: 0 on success, -1 on end, < -1 on non-recoverable errors
+# @data:      user data to pass to @func
+bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
+void bam_plp_destroy(bam_plp_t iter)
+int bam_plp_push(bam_plp_t iter, const bam1_t *b)
+const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
+const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
+void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt)
+void bam_plp_reset(bam_plp_t iter)
+bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data)
+# bam_mplp_init_overlaps() - if called, mpileup will detect overlapping
+# read pairs and for each base pair set the base quality of the
+# lower-quality base to zero, thus effectively discarding it from
+# calling. If the two bases are identical, the quality of the other base
+# is increased to the sum of their qualities (capped at 200), otherwise
+# it is multiplied by 0.8.
+void bam_mplp_init_overlaps(bam_mplp_t iter)
+void bam_mplp_destroy(bam_mplp_t iter)
+void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt)
+int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp)
+void bam_mplp_reset(bam_mplp_t iter)
+void bam_mplp_constructor(bam_mplp_t iter,
+		      int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd))
+void bam_mplp_destructor(bam_mplp_t iter,
+			     int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd))
+# Added by AH
+# ctypedef bam_pileup1_t * const_bam_pileup1_t_ptr "const bam_pileup1_t *"
+# // ---------------------------
+# // Base modification retrieval
+# /*! @typedef
+#  @abstract Holds a single base modification.
+#  @field modified_base     The short base code (m, h, etc) or -ChEBI (negative)
+#  @field canonical_base    The canonical base referred to in the MM tag.
+#                           One of A, C, G, T or N.  Note this may not be the
+#                           explicit base recorded in the SEQ column (esp. if N).
+#  @field strand            0 or 1, indicating + or - strand from MM tag.
+#  @field qual              Quality code (256*probability), or -1 if unknown
+#  @discussion
+#  Note this doesn't hold any location data or information on which other
+#  modifications may be possible at this site.
+ctypedef struct hts_base_mod:
+int modified_base
+int canonical_base
+int strand
+int qual
+# /// Allocates an hts_base_mode_state.
+# /**
+# * @return An hts_base_mode_state pointer on success,
+# *         NULL on failure.
+# *
+# * This just allocates the memory.  The initialisation of the contents is
+# * done using bam_parse_basemod.  Successive calls may be made to that
+# * without the need to free and allocate a new state.
+# *
+# * The state be destroyed using the hts_base_mode_state_free function.
+# */
+ctypedef struct hts_base_mod_state
+hts_base_mod_state *hts_base_mod_state_alloc()
+# /// Destroys an  hts_base_mode_state.
+# /**
+# * @param state    The base modification state pointer.
+# *
+# * The should have previously been created by hts_base_mode_state_alloc.
+# */
+void hts_base_mod_state_free(hts_base_mod_state *state)
+# /// Parses the Mm and Ml tags out of a bam record.
+# /**
+# * @param b        BAM alignment record
+# * @param state    The base modification state pointer.
+# * @return 0 on success,
+# *         -1 on failure.
+# *
+# * This fills out the contents of the modification state, resetting the
+# * iterator location to the first sequence base.
+# */
+int bam_parse_basemod(const bam1_t *b, hts_base_mod_state *state)
+# /// Finds the next location containing base modifications and returns them
+# /**
+# * @param b        BAM alignment record
+# * @param state    The base modification state pointer.
+# * @param mods     A supplied array for returning base modifications
+# * @param n_mods   The size of the mods array
+# * @return The number of modifications found on success,
+# *         0 if no more modifications are present,
+# *         -1 on failure.
+# *
+# * Unlike bam_mods_at_next_pos this skips ahead to the next site
+# * with modifications.
+# *
+# * If more than n_mods modifications are found, the total found is returned.
+# * Note this means the caller needs to check whether this is higher than
+# * n_mods.
+# */
+int bam_next_basemod(const bam1_t *b, hts_base_mod_state *state,hts_base_mod *mods, int n_mods, int *pos)
+# ***********************************
+# * BAQ calculation and realignment *
+# ***********************************/
+int sam_cap_mapq(bam1_t *b, const char *ref, int ref_len, int thres)
+int sam_prob_realn(bam1_t *b, const char *ref, int ref_len, int flag)
+cdef extern from "htslib/faidx.h" nogil:
+ctypedef struct faidx_t:
+pass
+# /// Build index for a FASTA or bgzip-compressed FASTA file.
+# /**  @param  fn  FASTA file name
+# @param  fnfai Name of .fai file to build.
+# @param  fngzi Name of .gzi file to build (if fn is bgzip-compressed).
+# @return     0 on success; or -1 on failure
+# If fnfai is NULL, ".fai" will be appended to fn to make the FAI file name.
+# If fngzi is NULL, ".gzi" will be appended to fn for the GZI file.  The GZI
+# file will only be built if fn is bgzip-compressed.
+# */
+int fai_build3(const char *fn,
+const char *fnfai,
+const char *fngzi)
+# /// Build index for a FASTA or bgzip-compressed FASTA file.
+# /** @param  fn  FASTA file name
+# @return     0 on success; or -1 on failure
+#
+# File "fn.fai" will be generated.  This function is equivalent to
+# fai_build3(fn, NULL, NULL);
+# */
+int fai_build(char *fn)
+# /// Destroy a faidx_t struct
+void fai_destroy(faidx_t *fai)
+# /// Load FASTA indexes.
+# /** @param  fn  File name of the FASTA file (can be compressed with bgzip).
+#     @param  fnfai File name of the FASTA index.
+#     @param  fngzi File name of the bgzip index.
+#     @param  flags Option flags to control index file caching and creation.
+#     @return Pointer to a faidx_t struct on success, NULL on failure.
+# If fnfai is NULL, ".fai" will be appended to fn to make the FAI file name.
+# If fngzi is NULL, ".gzi" will be appended to fn for the bgzip index name.
+# The bgzip index is only needed if fn is compressed.
+# If (flags & FAI_CREATE) is true, the index files will be built using
+# fai_build3() if they are not already present.
+# */
+faidx_t *fai_load3(const char *fn,
+const char *fnfai,
+const char *fngzi,
+int flags)
+# /// Load index from "fn.fai".
+# /** @param  fn  File name of the FASTA file
+#     @return Pointer to a faidx_t struct on success, NULL on failure.
+# This function is equivalent to fai_load3(fn, NULL, NULL, FAI_CREATE|FAI_CACHE);
+# */
+faidx_t *fai_load(char *fn)
+# /// Fetch the sequence in a region
+# /** @param  fai  Pointer to the faidx_t struct
+#     @param  reg  Region in the format "chr2:20,000-30,000"
+#     @param  len  Length of the region; -2 if seq not present, -1 general error
+#     @return      Pointer to the sequence; `NULL` on failure
+# The returned sequence is allocated by `malloc()` family and should be destroyed
+# by end users by calling `free()` on it.
+# */
+char *fai_fetch(faidx_t *fai,
+char *reg,
+int *len)
+# /// Fetch the sequence in a region
+# /** @param  fai  Pointer to the faidx_t struct
+#     @param  c_name Region name
+#     @param  p_beg_i  Beginning position number (zero-based)
+#     @param  p_end_i  End position number (zero-based)
+#     @param  len  Length of the region; -2 if c_name not present, -1 general error
+#     @return      Pointer to the sequence; null on failure
+# The returned sequence is allocated by `malloc()` family and should be destroyed
+# by end users by calling `free()` on it.
+# */
+char *faidx_fetch_seq(faidx_t *fai,
+char *c_name,
+int p_beg_i,
+int p_end_i,
+int *len)
+# /// Query if sequence is present
+# /**   @param  fai  Pointer to the faidx_t struct
+#   @param  seq  Sequence name
+#   @return      1 if present or 0 if absent
+#   */
+int faidx_has_seq(faidx_t *fai, const char *seq)
+# /// Fetch the number of sequences
+# /** @param  fai  Pointer to the faidx_t struct
+# @return      The number of sequences
+# */
+int faidx_nseq(const faidx_t *fai)
+# /// Return name of i-th sequence
+const char *faidx_iseq(const faidx_t *fai, int i)
+# /// Return sequence length, -1 if not present
+int faidx_seq_len(faidx_t *fai, const char *seq)
+# tabix support
+cdef extern from "htslib/tbx.h" nogil:
+# tbx.h definitions
+int8_t TBX_MAX_SHIFT
+int32_t TBX_GENERIC
+int32_t TBX_SAM
+int32_t TBX_VCF
+int32_t TBX_UCSC
+ctypedef struct tbx_conf_t:
+int32_t preset
+int32_t sc, bc, ec   # seq col., beg col. and end col.
+int32_t meta_char, line_skip
+ctypedef struct tbx_t:
+tbx_conf_t conf
+hts_idx_t *idx
+void * dict
+tbx_conf_t tbx_conf_gff
+tbx_conf_t tbx_conf_bed
+tbx_conf_t tbx_conf_psltbl
+tbx_conf_t tbx_conf_sam
+tbx_conf_t tbx_conf_vcf
+void tbx_itr_destroy(hts_itr_t * iter)
+hts_itr_t * tbx_itr_queryi(tbx_t * t, int tid, int bed, int end)
+hts_itr_t * tbx_itr_querys(tbx_t * t, char * s)
+int tbx_itr_next(htsFile * fp, tbx_t * t, hts_itr_t * iter, void * data)
+int tbx_name2id(tbx_t *tbx, char *ss)
+int tbx_index_build(char *fn, int min_shift, tbx_conf_t *conf)
+int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf)
+tbx_t * tbx_index_load(char *fn)
+tbx_t *tbx_index_load2(const char *fn, const char *fnidx)
+tbx_t *tbx_index_load3(const char *fn, const char *fnidx, int flags)
+# free the array but not the values
+char **tbx_seqnames(tbx_t *tbx, int *n)
+void tbx_destroy(tbx_t *tbx)
+# VCF/BCF API
+cdef extern from "htslib/vcf.h" nogil:
+# Header struct
+uint8_t BCF_HL_FLT   # header line
+uint8_t BCF_HL_INFO
+uint8_t BCF_HL_FMT
+uint8_t BCF_HL_CTG
+uint8_t BCF_HL_STR   # structured header line TAG=<A=..,B=..>
+uint8_t BCF_HL_GEN   # generic header line
+uint8_t BCF_HT_FLAG  # header type
+uint8_t BCF_HT_INT
+uint8_t BCF_HT_REAL
+uint8_t BCF_HT_STR
+uint8_t BCF_VL_FIXED # variable length
+uint8_t BCF_VL_VAR
+uint8_t BCF_VL_A
+uint8_t BCF_VL_G
+uint8_t BCF_VL_R
+# === Dictionary ===
+#
+# The header keeps three dictionaries. The first keeps IDs in the
+# "FILTER/INFO/FORMAT" lines, the second keeps the sequence names and lengths
+# in the "contig" lines and the last keeps the sample names. bcf_hdr_t::dict[]
+# is the actual hash table, which is opaque to the end users. In the hash
+# table, the key is the ID or sample name as a C string and the value is a
+# bcf_idinfo_t struct. bcf_hdr_t::id[] points to key-value pairs in the hash
+# table in the order that they appear in the VCF header. bcf_hdr_t::n[] is the
+# size of the hash table or, equivalently, the length of the id[] arrays.
+uint8_t BCF_DT_ID       # dictionary type
+uint8_t BCF_DT_CTG
+uint8_t BCF_DT_SAMPLE
+# Complete textual representation of a header line
+ctypedef struct bcf_hrec_t:
+int type            # One of the BCF_HL_* type
+char *key           # The part before '=', i.e. FILTER/INFO/FORMAT/contig/fileformat etc.
+char *value         # Set only for generic lines, NULL for FILTER/INFO, etc.
+int nkeys           # Number of structured fields
+char **keys         # The key=value pairs
+char **vals
+ctypedef struct bcf_idinfo_t:
+uint32_t info[3]     # stores Number:20, var:4, Type:4, ColType:4 in info[0..2]
+bcf_hrec_t *hrec[3]  # for BCF_HL_FLT,INFO,FMT and contig length in info[0] for BCF_HL_CTG
+int id
+ctypedef struct bcf_idpair_t:
+const char *key
+const bcf_idinfo_t *val
+ctypedef struct bcf_hdr_t:
+int32_t n[3]                # n:the size of the dictionary block in use, (allocated size, m, is below to preserve ABI)
+bcf_idpair_t *id[3]
+void *dict[3]               # ID dictionary, contig dict and sample dict
+char **samples
+bcf_hrec_t **hrec
+int nhrec, dirty
+int ntransl
+int *transl[2]              # for bcf_translate()
+int nsamples_ori            # for bcf_hdr_set_samples()
+uint8_t *keep_samples
+kstring_t mem
+int32_t m[3]                # m: allocated size of the dictionary block in use (see n above)
+uint8_t bcf_type_shift[]
+# * VCF record *
+uint8_t BCF_BT_NULL
+uint8_t BCF_BT_INT8
+uint8_t BCF_BT_INT16
+uint8_t BCF_BT_INT32
+uint8_t BCF_BT_FLOAT
+uint8_t BCF_BT_CHAR
+uint8_t VCF_REF
+uint8_t VCF_SNP
+uint8_t VCF_MNP
+uint8_t VCF_INDEL
+uint8_t VCF_OTHER
+uint8_t VCF_BND
+uint8_t VCF_OVERLAP
+ctypedef struct variant_t:
+int type, n     # variant type and the number of bases affected, negative for deletions
+ctypedef struct bcf_fmt_t:
+int id             # id: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$id].key
+int n, size, type  # n: number of values per-sample; size: number of bytes per-sample; type: one of BCF_BT_* types
+uint8_t *p         # same as vptr and vptr_* in bcf_info_t below
+uint32_t p_len
+uint32_t p_off
+uint8_t p_free
+union bcf_info_union_t:
+int32_t i      # integer value
+float f        # float value
+ctypedef struct bcf_info_t:
+int key        # key: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$key].key
+int type, len  # type: one of BCF_BT_* types; len: vector length, 1 for scalars
+# v1 union only set if $len==1; for easier access
+bcf_info_union_t v1
+uint8_t *vptr           # pointer to data array in bcf1_t->shared.s, excluding the size+type and tag id bytes
+uint32_t vptr_len       # length of the vptr block or, when set, of the vptr_mod block, excluding offset
+uint32_t vptr_off       # vptr offset, i.e., the size of the INFO key plus size+type bytes
+uint8_t  vptr_free      # indicates that vptr-vptr_off must be freed; set only when modified and the new
+# data block is bigger than the original
+uint8_t BCF1_DIRTY_ID
+uint8_t BCF1_DIRTY_ALS
+uint8_t BCF1_DIRTY_FLT
+uint8_t BCF1_DIRTY_INF
+ctypedef struct bcf_dec_t:
+int m_fmt, m_info, m_id, m_als, m_allele, m_flt  # allocated size (high-water mark); do not change
+int n_flt           # Number of FILTER fields
+int *flt            # FILTER keys in the dictionary
+char *id            # ID
+char *als           # REF+ALT block (\0-seperated)
+char **allele       # allele[0] is the REF (allele[] pointers to the als block); all null terminated
+bcf_info_t *info    # INFO
+bcf_fmt_t *fmt      # FORMAT and individual sample
+variant_t *var      # $var and $var_type set only when set_variant_types called
+int n_var, var_type
+int shared_dirty    # if set, shared.s must be recreated on BCF output
+int indiv_dirty     # if set, indiv.s must be recreated on BCF output
+uint8_t BCF_ERR_CTG_UNDEF
+uint8_t BCF_ERR_TAG_UNDEF
+uint8_t BCF_ERR_NCOLS
+uint8_t BCF_ERR_LIMITS
+uint8_t BCF_ERR_CHAR
+uint8_t BCF_ERR_CTG_INVALID
+uint8_t BCF_ERR_TAG_INVALID
+# The bcf1_t structure corresponds to one VCF/BCF line. Reading from VCF file
+# is slower because the string is first to be parsed, packed into BCF line
+# (done in vcf_parse), then unpacked into internal bcf1_t structure. If it
+# is known in advance that some of the fields will not be required (notably
+# the sample columns), parsing of these can be skipped by setting max_unpack
+# appropriately.
+# Similarly, it is fast to output a BCF line because the columns (kept in
+# shared.s, indiv.s, etc.) are written directly by bcf_write, whereas a VCF
+# line must be formatted in vcf_format.
+ctypedef struct bcf1_t:
+int32_t rid               # CHROM
+int32_t pos               # POS
+int32_t rlen              # length of REF
+float qual                # QUAL
+uint32_t n_info, n_allele
+uint32_t n_fmt, n_sample
+kstring_t shared, indiv
+bcf_dec_t d               # lazy evaluation: $d is not generated by bcf_read(), but by explicitly calling bcf_unpack()
+int max_unpack            # Set to BCF_UN_STR, BCF_UN_FLT, or BCF_UN_INFO to boost performance of vcf_parse when some of the fields won't be needed
+int unpacked              # remember what has been unpacked to allow calling bcf_unpack() repeatedly without redoing the work
+int unpack_size[3]        # the original block size of ID, REF+ALT and FILTER
+int errcode               # one of BCF_ERR_* codes
+####### API #######
+# BCF and VCF I/O
+#
+# A note about naming conventions: htslib internally represents VCF
+# records as bcf1_t data structures, therefore most functions are
+# prefixed with bcf_. There are a few exceptions where the functions must
+# be aware of both BCF and VCF worlds, such as bcf_parse vs vcf_parse. In
+# these cases, functions prefixed with bcf_ are more general and work
+# with both BCF and VCF.
+# bcf_hdr_init() - create an empty BCF header.
+# @param mode    "r" or "w"
+#
+# When opened for writing, the mandatory fileFormat and
+# FILTER=PASS lines are added automatically.
+bcf_hdr_t *bcf_hdr_init(const char *mode)
+# Destroy a BCF header struct
+void bcf_hdr_destroy(bcf_hdr_t *h)
+# Initialize a bcf1_t object; equivalent to calloc(1, sizeof(bcf1_t))
+bcf1_t *bcf_init()
+# Deallocate a bcf1_t object
+void bcf_destroy(bcf1_t *v)
+# Same as bcf_destroy() but frees only the memory allocated by bcf1_t,
+# not the bcf1_t object itself.
+void bcf_empty(bcf1_t *v)
+# Make the bcf1_t object ready for next read. Intended mostly for
+# internal use, the user should rarely need to call this function
+# directly.
+void bcf_clear(bcf1_t *v)
+# Reads VCF or BCF header
+bcf_hdr_t *bcf_hdr_read(htsFile *fp)
+# bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed
+# @samples: samples to include or exclude from file or as a comma-separated string.
+#             LIST|FILE   .. select samples in list/file
+#             ^LIST|FILE  .. exclude samples from list/file
+#             -           .. include all samples
+#             NULL        .. exclude all samples
+# @is_file: @samples is a file (1) or a comma-separated list (0)
+#
+# The bottleneck of VCF reading is parsing of genotype fields. If the
+# reader knows in advance that only subset of samples is needed (possibly
+# no samples at all), the performance of bcf_read() can be significantly
+# improved by calling bcf_hdr_set_samples after bcf_hdr_read().
+# The function bcf_read() will subset the VCF/BCF records automatically
+# with the notable exception when reading records via bcf_itr_next().
+# In this case, bcf_subset_format() must be called explicitly, because
+# bcf_readrec() does not see the header.
+#
+# Returns 0 on success, -1 on error or a positive integer if the list
+# contains samples not present in the VCF header. In such a case, the
+# return value is the index of the offending sample.
+#
+int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file)
+int bcf_subset_format(const bcf_hdr_t *hdr, bcf1_t *rec)
+# Writes VCF or BCF header
+int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h)
+# Parse VCF line contained in kstring and populate the bcf1_t struct
+int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)
+# The opposite of vcf_parse. It should rarely be called directly, see vcf_write
+int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s)
+# bcf_read() - read next VCF or BCF record
+#
+# Returns -1 on critical errors, 0 otherwise. On errors which are not
+# critical for reading, such as missing header definitions, v->errcode is
+# set to one of BCF_ERR* code and must be checked before calling
+# vcf_write().
+int bcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+# bcf_unpack() - unpack/decode a BCF record (fills the bcf1_t::d field)
+#
+# Note that bcf_unpack() must be called even when reading VCF. It is safe
+# to call the function repeatedly, it will not unpack the same field
+# twice.
+uint8_t BCF_UN_STR        # up to ALT inclusive
+uint8_t BCF_UN_FLT        # up to FILTER
+uint8_t BCF_UN_INFO       # up to INFO
+uint8_t BCF_UN_SHR        # all shared information
+uint8_t BCF_UN_FMT        # unpack format and each sample
+uint8_t BCF_UN_IND        # a synonymo of BCF_UN_FMT
+uint8_t BCF_UN_ALL        # everything
+int bcf_unpack(bcf1_t *b, int which)
+# bcf_dup() - create a copy of BCF record.
+#
+# Note that bcf_unpack() must be called on the returned copy as if it was
+# obtained from bcf_read(). Also note that bcf_dup() calls bcf_sync1(src)
+# internally to reflect any changes made by bcf_update_* functions.
+bcf1_t *bcf_dup(bcf1_t *src)
+bcf1_t *bcf_copy(bcf1_t *dst, bcf1_t *src)
+# bcf_write() - write one VCF or BCF record. The type is determined at the open() call.
+int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v)
+# The following functions work only with VCFs and should rarely be called
+# directly. Usually one wants to use their bcf_* alternatives, which work
+# transparently with both VCFs and BCFs.
+bcf_hdr_t *vcf_hdr_read(htsFile *fp)
+int vcf_hdr_write(htsFile *fp, const bcf_hdr_t *h)
+int vcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+#************************************************************************
+# Header querying and manipulation routines
+#************************************************************************
+# Create a new header using the supplied template
+bcf_hdr_t *bcf_hdr_dup(const bcf_hdr_t *hdr)
+# Copy header lines from src to dst if not already present in dst. See also bcf_translate().
+# Returns 0 on success or sets a bit on error:
+#     1 .. conflicting definitions of tag length
+#     # todo
+int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src)
+# bcf_hdr_merge() - copy header lines from src to dst, see also bcf_translate()
+# @param dst: the destination header to be merged into, NULL on the first pass
+# @param src: the source header
+#
+# Notes:
+#     - use as:
+#         bcf_hdr_t *dst = NULL;
+#         for (i=0; i<nsrc; i++) dst = bcf_hdr_merge(dst,src[i]);
+#
+#     - bcf_hdr_merge() replaces bcf_hdr_combine() which had a problem when
+#     combining multiple BCF headers. The current bcf_hdr_combine()
+#     does not have this problem, but became slow when used for many files.
+bcf_hdr_t *bcf_hdr_merge(bcf_hdr_t *dst, const bcf_hdr_t *src)
+# bcf_hdr_add_sample() - add a new sample.
+# @param sample:  sample name to be added
+int bcf_hdr_add_sample(bcf_hdr_t *hdr, const char *sample)
+# Read VCF header from a file and update the header
+int bcf_hdr_set(bcf_hdr_t *hdr, const char *fname)
+# Appends formatted header text to _str_.
+# If _is_bcf_ is zero, `IDX` fields are discarded.
+#  @return 0 if successful, or negative if an error occurred
+#  @since 1.4
+int bcf_hdr_format(const bcf_hdr_t *hdr, int is_bcf, kstring_t *str);
+# Returns formatted header (newly allocated string) and its length,
+# excluding the terminating \0. If is_bcf parameter is unset, IDX
+# fields are discarded.
+char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
+# Append new VCF header line, returns 0 on success
+int bcf_hdr_append(bcf_hdr_t *h, const char *line)
+int bcf_hdr_printf(bcf_hdr_t *h, const char *format, ...)
+# VCF version, e.g. VCFv4.2
+const char *bcf_hdr_get_version(const bcf_hdr_t *hdr)
+void bcf_hdr_set_version(bcf_hdr_t *hdr, const char *version)
+# bcf_hdr_remove() - remove VCF header tag
+# @param type:      one of BCF_HL_*
+# @param key:       tag name or NULL to remove all tags of the given type
+void bcf_hdr_remove(bcf_hdr_t *h, int type, const char *key)
+# bcf_hdr_subset() - creates a new copy of the header removing unwanted samples
+# @param n:        number of samples to keep
+# @param samples:  names of the samples to keep
+# @param imap:     mapping from index in @samples to the sample index in the original file
+#
+# Sample names not present in h0 are ignored. The number of unmatched samples can be checked
+# by comparing n and bcf_hdr_nsamples(out_hdr).
+# This function can be used to reorder samples.
+# See also bcf_subset() which subsets individual records.
+#
+bcf_hdr_t *bcf_hdr_subset(const bcf_hdr_t *h0, int n, char *const* samples, int *imap)
+# Creates a list of sequence names. It is up to the caller to free the list (but not the sequence names)
+const char **bcf_hdr_seqnames(const bcf_hdr_t *h, int *nseqs)
+# Get number of samples
+int32_t bcf_hdr_nsamples(const bcf_hdr_t *h)
+# The following functions are for internal use and should rarely be called directly
+int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt)
+int bcf_hdr_sync(bcf_hdr_t *h)
+bcf_hrec_t *bcf_hdr_parse_line(const bcf_hdr_t *h, const char *line, int *len)
+void bcf_hrec_format(const bcf_hrec_t *hrec, kstring_t *str)
+int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
+# bcf_hdr_get_hrec() - get header line info
+# @param type:  one of the BCF_HL_* types: FLT,INFO,FMT,CTG,STR,GEN
+# @param key:   the header key for generic lines (e.g. "fileformat"), any field
+#                 for structured lines, typically "ID".
+# @param value: the value which pairs with key. Can be be NULL for BCF_HL_GEN
+# @param str_class: the class of BCF_HL_STR line (e.g. "ALT" or "SAMPLE"), otherwise NULL
+#
+bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *key, const char *value, const char *str_class)
+bcf_hrec_t *bcf_hrec_dup(bcf_hrec_t *hrec)
+void bcf_hrec_add_key(bcf_hrec_t *hrec, const char *str, int len)
+void bcf_hrec_set_val(bcf_hrec_t *hrec, int i, const char *str, int len, int is_quoted)
+int bcf_hrec_find_key(bcf_hrec_t *hrec, const char *key)
+void hrec_add_idx(bcf_hrec_t *hrec, int idx)
+void bcf_hrec_destroy(bcf_hrec_t *hrec)
+#************************************************************************
+# Individual record querying and manipulation routines
+#************************************************************************
+# See the description of bcf_hdr_subset()
+int bcf_subset(const bcf_hdr_t *h, bcf1_t *v, int n, int *imap)
+# bcf_translate() - translate tags ids to be consistent with different header. This function
+#                   is useful when lines from multiple VCF need to be combined.
+# @dst_hdr:   the destination header, to be used in bcf_write(), see also bcf_hdr_combine()
+# @src_hdr:   the source header, used in bcf_read()
+# @src_line:  line obtained by bcf_read()
+int bcf_translate(const bcf_hdr_t *dst_hdr, bcf_hdr_t *src_hdr, bcf1_t *src_line)
+# bcf_get_variant_type[s]()  - returns one of VCF_REF, VCF_SNP, etc
+int bcf_get_variant_types(bcf1_t *rec)
+int bcf_get_variant_type(bcf1_t *rec, int ith_allele)
+int bcf_is_snp(bcf1_t *v)
+# bcf_update_filter() - sets the FILTER column
+# @flt_ids:  The filter IDs to set, numeric IDs returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS")
+# @n:        Number of filters. If n==0, all filters are removed
+int bcf_update_filter(const bcf_hdr_t *hdr, bcf1_t *line, int *flt_ids, int n)
+# bcf_add_filter() - adds to the FILTER column
+# @flt_id:   The filter IDs to add, numeric IDs returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS")
+#
+# If flt_id is PASS, all existing filters are removed first. If other than PASS, existing PASS is removed.
+int bcf_add_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id)
+# bcf_remove_filter() - removes from the FILTER column
+# @flt_id:   filter ID to remove, numeric ID returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS")
+# @pass:     when set to 1 and no filters are present, set to PASS
+int bcf_remove_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id, int set_pass)
+# Returns 1 if present, 0 if absent, or -1 if filter does not exist. "PASS" and "." can be used interchangeably.
+int bcf_has_filter(const bcf_hdr_t *hdr, bcf1_t *line, char *filter)
+# bcf_update_alleles() and bcf_update_alleles_str() - update REF and ALT column
+# @alleles:           Array of alleles
+# @nals:              Number of alleles
+# @alleles_string:    Comma-separated alleles, starting with the REF allele
+int bcf_update_alleles(const bcf_hdr_t *hdr, bcf1_t *line, const char **alleles, int nals)
+int bcf_update_alleles_str(const bcf_hdr_t *hdr, bcf1_t *line, const char *alleles_string)
+# bcf_update_id() - sets new ID string
+# bcf_add_id() - adds to the ID string checking for duplicates
+int bcf_update_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id)
+int bcf_add_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id)
+# bcf_update_info_*() - functions for updating INFO fields
+# @hdr:       the BCF header
+# @line:      VCF line to be edited
+# @key:       the INFO tag to be updated
+# @values:    pointer to the array of values. Pass NULL to remove the tag.
+# @n:         number of values in the array. When set to 0, the INFO tag is removed
+#
+# The @string in bcf_update_info_flag() is optional, @n indicates whether
+# the flag is set or removed.
+#
+# Returns 0 on success or negative value on error.
+#
+int bcf_update_info_int32(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const int32_t *values, int n)
+int bcf_update_info_float(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const float *values, int n)
+int bcf_update_info_flag(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char *values, int n)
+int bcf_update_info_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char *values, int n)
+int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type)
+# bcf_update_format_*() - functions for updating FORMAT fields
+# @values:    pointer to the array of values, the same number of elements
+#             is expected for each sample. Missing values must be padded
+#             with bcf_*_missing or bcf_*_vector_end values.
+# @n:         number of values in the array. If n==0, existing tag is removed.
+#
+# The function bcf_update_format_string() is a higher-level (slower) variant of
+# bcf_update_format_char(). The former accepts array of \0-terminated strings
+# whereas the latter requires that the strings are collapsed into a single array
+# of fixed-length strings. In case of strings with variable length, shorter strings
+# can be \0-padded. Note that the collapsed strings passed to bcf_update_format_char()
+# are not \0-terminated.
+#
+# Returns 0 on success or negative value on error.
+#
+int bcf_update_format_int32(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const int32_t *values, int n)
+int bcf_update_format_float(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const float *values, int n)
+int bcf_update_format_char(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char *values, int n)
+int bcf_update_genotypes(const bcf_hdr_t *hdr, bcf1_t *line, const int32_t *values, int n)
+int bcf_update_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char **values, int n)
+int bcf_update_format(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type)
+# Macros for setting genotypes correctly, for use with bcf_update_genotypes only; idx corresponds
+# to VCF's GT (1-based index to ALT or 0 for the reference allele) and val is the opposite, obtained
+# from bcf_get_genotypes() below.
+uint32_t bcf_gt_phased(uint32_t idx)
+uint32_t bcf_gt_unphased(uint32_t idx)
+uint32_t bcf_gt_missing
+uint32_t bcf_gt_is_missing(uint32_t val)
+uint32_t bcf_gt_is_phased(uint32_t idx)
+uint32_t bcf_gt_allele(uint32_t val)
+# Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based)
+uint32_t bcf_alleles2gt(uint32_t a, uint32_t b)
+void bcf_gt2alleles(int igt, int *a, int *b)
+# bcf_get_fmt() - returns pointer to FORMAT's field data
+# @header: for access to BCF_DT_ID dictionary
+# @line:   VCF line obtained from vcf_parse1
+# @fmt:    one of GT,PL,...
+#
+# Returns bcf_fmt_t* if the call succeeded, or returns NULL when the field
+# is not available.
+#
+bcf_fmt_t *bcf_get_fmt(const bcf_hdr_t *hdr, bcf1_t *line, const char *key)
+bcf_info_t *bcf_get_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key)
+# bcf_get_*_id() - returns pointer to FORMAT/INFO field data given the header index instead of the string ID
+# @line: VCF line obtained from vcf_parse1
+# @id:  The header index for the tag, obtained from bcf_hdr_id2int()
+#
+# Returns bcf_fmt_t* / bcf_info_t*. These functions do not check if the index is valid
+# as their goal is to avoid the header lookup.
+#
+bcf_fmt_t *bcf_get_fmt_id(bcf1_t *line, const int id)
+bcf_info_t *bcf_get_info_id(bcf1_t *line, const int id)
+# bcf_get_info_*() - get INFO values, integers or floats
+# @hdr:       BCF header
+# @line:      BCF record
+# @tag:       INFO tag to retrieve
+# @dst:       *dst is pointer to a memory location, can point to NULL
+# @ndst:      pointer to the size of allocated memory
+#
+# Returns negative value on error or the number of written values on
+# success. bcf_get_info_string() returns on success the number of
+# characters written excluding the null-terminating byte. bcf_get_info_flag()
+# returns 1 when flag is set or 0 if not.
+#
+# List of return codes:
+#     -1 .. no such INFO tag defined in the header
+#     -2 .. clash between types defined in the header and encountered in the VCF record
+#     -3 .. tag is not present in the VCF record
+#
+int bcf_get_info_int32(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, int32_t **dst, int *ndst)
+int bcf_get_info_float(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, float **dst, int *ndst)
+int bcf_get_info_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, char **dst, int *ndst)
+int bcf_get_info_flag(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, int **dst, int *ndst)
+int bcf_get_info_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type)
+# bcf_get_format_*() - same as bcf_get_info*() above
+#
+# The function bcf_get_format_string() is a higher-level (slower) variant of bcf_get_format_char().
+# see the description of bcf_update_format_string() and bcf_update_format_char() above.
+# Unlike other bcf_get_format__*() functions, bcf_get_format_string() allocates two arrays:
+# a single block of \0-terminated strings collapsed into a single array and an array of pointers
+# to these strings. Both arrays must be cleaned by the user.
+#
+# Returns negative value on error or the number of written values on success.
+#
+# Example:
+#     int ndst = 0; char **dst = NULL
+#     if ( bcf_get_format_string(hdr, line, "XX", &dst, &ndst) > 0 )
+#         for (i=0; i<bcf_hdr_nsamples(hdr); i++) printf("%s\n", dst[i])
+#     free(dst[0]); free(dst)
+#
+# Example:
+#     int ngt, *gt_arr = NULL, ngt_arr = 0
+#     ngt = bcf_get_genotypes(hdr, line, &gt_arr, &ngt_arr)
+#
+int bcf_get_format_int32(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, int32_t **dst, int *ndst)
+int bcf_get_format_float(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, float **dst, int *ndst)
+int bcf_get_format_char(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, char **dst, int *ndst)
+int bcf_get_genotypes(const bcf_hdr_t *hdr, bcf1_t *line, int32_t **dst, int *ndst)
+int bcf_get_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, char ***dst, int *ndst)
+int bcf_get_format_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type)
+#************************************************************************
+# Helper functions
+#************************************************************************
+#
+# bcf_hdr_id2int() - Translates string into numeric ID
+# bcf_hdr_int2id() - Translates numeric ID into string
+# @type:     one of BCF_DT_ID, BCF_DT_CTG, BCF_DT_SAMPLE
+# @id:       tag name, such as: PL, DP, GT, etc.
+#
+# Returns -1 if string is not in dictionary, otherwise numeric ID which identifies
+# fields in BCF records.
+#
+int bcf_hdr_id2int(const bcf_hdr_t *hdr, int type, const char *id)
+const char *bcf_hdr_int2id(const bcf_hdr_t *hdr, int type, int int_id)
+# bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID
+# bcf_hdr_id2name() - Translates numeric ID to sequence name
+#
+int bcf_hdr_name2id(const bcf_hdr_t *hdr, const char *id)
+const char *bcf_hdr_id2name(const bcf_hdr_t *hdr, int rid)
+const char *bcf_seqname(const bcf_hdr_t *hdr, bcf1_t *rec)
+#
+# bcf_hdr_id2*() - Macros for accessing bcf_idinfo_t
+# @type:      one of BCF_HL_FLT, BCF_HL_INFO, BCF_HL_FMT
+# @int_id:    return value of bcf_hdr_id2int, must be >=0
+#
+# The returned values are:
+#    bcf_hdr_id2length   ..  whether the number of values is fixed or variable, one of BCF_VL_*
+#    bcf_hdr_id2number   ..  the number of values, 0xfffff for variable length fields
+#    bcf_hdr_id2type     ..  the field type, one of BCF_HT_*
+#    bcf_hdr_id2coltype  ..  the column type, one of BCF_HL_*
+#
+# Notes: Prior to using the macros, the presence of the info should be
+# tested with bcf_hdr_idinfo_exists().
+#
+int bcf_hdr_id2length(const bcf_hdr_t *hdr, int type, int int_id)
+int bcf_hdr_id2number(const bcf_hdr_t *hdr, int type, int int_id)
+int bcf_hdr_id2type(const bcf_hdr_t *hdr, int type, int int_id)
+int bcf_hdr_id2coltype(const bcf_hdr_t *hdr, int type, int int_id)
+int bcf_hdr_idinfo_exists(const bcf_hdr_t *hdr, int type, int int_id)
+bcf_hrec_t *bcf_hdr_id2hrec(const bcf_hdr_t *hdr, int type, int col_type, int int_id)
+void bcf_fmt_array(kstring_t *s, int n, int type, void *data)
+uint8_t *bcf_fmt_sized_array(kstring_t *s, uint8_t *ptr)
+void bcf_enc_vchar(kstring_t *s, int l, const char *a)
+void bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize)
+void bcf_enc_vfloat(kstring_t *s, int n, float *a)
+#************************************************************************
+# BCF index
+#
+# Note that these functions work with BCFs only. See synced_bcf_reader.h
+# which provides (amongst other things) an API to work transparently with
+# both indexed BCFs and VCFs.
+#************************************************************************
+hts_idx_t *bcf_index_load2(const char *fn, const char *fnidx)
+hts_idx_t *bcf_index_load3(const char *fn, const char *fnidx, int flags)
+int bcf_index_build(const char *fn, int min_shift)
+int bcf_index_build2(const char *fn, const char *fnidx, int min_shift)
+#*******************
+# Typed value I/O *
+#******************
+# Note that in contrast with BCFv2.1 specification, HTSlib implementation
+# allows missing values in vectors. For integer types, the values 0x80,
+# 0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001,
+# 0x80000001 as end-of-vector indicators.  Similarly for floats, the value of
+# 0x7F800001 is interpreted as a missing value and 0x7F800002 as an
+# end-of-vector indicator.
+# Note that the end-of-vector byte is not part of the vector.
+# This trial BCF version (v2.2) is compatible with the VCF specification and
+# enables to handle correctly vectors with different ploidy in presence of
+# missing values.
+int32_t bcf_int8_vector_end
+int32_t bcf_int16_vector_end
+int32_t bcf_int32_vector_end
+int32_t bcf_str_vector_end
+int32_t bcf_int8_missing
+int32_t bcf_int16_missing
+int32_t bcf_int32_missing
+int32_t bcf_str_missing
+uint32_t bcf_float_vector_end
+uint32_t bcf_float_missing
+void bcf_float_set(float *ptr, uint32_t value)
+void bcf_float_set_vector_end(float *x)
+void bcf_float_set_missing(float *x)
+int bcf_float_is_missing(float f)
+int bcf_float_is_vector_end(float f)
+void bcf_format_gt(bcf_fmt_t *fmt, int isample, kstring_t *str)
+void bcf_enc_size(kstring_t *s, int size, int type)
+int bcf_enc_inttype(long x)
+void bcf_enc_int1(kstring_t *s, int32_t x)
+int32_t bcf_dec_int1(const uint8_t *p, int type, uint8_t **q)
+int32_t bcf_dec_typed_int1(const uint8_t *p, uint8_t **q)
+int32_t bcf_dec_size(const uint8_t *p, uint8_t **q, int *type)
+# These trivial wrappers are defined only for consistency with other parts of htslib
+bcf1_t *bcf_init1()
+int bcf_read1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+int vcf_read1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+int bcf_write1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+int vcf_write1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+void bcf_destroy1(bcf1_t *v)
+void bcf_empty1(bcf1_t *v)
+int vcf_parse1(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)
+void bcf_clear1(bcf1_t *v)
+int vcf_format1(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s)
+# Other nice wrappers
+void bcf_itr_destroy(hts_itr_t *iter)
+hts_itr_t *bcf_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end)
+hts_itr_t *bcf_itr_querys(const hts_idx_t *idx, const bcf_hdr_t *hdr, char *s)
+int bcf_itr_next(htsFile *fp, hts_itr_t *iter, void *r)
+hts_idx_t *bcf_index_load(const char *fn)
+const char **bcf_index_seqnames(const hts_idx_t *idx, const bcf_hdr_t *hdr, int *nptr)
+# VCF/BCF utility functions
+cdef extern from "htslib/vcfutils.h" nogil:
+struct kbitset_t
+# bcf_trim_alleles() - remove ALT alleles unused in genotype fields
+# @header:  for access to BCF_DT_ID dictionary
+# @line:    VCF line obtain from vcf_parse1
+#
+# Returns the number of removed alleles on success or negative
+# on error:
+#     -1 .. some allele index is out of bounds
+int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line)
+# bcf_remove_alleles() - remove ALT alleles according to bitmask @mask
+# @header:  for access to BCF_DT_ID dictionary
+# @line:    VCF line obtained from vcf_parse1
+# @mask:    alleles to remove
+#
+# If you have more than 31 alleles, then the integer bit mask will
+# overflow, so use bcf_remove_allele_set instead
+void bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int mask)
+# bcf_remove_allele_set() - remove ALT alleles according to bitset @rm_set
+# @header:  for access to BCF_DT_ID dictionary
+# @line:    VCF line obtained from vcf_parse1
+# @rm_set:  pointer to kbitset_t object with bits set for allele
+#           indexes to remove
+#
+# Number=A,R,G INFO and FORMAT fields will be updated accordingly.
+void bcf_remove_allele_set(const bcf_hdr_t *header, bcf1_t *line, kbitset_t *rm_set)
+# bcf_calc_ac() - calculate the number of REF and ALT alleles
+# @header:  for access to BCF_DT_ID dictionary
+# @line:    VCF line obtained from vcf_parse1
+# @ac:      array of length line->n_allele
+# @which:   determine if INFO/AN,AC and indv fields be used
+#
+# Returns 1 if the call succeeded, or 0 if the value could not
+# be determined.
+#
+# The value of @which determines if existing INFO/AC,AN can be
+# used (BCF_UN_INFO) and and if indv fields can be split (BCF_UN_FMT).
+int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which)
+# bcf_gt_type() - determines type of the genotype
+# @fmt_ptr:  the GT format field as set for example by set_fmt_ptr
+# @isample:  sample index (starting from 0)
+# @ial:      index of the 1st non-reference allele (starting from 1)
+# @jal:      index of the 2nd non-reference allele (starting from 1)
+#
+# Returns the type of the genotype (one of GT_HOM_RR, GT_HET_RA,
+# GT_HOM_AA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A or GT_UNKN). If $ial
+# is not NULL and the genotype has one or more non-reference
+# alleles, $ial will be set. In case of GT_HET_AA, $ial is the
+# position of the allele which appeared first in ALT. If $jal is
+# not null and the genotype is GT_HET_AA, $jal will be set and is
+# the position of the second allele in ALT.
+uint8_t GT_HOM_RR    # note: the actual value of GT_* matters, used in dosage r2 calculation
+uint8_t GT_HOM_AA
+uint8_t GT_HET_RA
+uint8_t GT_HET_AA
+uint8_t GT_HAPL_R
+uint8_t GT_HAPL_A
+uint8_t GT_UNKN
+int bcf_gt_type(bcf_fmt_t *fmt_ptr, int isample, int *ial, int *jal)
+int bcf_acgt2int(char c)
+char bcf_int2acgt(int i)
+# bcf_ij2G() - common task: allele indexes to Number=G index (diploid)
+# @i,j:  allele indexes, 0-based, i<=j
+# Returns index to the Number=G diploid array
+uint32_t bcf_ij2G(uint32_t i, uint32_t j)
+cdef extern from "htslib/cram.h" nogil:
+enum cram_block_method:
+ERROR
+RAW
+GZIP
+BZIP2
+LZMA
+RANS
+RANS0
+RANS1
+GZIP_RLE
+enum cram_content_type:
+CT_ERROR
+FILE_HEADER
+COMPRESSION_HEADER
+MAPPED_SLICE
+UNMAPPED_SLICE
+EXTERNAL
+CORE
+# Opaque data types, see cram_structs for the fully fledged versions.
+ctypedef struct SAM_hdr
+ctypedef struct cram_file_def
+ctypedef struct cram_fd
+ctypedef struct cram_container
+ctypedef struct cram_block
+ctypedef struct cram_slice
+ctypedef struct cram_metrics
+ctypedef struct cram_block_slice_hdr
+ctypedef struct cram_block_compression_hdr
+ctypedef struct refs_t
+# Accessor functions
+#
+#-----------------------------------------------------------------------------
+# cram_fd
+#
+SAM_hdr *cram_fd_get_header(cram_fd *fd)
+void cram_fd_set_header(cram_fd *fd, SAM_hdr *hdr)
+int cram_fd_get_version(cram_fd *fd)
+void cram_fd_set_version(cram_fd *fd, int vers)
+int cram_major_vers(cram_fd *fd)
+int cram_minor_vers(cram_fd *fd)
+hFILE *cram_fd_get_fp(cram_fd *fd)
+void cram_fd_set_fp(cram_fd *fd, hFILE *fp)
+#
+#-----------------------------------------------------------------------------
+# cram_container
+#
+int32_t cram_container_get_length(cram_container *c)
+void cram_container_set_length(cram_container *c, int32_t length)
+int32_t cram_container_get_num_blocks(cram_container *c)
+void cram_container_set_num_blocks(cram_container *c, int32_t num_blocks)
+int32_t *cram_container_get_landmarks(cram_container *c, int32_t *num_landmarks)
+void cram_container_set_landmarks(cram_container *c, int32_t num_landmarks,
+				      int32_t *landmarks)
+# Returns true if the container is empty (EOF marker) */
+int cram_container_is_empty(cram_fd *fd)
+#
+#-----------------------------------------------------------------------------
+# cram_block
+#
+int32_t cram_block_get_content_id(cram_block *b)
+int32_t cram_block_get_comp_size(cram_block *b)
+int32_t cram_block_get_uncomp_size(cram_block *b)
+int32_t cram_block_get_crc32(cram_block *b)
+void *  cram_block_get_data(cram_block *b)
+cram_content_type cram_block_get_content_type(cram_block *b)
+void cram_block_set_content_id(cram_block *b, int32_t id)
+void cram_block_set_comp_size(cram_block *b, int32_t size)
+void cram_block_set_uncomp_size(cram_block *b, int32_t size)
+void cram_block_set_crc32(cram_block *b, int32_t crc)
+void cram_block_set_data(cram_block *b, void *data)
+int cram_block_append(cram_block *b, void *data, int size)
+void cram_block_update_size(cram_block *b)
+# Offset is known as "size" internally, but it can be confusing.
+size_t cram_block_get_offset(cram_block *b)
+void cram_block_set_offset(cram_block *b, size_t offset)
+#
+# Computes the size of a cram block, including the block
+# header itself.
+#
+uint32_t cram_block_size(cram_block *b)
+#
+# Renumbers RG numbers in a cram compression header.
+#
+# CRAM stores RG as the Nth number in the header, rather than a
+# string holding the ID: tag.  This is smaller in space, but means
+# "samtools cat" to join files together that contain single but
+# different RG lines needs a way of renumbering them.
+#
+# The file descriptor is expected to be immediately after the
+# cram_container structure (ie before the cram compression header).
+# Due to the nature of the CRAM format, this needs to read and write
+# the blocks itself.  Note that there may be multiple slices within
+# the container, meaning multiple compression headers to manipulate.
+# Changing RG may change the size of the compression header and
+# therefore the length field in the container.  Hence we rewrite all
+# blocks just in case and also emit the adjusted container.
+#
+# The current implementation can only cope with renumbering a single
+# RG (and only then if it is using HUFFMAN or BETA codecs).  In
+# theory it *may* be possible to renumber multiple RGs if they use
+# HUFFMAN to the CORE block or use an external block unshared by any
+# other data series.  So we have an API that can be upgraded to
+# support this, but do not implement it for now.  An example
+# implementation of RG as an EXTERNAL block would be to find that
+# block and rewrite it, returning the number of blocks consumed.
+#
+# Returns 0 on success;
+#        -1 if unable to edit;
+#        -2 on other errors (eg I/O).
+#
+int cram_transcode_rg(cram_fd *input, cram_fd *output,
+			  cram_container *c,
+			  int nrg, int *in_rg, int *out_rg)
+#
+# Copies the blocks representing the next num_slice slices from a
+# container from 'in' to 'out'.  It is expected that the file pointer
+# is just after the read of the cram_container and cram compression
+# header.
+#
+# Returns 0 on success
+#        -1 on failure
+#
+int cram_copy_slice(cram_fd *input, cram_fd *output, int32_t num_slice)
+#
+#-----------------------------------------------------------------------------
+# SAM_hdr
+#
+# Tokenises a SAM header into a hash table.
+#
+# Also extracts a few bits on specific data types, such as @RG lines.
+#
+# @return
+# Returns a SAM_hdr struct on success (free with sam_hdr_free())
+#         NULL on failure
+#
+SAM_hdr *sam_hdr_parse_(const char *hdr, int len)
+#
+#-----------------------------------------------------------------------------
+# cram_io basics
+#
+# CRAM blocks - the dynamically growable data block. We have code to
+# create, update, (un)compress and read/write.
+#
+# These are derived from the deflate_interlaced.c blocks, but with the
+# CRAM extension of content types and IDs.
+#
+# Allocates a new cram_block structure with a specified content_type and
+# id.
+#
+# @return
+# Returns block pointer on success;
+#         NULL on failure
+#
+cram_block *cram_new_block(cram_content_type content_type,
+			       int content_id)
+# Reads a block from a cram file.
+#
+# @return
+# Returns cram_block pointer on success;
+#         NULL on failure
+#
+cram_block *cram_read_block(cram_fd *fd)
+# Writes a CRAM block.
+#
+# @return
+# Returns 0 on success;
+#        -1 on failure
+#
+int cram_write_block(cram_fd *fd, cram_block *b)
+# Frees a CRAM block, deallocating internal data too.
+#
+void cram_free_block(cram_block *b)
+# Uncompresses a CRAM block, if compressed.
+#
+# @return
+# Returns 0 on success;
+#        -1 on failure
+#
+int cram_uncompress_block(cram_block *b)
+# Compresses a block.
+#
+# Compresses a block using one of two different zlib strategies. If we only
+# want one choice set strat2 to be -1.
+#
+# The logic here is that sometimes Z_RLE does a better job than Z_FILTERED
+# or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is
+# significantly faster.
+#
+# @return
+# Returns 0 on success;
+#        -1 on failure
+#
+int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics,
+			    int method, int level)
+# Containers
+#
+# Creates a new container, specifying the maximum number of slices
+# and records permitted.
+#
+# @return
+# Returns cram_container ptr on success;
+#         NULL on failure
+#
+cram_container *cram_new_container(int nrec, int nslice)
+void cram_free_container(cram_container *c)
+# Reads a container header.
+#
+# @return
+# Returns cram_container on success;
+#         NULL on failure or no container left (fd->err == 0).
+#
+cram_container *cram_read_container(cram_fd *fd)
+# Writes a container structure.
+#
+# @return
+# Returns 0 on success;
+#        -1 on failure
+#
+int cram_write_container(cram_fd *fd, cram_container *h)
+#
+# Stores the container structure in dat and returns *size as the
+# number of bytes written to dat[].  The input size of dat is also
+# held in *size and should be initialised to cram_container_size(c).
+#
+# Returns 0 on success;
+#        -1 on failure
+#
+int cram_store_container(cram_fd *fd, cram_container *c, char *dat, int *size)
+int cram_container_size(cram_container *c)
+# The top-level cram opening, closing and option handling
+#
+# Opens a CRAM file for read (mode "rb") or write ("wb").
+#
+# The filename may be "-" to indicate stdin or stdout.
+#
+# @return
+# Returns file handle on success;
+#         NULL on failure.
+#
+cram_fd *cram_open(const char *filename, const char *mode)
+# Opens an existing stream for reading or writing.
+#
+# @return
+# Returns file handle on success;
+#         NULL on failure.
+#
+cram_fd *cram_dopen(hFILE *fp, const char *filename, const char *mode)
+# Closes a CRAM file.
+#
+# @return
+# Returns 0 on success;
+#        -1 on failure
+#
+int cram_close(cram_fd *fd)
+#
+# Seek within a CRAM file.
+#
+# Returns 0 on success
+#        -1 on failure
+#
+int cram_seek(cram_fd *fd, off_t offset, int whence)
+#
+# Flushes a CRAM file.
+# Useful for when writing to stdout without wishing to close the stream.
+#
+# Returns 0 on success
+#        -1 on failure
+#
+int cram_flush(cram_fd *fd)
+# Checks for end of file on a cram_fd stream.
+#
+# @return
+# Returns 0 if not at end of file
+#         1 if we hit an expected EOF (end of range or EOF block)
+#         2 for other EOF (end of stream without EOF block)
+#
+int cram_eof(cram_fd *fd)
+# Sets options on the cram_fd.
+#
+# See CRAM_OPT_* definitions in hts.h.
+# Use this immediately after opening.
+#
+# @return
+# Returns 0 on success;
+#        -1 on failure
+#
+int cram_set_option(cram_fd *fd, hts_fmt_option opt, ...)
+# Sets options on the cram_fd.
+#
+# See CRAM_OPT_* definitions in hts.h.
+# Use this immediately after opening.
+#
+# @return
+# Returns 0 on success;
+#        -1 on failure
+#
+int cram_set_voption(cram_fd *fd, hts_fmt_option opt, va_list args)
+#
+# Attaches a header to a cram_fd.
+#
+# This should be used when creating a new cram_fd for writing where
+# we have an SAM_hdr already constructed (eg from a file we've read
+# in).
+#
+# @return
+# Returns 0 on success;
+#        -1 on failure
+#
+int cram_set_header(cram_fd *fd, SAM_hdr *hdr)
+# Check if this file has a proper EOF block
+#
+# @return
+# Returns 3 if the file is a version of CRAM that does not contain EOF blocks
+#         2 if the file is a stream and thus unseekable
+#         1 if the file contains an EOF block
+#         0 if the file does not contain an EOF block
+#        -1 if an error occurred whilst reading the file or we could not seek back to where we were
+#
+#
+int cram_check_EOF(cram_fd *fd)
+# As int32_decoded/encode, but from/to blocks instead of cram_fd */
+int int32_put_blk(cram_block *b, int32_t val)
+# Deallocates all storage used by a SAM_hdr struct.
+#
+# This also decrements the header reference count. If after decrementing
+# it is still non-zero then the header is assumed to be in use by another
+# caller and the free is not done.
+#
+# This is a synonym for sam_hdr_dec_ref().
+#
+void sam_hdr_free(SAM_hdr *hdr)
+# Returns the current length of the SAM_hdr in text form.
+#
+# Call sam_hdr_rebuild() first if editing has taken place.
+#
+int sam_hdr_length(SAM_hdr *hdr)
+# Returns the string form of the SAM_hdr.
+#
+# Call sam_hdr_rebuild() first if editing has taken place.
+#
+char *sam_hdr_str(SAM_hdr *hdr)
+# Appends a formatted line to an existing SAM header.
+#
+# Line is a full SAM header record, eg "@SQ\tSN:foo\tLN:100", with
+# optional new-line. If it contains more than 1 line then multiple lines
+# will be added in order.
+#
+# Len is the length of the text data, or 0 if unknown (in which case
+# it should be null terminated).
+#
+# @return
+# Returns 0 on success;
+#        -1 on failure
+#
+# Add an @PG line.
+#
+# If we wish complete control over this use sam_hdr_add() directly. This
+# function uses that, but attempts to do a lot of tedious house work for
+# you too.
+#
+# - It will generate a suitable ID if the supplied one clashes.
+# - It will generate multiple @PG records if we have multiple PG chains.
+#
+# Call it as per sam_hdr_add() with a series of key,value pairs ending
+# in NULL.
+#
+# @return
+# Returns 0 on success;
+#        -1 on failure
+#
+int sam_hdr_add_PG(SAM_hdr *sh, const char *name, ...)
+#
+# A function to help with construction of CL tags in @PG records.
+# Takes an argc, argv pair and returns a single space-separated string.
+# This string should be deallocated by the calling function.
+#
+# @return
+# Returns malloced char * on success;
+#         NULL on failure
+#
+char *stringify_argv(int argc, char *argv[])
+#
+# Returns the refs_t structure used by a cram file handle.
+#
+# This may be used in conjunction with option CRAM_OPT_SHARED_REF to
+# share reference memory between multiple file handles.
+#
+# @return
+# Returns NULL if none exists or the file handle is not a CRAM file.
+#
+refs_t *cram_get_refs(htsFile *fd)
+cdef class HTSFile(object):
+cdef          htsFile *htsfile       # pointer to htsFile structure
+cdef          int64_t start_offset   # BGZF offset of first record
+cdef readonly object  filename       # filename as supplied by user
+cdef readonly object  mode           # file opening mode
+cdef readonly object  threads        # number of threads to use
+cdef readonly object  index_filename # filename of index, if supplied by user
+cdef readonly bint    is_stream      # Is htsfile a non-seekable stream
+cdef readonly bint    is_remote      # Is htsfile a remote stream
+cdef readonly bint	  duplicate_filehandle   # Duplicate filehandle when opening via fh
+cdef htsFile *_open_htsfile(self) except? NULL

Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libchtslib.pxd @ 69:33d812a61356