- 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_compress_block2
int cram_compress_block2(cram_fd* fd, cram_slice* s, 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. Be warned that the author may not have intended to support it.
- sam_hdr_parse_
SAM_hdr* sam_hdr_parse_(const(char)* hdr, size_t len)
Undocumented in source. Be warned that the author may not have intended to support it.
@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).