htslib.cram

@file Consider using the higher level hts_*() API for programs that wish to be file format agnostic (see htslib/hts.h).

This API should be used for CRAM specific code. The specifics of the public API are implemented in cram_io.h, cram_encode.h and cram_decode.h although these should not be included directly (use this file instead).

Members

Aliases

SAM_hdr alias SAM_hdr = sam_hdr_t: @{ ------------------------------------------------------------------- Old typedef and function names for compatibility with existing code. Header functionality is now provided by sam.h's sam_hdr_t functions.
sam_hdr_add_PG alias sam_hdr_add_PG = sam_hdr_add_pg: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Enums

cram_block_method enum cram_block_method: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_content_type enum cram_content_type: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Functions

cram_block_append int cram_block_append(cram_block* b, const(void)* data, int size): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_get_comp_size int cram_block_get_comp_size(cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_get_content_id int cram_block_get_content_id(cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_get_content_type cram_content_type cram_block_get_content_type(cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_get_crc32 int cram_block_get_crc32(cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_get_data void* cram_block_get_data(cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_get_offset size_t cram_block_get_offset(cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_get_uncomp_size int cram_block_get_uncomp_size(cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_set_comp_size void cram_block_set_comp_size(cram_block* b, int size): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_set_content_id void cram_block_set_content_id(cram_block* b, int id): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_set_crc32 void cram_block_set_crc32(cram_block* b, int crc): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_set_data void cram_block_set_data(cram_block* b, void* data): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_set_offset void cram_block_set_offset(cram_block* b, size_t offset): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_set_uncomp_size void cram_block_set_uncomp_size(cram_block* b, int size): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_size uint cram_block_size(cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_update_size void cram_block_update_size(cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_check_EOF int cram_check_EOF(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_close int cram_close(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_compress_block int cram_compress_block(cram_fd* fd, cram_block* b, cram_metrics* metrics, int method, int level): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_container_get_landmarks int* cram_container_get_landmarks(cram_container* c, int* num_landmarks): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_container_get_length int cram_container_get_length(cram_container* c): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_container_get_num_blocks int cram_container_get_num_blocks(cram_container* c): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_container_is_empty int cram_container_is_empty(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_container_set_landmarks void cram_container_set_landmarks(cram_container* c, int num_landmarks, int* landmarks): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_container_set_length void cram_container_set_length(cram_container* c, int length): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_container_set_num_blocks void cram_container_set_num_blocks(cram_container* c, int num_blocks): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_container_size int cram_container_size(cram_container* c): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_copy_slice int cram_copy_slice(cram_fd* in_, cram_fd* out_, int num_slice): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_dopen cram_fd* cram_dopen(hFILE* fp, const(char)* filename, const(char)* mode): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_eof int cram_eof(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_fd_get_fp hFILE* cram_fd_get_fp(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_fd_get_header sam_hdr_t* cram_fd_get_header(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_fd_get_version int cram_fd_get_version(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_fd_set_fp void cram_fd_set_fp(cram_fd* fd, hFILE* fp): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_fd_set_header void cram_fd_set_header(cram_fd* fd, sam_hdr_t* hdr): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_fd_set_version void cram_fd_set_version(cram_fd* fd, int vers): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_flush int cram_flush(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_free_block void cram_free_block(cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_free_container void cram_free_container(cram_container* c): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_get_refs refs_t* cram_get_refs(htsFile* fd): @{ -------------------------------------------------------------------
cram_major_vers int cram_major_vers(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_minor_vers int cram_minor_vers(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_new_block cram_block* cram_new_block(cram_content_type content_type, int content_id): @{ ---------------------------------------------------------------------- CRAM blocks - the dynamically growable data block. We have code to create, update, (un)compress and read/write.
cram_new_container cram_container* cram_new_container(int nrec, int nslice): @{ ---------------------------------------------------------------------- Containers
cram_open cram_fd* cram_open(const(char)* filename, const(char)* mode): @{ ---------------------------------------------------------------------- The top-level cram opening, closing and option handling
cram_read_block cram_block* cram_read_block(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_read_container cram_container* cram_read_container(cram_fd* fd): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_seek int cram_seek(cram_fd* fd, off_t offset, int whence): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_set_header int cram_set_header(cram_fd* fd, sam_hdr_t* hdr): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_set_option int cram_set_option(cram_fd* fd, hts_fmt_option opt, ...): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_set_voption int cram_set_voption(cram_fd* fd, hts_fmt_option opt, va_list args): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_store_container int cram_store_container(cram_fd* fd, cram_container* c, char* dat, int* size): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_transcode_rg int cram_transcode_rg(cram_fd* in_, cram_fd* out_, cram_container* c, int nrg, int* in_rg, int* out_rg): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_uncompress_block int cram_uncompress_block(cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_write_block int cram_write_block(cram_fd* fd, cram_block* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_write_container int cram_write_container(cram_fd* fd, cram_container* h): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
int32_put_blk int int32_put_blk(cram_block* b, int val): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_hdr_free void sam_hdr_free(SAM_hdr* hdr): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_hdr_parse_ SAM_hdr* sam_hdr_parse_(const(char)* hdr, size_t len): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Structs

cram_block struct cram_block: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_compression_hdr struct cram_block_compression_hdr: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_block_slice_hdr struct cram_block_slice_hdr: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_container struct cram_container: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_fd struct cram_fd: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_file_def struct cram_file_def: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_metrics struct cram_metrics: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
cram_slice struct cram_slice: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
hFILE struct hFILE: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
refs_t struct refs_t: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.