# 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 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= 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 0 ) # for (i=0; i=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? 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