htslib.sam

@file htslib/sam.h High-level SAM/BAM/CRAM sequence file operations.

Members

Aliases

bam_hdr_t alias bam_hdr_t = sam_hdr_t: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_itr_destroy alias bam_itr_destroy = hts_itr_destroy: ** BAM/CRAM indexing ***
bam_itr_queryi alias bam_itr_queryi = sam_itr_queryi: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_itr_querys alias bam_itr_querys = sam_itr_querys: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_mplp_t alias bam_mplp_t = __bam_mplp_t*: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_plp_auto_f alias bam_plp_auto_f = int function(void* data, bam1_t* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_plp_t alias bam_plp_t = __bam_plp_t*: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
samFile alias samFile = htsFile: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_close alias sam_close = hts_close: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_itr_destroy alias sam_itr_destroy = hts_itr_destroy: Free a SAM iterator @param iter Iterator to free
sam_itr_multi_next alias sam_itr_multi_next = sam_itr_next: @param htsfp Htsfile pointer for the input file @param itr Iterator @param r Pointer to a bam1_t struct @return >= 0 on success; -1 when there is no more data; < -1 on error
sam_open alias sam_open = hts_open: ** SAM I/O ***
sam_open_format alias sam_open_format = hts_open_format: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Functions

bam_aux2A char bam_aux2A(const(ubyte)* s): @param s Pointer to the tag data, as returned by bam_aux_get(). @return The value, or 0 if the tag was not a character ('A') type If the tag is not a character type, errno is set to EINVAL.
bam_aux2Z char* bam_aux2Z(const(ubyte)* s): @param s Pointer to the tag data, as returned by bam_aux_get(). @return Pointer to the string, or NULL if the tag was not a string type If the tag is not a string type ('Z' or 'H'), errno is set to EINVAL.
bam_aux2f double bam_aux2f(const(ubyte)* s): @param s Pointer to the tag data, as returned by bam_aux_get() @return The value, or 0 if the tag was not an integer type If the tag is not an numeric type, errno is set to EINVAL. The value of integer flags will be returned cast to a double.
bam_aux2i long bam_aux2i(const(ubyte)* s): @param s Pointer to the tag data, as returned by bam_aux_get() @return The value, or 0 if the tag was not an integer type If the tag is not an integer type, errno is set to EINVAL. This function will not return the value of floating-point tags.
bam_auxB2f double bam_auxB2f(const(ubyte)* s, uint idx): @param s Pointer to the tag data, as returned by bam_aux_get(). @param idx 0-based Index into the array @return The idx'th value, or 0.0 on error. If the array is not a numeric type, errno is set to EINVAL. This can only actually happen if the input record has an invalid type field. If idx is greater than or equal to the value returned by bam_auxB_len(s), errno is set to ERANGE. In both cases, 0.0 will be returned.
bam_auxB2i long bam_auxB2i(const(ubyte)* s, uint idx): @param s Pointer to the tag data, as returned by bam_aux_get(). @param idx 0-based Index into the array @return The idx'th value, or 0 on error. If the array is not an integer type, errno is set to EINVAL. If idx is greater than or equal to the value returned by bam_auxB_len(s), errno is set to ERANGE. In both cases, 0 will be returned.
bam_auxB_len uint bam_auxB_len(const(ubyte)* s): @param s Pointer to the tag data, as returned by bam_aux_get(). @return The length of the array, or 0 if the tag is not an array type. If the tag is not an array type, errno is set to EINVAL.
bam_aux_append int bam_aux_append(bam1_t* b, const(char)[2] tag, char type, int len, const(ubyte)* data): Append tag data to a bam record
bam_aux_del int bam_aux_del(bam1_t* b, ubyte* s): Delete tag data from a bam record
bam_aux_get ubyte* bam_aux_get(const(bam1_t)* b, const(char)[2] tag): @param b Pointer to the bam record @param tag Desired aux tag @return Pointer to the tag data, or NULL if tag is not present or on error If the tag is not present, this function returns NULL and sets errno to ENOENT. If the bam record's aux data is corrupt (either a tag has an invalid type, or the last record is incomplete) then errno is set to EINVAL and NULL is returned.
bam_aux_update_array int bam_aux_update_array(bam1_t* b, const(char)[2] tag, ubyte type, uint items, void* data): Update or add an array tag
bam_aux_update_float int bam_aux_update_float(bam1_t* b, const(char)[2] tag, float val): Update or add a floating-point tag
bam_aux_update_int int bam_aux_update_int(bam1_t* b, const(char)[2] tag, long val): Update or add an integer tag
bam_aux_update_str int bam_aux_update_str(bam1_t* b, const(char)[2] tag, int len, const(char)* data): Update or add a string-type tag
bam_cigar2qlen hts_pos_t bam_cigar2qlen(int n_cigar, const(uint)* cigar): @param n_cigar Number of items in @p cigar @param cigar CIGAR data @return Query length
bam_cigar2rlen hts_pos_t bam_cigar2rlen(int n_cigar, const(uint)* cigar): @param n_cigar Number of items in @p cigar @param cigar CIGAR data @return Reference length
bam_cigar_gen auto bam_cigar_gen(T0 l, T1 o): Undocumented in source. Be warned that the author may not have intended to support it.
bam_cigar_op auto bam_cigar_op(T c): Undocumented in source. Be warned that the author may not have intended to support it.
bam_cigar_oplen auto bam_cigar_oplen(T c): Undocumented in source. Be warned that the author may not have intended to support it.
bam_cigar_type auto bam_cigar_type(T o): Undocumented in source. Be warned that the author may not have intended to support it.
bam_copy1 bam1_t* bam_copy1(bam1_t* bdst, const(bam1_t)* bsrc): @param bdst Destination alignment record @param bsrc Source alignment record @return bdst on success; NULL on failure
bam_destroy1 void bam_destroy1(bam1_t* b): @param b structure to destroy
bam_dup1 bam1_t* bam_dup1(const(bam1_t)* bsrc): @param bsrc Source alignment record @return Pointer to a new alignment record on success; NULL on failure
bam_endpos hts_pos_t bam_endpos(const(bam1_t)* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_flag2str char* bam_flag2str(int flag): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_get_aux auto bam_get_aux(T b): Undocumented in source. Be warned that the author may not have intended to support it.
bam_get_cigar auto bam_get_cigar(bam1_t* b): Undocumented in source. Be warned that the author may not have intended to support it.
bam_get_l_aux auto bam_get_l_aux(T b): Undocumented in source. Be warned that the author may not have intended to support it.
bam_get_mempolicy uint bam_get_mempolicy(bam1_t* b): @param b Alignment record
bam_get_qname auto bam_get_qname(T b): Undocumented in source. Be warned that the author may not have intended to support it.
bam_get_qual auto bam_get_qual(T b): Undocumented in source. Be warned that the author may not have intended to support it.
bam_get_seq auto bam_get_seq(T b): Undocumented in source. Be warned that the author may not have intended to support it.
bam_hdr_destroy void bam_hdr_destroy(sam_hdr_t* h): Undocumented in source. Be warned that the author may not have intended to support it.
bam_hdr_dup sam_hdr_t* bam_hdr_dup(const(sam_hdr_t)* h0): Undocumented in source. Be warned that the author may not have intended to support it.
bam_hdr_init sam_hdr_t* bam_hdr_init(): Undocumented in source. Be warned that the author may not have intended to support it.
bam_hdr_read sam_hdr_t* bam_hdr_read(BGZF* fp): Read the header from a BAM compressed file.
bam_hdr_write int bam_hdr_write(BGZF* fp, const(sam_hdr_t)* h): Writes the header to a BAM file.
bam_index_build auto bam_index_build(T0 fn, T1 min_shift): Undocumented in source. Be warned that the author may not have intended to support it.
bam_index_load auto bam_index_load(T fn): Undocumented in source. Be warned that the author may not have intended to support it.
bam_init1 bam1_t* bam_init1(): @return An empty bam1_t structure on success, NULL on failure
bam_is_mrev auto bam_is_mrev(T b): Undocumented in source. Be warned that the author may not have intended to support it.
bam_is_rev auto bam_is_rev(T b): Undocumented in source. Be warned that the author may not have intended to support it.
bam_itr_next auto bam_itr_next(T0 htsfp, T1 itr, T2 r): Undocumented in source. Be warned that the author may not have intended to support it.
bam_mplp64_auto int bam_mplp64_auto(bam_mplp_t iter, int* _tid, hts_pos_t* _pos, int* n_plp, const(bam_pileup1_t*)* plp): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_mplp_auto int bam_mplp_auto(bam_mplp_t iter, int* _tid, int* _pos, int* n_plp, const(bam_pileup1_t*)* plp): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_mplp_constructor void bam_mplp_constructor(bam_mplp_t iter, int function(void* data, const(bam1_t)* b, bam_pileup_cd* cd) func): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_mplp_destroy void bam_mplp_destroy(bam_mplp_t iter): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_mplp_destructor void bam_mplp_destructor(bam_mplp_t iter, int function(void* data, const(bam1_t)* b, bam_pileup_cd* cd) func): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_mplp_init
bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void** data): The struct returned by a successful call should be freed via bam_mplp_destroy() when it is no longer needed.
bam_mplp_init_overlaps int bam_mplp_init_overlaps(bam_mplp_t iter): @param iter mpileup iterator @return 0 on success; a negative value on error
bam_mplp_reset void bam_mplp_reset(bam_mplp_t iter): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_mplp_set_maxcnt void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_name2id int bam_name2id(sam_hdr_t* h, const(char)* ref_): Alias of sam_hdr_name2tid(), for backwards compatibility.
bam_plp64_auto const(bam_pileup1_t)* bam_plp64_auto(bam_plp_t iter, int* _tid, hts_pos_t* _pos, int* _n_plp): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_plp64_next const(bam_pileup1_t)* bam_plp64_next(bam_plp_t iter, int* _tid, hts_pos_t* _pos, int* _n_plp): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_plp_auto const(bam_pileup1_t)* bam_plp_auto(bam_plp_t iter, int* _tid, int* _pos, int* _n_plp): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_plp_constructor void bam_plp_constructor(bam_plp_t plp, int function(void* data, const(bam1_t)* b, bam_pileup_cd* cd) func): bam_plp_constructor() - sets a callback to initialise any per-pileup1_t fields. @plp: The bam_plp_t initialised using bam_plp_init. @func: The callback function itself. When called, it is given the data argument (specified in bam_plp_init), the bam structure and a pointer to a locally allocated bam_pileup_cd union. This union will also be present in each bam_pileup1_t created.
bam_plp_destroy void bam_plp_destroy(bam_plp_t iter): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_plp_destructor void bam_plp_destructor(bam_plp_t plp, int function(void* data, const(bam1_t)* b, bam_pileup_cd* cd) func): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_plp_init bam_plp_t bam_plp_init(bam_plp_auto_f func, void* data): 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_insertion int bam_plp_insertion(const(bam_pileup1_t)* p, kstring_t* ins, int* del_len): @param p pileup data @param ins the kstring where the insertion sequence will be written @param del_len location for deletion length @return the length of insertion string on success; -1 on failure.
bam_plp_next const(bam_pileup1_t)* bam_plp_next(bam_plp_t iter, int* _tid, int* _pos, int* _n_plp): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_plp_push int bam_plp_push(bam_plp_t iter, const(bam1_t)* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_plp_reset void bam_plp_reset(bam_plp_t iter): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_plp_set_maxcnt void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_read1 int bam_read1(BGZF* fp, bam1_t* b): @param fp BGZF file being read @param b Destination for the alignment data @return number of bytes read on success -1 at end of file < -1 on failure
bam_seqi auto bam_seqi(T0 s, T1 i): Undocumented in source. Be warned that the author may not have intended to support it.
bam_set_mempolicy void bam_set_mempolicy(bam1_t* b, uint policy): @param b Alignment record @param policy Desired policy
bam_set_qname int bam_set_qname(bam1_t* b, const(char)* qname): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_str2flag int bam_str2flag(const(char)* str): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_write1 int bam_write1(BGZF* fp, const(bam1_t)* b): @param fp BGZF file being written @param b Alignment record to write @return number of bytes written on success -1 on error
sam_cap_mapq int sam_cap_mapq(bam1_t* b, const(char)* ref_, hts_pos_t ref_len, int thres): BAQ calculation and realignment *
sam_format1 int sam_format1(const(sam_hdr_t)* h, const(bam1_t)* b, kstring_t* str): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_hdr_add_line int sam_hdr_add_line(sam_hdr_t* h, const(char)* type, ...): Adds a single line to an existing header.
sam_hdr_add_lines int sam_hdr_add_lines(sam_hdr_t* h, const(char)* lines, size_t len): Add formatted lines to an existing header.
sam_hdr_add_pg int sam_hdr_add_pg(sam_hdr_t* h, const(char)* name, ...): Add an \@PG line.
sam_hdr_change_HD int sam_hdr_change_HD(sam_hdr_t* h, const(char)* key, const(char)* 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_count_lines int sam_hdr_count_lines(sam_hdr_t* h, const(char)* type): Count the number of lines for a given header type
sam_hdr_destroy void sam_hdr_destroy(sam_hdr_t* h): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_hdr_dup sam_hdr_t* sam_hdr_dup(const(sam_hdr_t)* h0): Duplicate a header structure.
sam_hdr_find_hd auto sam_hdr_find_hd(T0 h, T1 ks): Returns the SAM formatted text of the \@HD header line
sam_hdr_find_line_id int sam_hdr_find_line_id(sam_hdr_t* h, const(char)* type, const(char)* ID_key, const(char)* ID_val, kstring_t* ks): Returns a complete line of formatted text for a given type and ID.
sam_hdr_find_line_pos int sam_hdr_find_line_pos(sam_hdr_t* h, const(char)* type, int pos, kstring_t* ks): Returns a complete line of formatted text for a given type and index.
sam_hdr_find_tag_hd auto sam_hdr_find_tag_hd(T0 h, T1 key, T2 ks): Returns the value associated with a given \@HD line tag
sam_hdr_find_tag_id int sam_hdr_find_tag_id(sam_hdr_t* h, const(char)* type, const(char)* ID_key, const(char)* ID_value, const(char)* key, kstring_t* ks): Return the value associated with a key for a header line identified by ID_key:ID_val
sam_hdr_find_tag_pos int sam_hdr_find_tag_pos(sam_hdr_t* h, const(char)* type, int pos, const(char)* key, kstring_t* ks): Return the value associated with a key for a header line identified by position
sam_hdr_incr_ref void sam_hdr_incr_ref(sam_hdr_t* h): Increments the reference count on a header
sam_hdr_init sam_hdr_t* sam_hdr_init(): ** BAM I/O *** Generates a new unpopulated header structure.
sam_hdr_length size_t sam_hdr_length(sam_hdr_t* h): Returns the current length of the header text.
sam_hdr_line_index int sam_hdr_line_index(sam_hdr_t* bh, const(char)* type, const(char)* key): Index of the line for the types that have dedicated look-up tables (SQ, RG, PG)
sam_hdr_line_name const(char)* sam_hdr_line_name(sam_hdr_t* bh, const(char)* type, int pos): Id key of the line for the types that have dedicated look-up tables (SQ, RG, PG)
sam_hdr_name2tid int sam_hdr_name2tid(sam_hdr_t* h, const(char)* ref_): Get the target id for a given reference sequence name
sam_hdr_nref int sam_hdr_nref(const(sam_hdr_t)* h): Returns the number of references in the header.
sam_hdr_parse sam_hdr_t* sam_hdr_parse(size_t l_text, const(char)* text): Create a header from existing text.
sam_hdr_pg_id const(char)* sam_hdr_pg_id(sam_hdr_t* h, const(char)* name): Generate a unique \@PG ID: value
sam_hdr_read sam_hdr_t* sam_hdr_read(samFile* fp): Read a header from a SAM, BAM or CRAM file.
sam_hdr_remove_except int sam_hdr_remove_except(sam_hdr_t* h, const(char)* type, const(char)* ID_key, const(char)* ID_value): Remove all lines of a given type from a header, except the one matching an ID
sam_hdr_remove_line_id int sam_hdr_remove_line_id(sam_hdr_t* h, const(char)* type, const(char)* ID_key, const(char)* ID_value): Remove a line with given type / id from a header
sam_hdr_remove_line_pos int sam_hdr_remove_line_pos(sam_hdr_t* h, const(char)* type, int position): Remove nth line of a given type from a header
sam_hdr_remove_lines int sam_hdr_remove_lines(sam_hdr_t* h, const(char)* type, const(char)* id, void* rh): Remove header lines of a given type, except those in a given ID set
sam_hdr_remove_tag_hd auto sam_hdr_remove_tag_hd(T0 h, T1 key): Removes the \@HD line tag with the given key
sam_hdr_remove_tag_id int sam_hdr_remove_tag_id(sam_hdr_t* h, const(char)* type, const(char)* ID_key, const(char)* ID_value, const(char)* key): Remove the key from the line identified by type, ID_key and ID_value.
sam_hdr_str const(char)* sam_hdr_str(sam_hdr_t* h): Returns the text representation of the header.
sam_hdr_tid2len hts_pos_t sam_hdr_tid2len(const(sam_hdr_t)* h, int tid): Get the reference sequence length from a target index
sam_hdr_tid2name const(char)* sam_hdr_tid2name(const(sam_hdr_t)* h, int tid): Get the reference sequence name from a target index
sam_hdr_update_hd auto sam_hdr_update_hd(T h, A a): Adds or updates tags on the header \@HD line
sam_hdr_update_line int sam_hdr_update_line(sam_hdr_t* h, const(char)* type, const(char)* ID_key, const(char)* ID_value, ...): Add or update tag key,value pairs in a header line.
sam_hdr_write int sam_hdr_write(samFile* fp, const(sam_hdr_t)* h): Write a header to a SAM, BAM or CRAM file.
sam_idx_init int sam_idx_init(htsFile* fp, sam_hdr_t* h, int min_shift, const(char)* fnidx): @param fp File handle for the data file being written. @param h Bam header structured (needed for BAI and CSI). @param min_shift 0 for BAI, or larger for CSI (CSI defaults to 14). @param fnidx Filename to write index to. This pointer must remain valid until after sam_idx_save is called. @return 0 on success, <0 on failure.
sam_idx_save int sam_idx_save(htsFile* fp): @param fp File handle for the data file being written. @return 0 on success, <0 on filaure.
sam_index_build int sam_index_build(const(char)* fn, int min_shift): @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; -4: failed to create and/or save the index)
sam_index_build2 int sam_index_build2(const(char)* fn, const(char)* fnidx, int min_shift): @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 (see sam_index_build for error codes)
sam_index_build3 int sam_index_build3(const(char)* fn, const(char)* fnidx, int min_shift, int nthreads): @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 @param nthreads Number of threads to use when building the index @return 0 if successful, or negative if an error occurred (see sam_index_build for error codes)
sam_index_load hts_idx_t* sam_index_load(htsFile* fp, const(char)* fn): @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.
sam_index_load2 hts_idx_t* sam_index_load2(htsFile* fp, const(char)* fn, const(char)* fnidx): @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.
sam_index_load3 hts_idx_t* sam_index_load3(htsFile* fp, const(char)* fn, const(char)* fnidx, int flags): @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 (see description) @return The index, or NULL if an error occurred.
sam_itr_next int sam_itr_next(htsFile* htsfp, hts_itr_t* itr, bam1_t* r): @param htsfp Htsfile pointer for the input file @param itr Iterator @param r Pointer to a bam1_t struct @return >= 0 on success; -1 when there is no more data; < -1 on error
sam_itr_queryi hts_itr_t* sam_itr_queryi(const(hts_idx_t)* idx, int tid, hts_pos_t beg, hts_pos_t end): @param idx Index @param tid Target id @param beg Start position in target @param end End position in target @return An iterator on success; NULL on failure
sam_itr_querys hts_itr_t* sam_itr_querys(const(hts_idx_t)* idx, sam_hdr_t* hdr, const(char)* region): @param idx Index @param hdr Header @param region Region specification @return An iterator on success; NULL on failure
sam_itr_regarray
hts_itr_t* sam_itr_regarray(const(hts_idx_t)* idx, sam_hdr_t* hdr, char** regarray, uint regcount): @param idx Index @param hdr Header @param regarray Array of ref:interval region specifiers @param regcount Number of items in regarray
sam_itr_regions hts_itr_t* sam_itr_regions(const(hts_idx_t)* idx, sam_hdr_t* hdr, hts_reglist_t* reglist, uint regcount): @param idx Index @param hdr Header @param reglist Array of regions to iterate over @param regcount Number of items in reglist
sam_open_mode int sam_open_mode(char* mode, const(char)* fn, const(char)* format): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_open_mode_opts char* sam_open_mode_opts(const(char)* fn, const(char)* mode, const(char)* format): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_parse1 int sam_parse1(kstring_t* s, sam_hdr_t* h, bam1_t* b): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_parse_region const(char)* sam_parse_region(sam_hdr_t* h, const(char)* s, int* tid, hts_pos_t* beg, hts_pos_t* end, int flags): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_prob_realn int sam_prob_realn(bam1_t* b, const(char)* ref_, hts_pos_t ref_len, int flag): @param b BAM record @param ref Reference sequence @param ref_len Reference sequence length @param flag Flags, see description @return 0 on success \n -1 if the read was unmapped, zero length, had no quality values, did not have at least one M, X or = CIGAR operator, or included a reference skip. \n -3 if BAQ alignment has already been done and does not need to be applied, or has already been applied. \n -4 if alignment failed (most likely due to running out of memory)
sam_read1 int sam_read1(samFile* fp, sam_hdr_t* h, bam1_t* b): @param fp Pointer to the source file @param h Pointer to the header previously read (fully or partially) @param b Pointer to the record placeholder @return >= 0 on successfully reading a new record, -1 on end of stream, < -1 on error
sam_write1 int sam_write1(samFile* fp, const(sam_hdr_t)* h, const(bam1_t)* b): @param fp Pointer to the destination file @param h Pointer to the header structure previously read @param b Pointer to the record to be written @return >= 0 on successfully writing the record, -1 on error
stringify_argv
char* stringify_argv(int argc, char** argv): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Manifest constants

BAM_CBACK enum BAM_CBACK;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CDEL enum BAM_CDEL;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CDIFF enum BAM_CDIFF;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CEQUAL enum BAM_CEQUAL;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CHARD_CLIP enum BAM_CHARD_CLIP;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CIGAR_MASK enum BAM_CIGAR_MASK;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CIGAR_SHIFT enum BAM_CIGAR_SHIFT;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CIGAR_STR enum BAM_CIGAR_STR;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CIGAR_TYPE enum BAM_CIGAR_TYPE;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CINS enum BAM_CINS;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CMATCH enum BAM_CMATCH;: ** CIGAR related macros ***
BAM_CPAD enum BAM_CPAD;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CREF_SKIP enum BAM_CREF_SKIP;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_CSOFT_CLIP enum BAM_CSOFT_CLIP;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FDUP enum BAM_FDUP;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FMREVERSE enum BAM_FMREVERSE;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FMUNMAP enum BAM_FMUNMAP;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FPAIRED enum BAM_FPAIRED;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FPROPER_PAIR enum BAM_FPROPER_PAIR;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FQCFAIL enum BAM_FQCFAIL;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FREAD1 enum BAM_FREAD1;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FREAD2 enum BAM_FREAD2;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FREVERSE enum BAM_FREVERSE;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FSECONDARY enum BAM_FSECONDARY;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FSUPPLEMENTARY enum BAM_FSUPPLEMENTARY;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_FUNMAP enum BAM_FUNMAP;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_USER_OWNS_DATA enum BAM_USER_OWNS_DATA;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BAM_USER_OWNS_STRUCT enum BAM_USER_OWNS_STRUCT;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
SAM_FORMAT_VERSION enum SAM_FORMAT_VERSION;: Highest SAM format version supported by this library

Static variables

bam_cigar_table const(byte)[256] bam_cigar_table;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Structs

__bam_mplp_t struct __bam_mplp_t: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
__bam_plp_t struct __bam_plp_t: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam1_core_t struct bam1_core_t: ** Alignment records ***
bam1_t struct bam1_t: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bam_pileup1_t struct bam_pileup1_t: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_hdr_t struct sam_hdr_t: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
sam_hrecs_t struct sam_hrecs_t: ** SAM/BAM/CRAM header ***

Unions

bam_pileup_cd union bam_pileup_cd: ** Pileup and Mpileup ***