dhtslib ~master (2020-09-09T05:17:46Z)
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sam_open
htslib
sam
** SAM I/O ***
extern (
C
)
alias
sam_open
=
hts_open
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htslib
sam
aliases
bam_hdr_t
bam_itr_destroy
bam_itr_queryi
bam_itr_querys
bam_mplp_t
bam_plp_auto_f
bam_plp_t
samFile
sam_close
sam_itr_destroy
sam_itr_multi_next
sam_open
sam_open_format
functions
bam_aux2A
bam_aux2Z
bam_aux2f
bam_aux2i
bam_auxB2f
bam_auxB2i
bam_auxB_len
bam_aux_append
bam_aux_del
bam_aux_get
bam_aux_update_array
bam_aux_update_float
bam_aux_update_int
bam_aux_update_str
bam_cigar2qlen
bam_cigar2rlen
bam_cigar_gen
bam_cigar_op
bam_cigar_oplen
bam_cigar_type
bam_copy1
bam_destroy1
bam_dup1
bam_endpos
bam_flag2str
bam_get_aux
bam_get_cigar
bam_get_l_aux
bam_get_mempolicy
bam_get_qname
bam_get_qual
bam_get_seq
bam_hdr_destroy
bam_hdr_dup
bam_hdr_init
bam_hdr_read
bam_hdr_write
bam_index_build
bam_index_load
bam_init1
bam_is_mrev
bam_is_rev
bam_itr_next
bam_mplp64_auto
bam_mplp_auto
bam_mplp_constructor
bam_mplp_destroy
bam_mplp_destructor
bam_mplp_init
bam_mplp_init_overlaps
bam_mplp_reset
bam_mplp_set_maxcnt
bam_name2id
bam_plp64_auto
bam_plp64_next
bam_plp_auto
bam_plp_constructor
bam_plp_destroy
bam_plp_destructor
bam_plp_init
bam_plp_insertion
bam_plp_next
bam_plp_push
bam_plp_reset
bam_plp_set_maxcnt
bam_read1
bam_seqi
bam_set_mempolicy
bam_set_qname
bam_str2flag
bam_write1
sam_cap_mapq
sam_format1
sam_hdr_add_line
sam_hdr_add_lines
sam_hdr_add_pg
sam_hdr_change_HD
sam_hdr_count_lines
sam_hdr_destroy
sam_hdr_dup
sam_hdr_find_hd
sam_hdr_find_line_id
sam_hdr_find_line_pos
sam_hdr_find_tag_hd
sam_hdr_find_tag_id
sam_hdr_find_tag_pos
sam_hdr_incr_ref
sam_hdr_init
sam_hdr_length
sam_hdr_line_index
sam_hdr_line_name
sam_hdr_name2tid
sam_hdr_nref
sam_hdr_parse
sam_hdr_pg_id
sam_hdr_read
sam_hdr_remove_except
sam_hdr_remove_line_id
sam_hdr_remove_line_pos
sam_hdr_remove_lines
sam_hdr_remove_tag_hd
sam_hdr_remove_tag_id
sam_hdr_str
sam_hdr_tid2len
sam_hdr_tid2name
sam_hdr_update_hd
sam_hdr_update_line
sam_hdr_write
sam_idx_init
sam_idx_save
sam_index_build
sam_index_build2
sam_index_build3
sam_index_load
sam_index_load2
sam_index_load3
sam_itr_next
sam_itr_queryi
sam_itr_querys
sam_itr_regarray
sam_itr_regions
sam_open_mode
sam_open_mode_opts
sam_parse1
sam_parse_region
sam_prob_realn
sam_read1
sam_write1
stringify_argv
manifest constants
BAM_CBACK
BAM_CDEL
BAM_CDIFF
BAM_CEQUAL
BAM_CHARD_CLIP
BAM_CIGAR_MASK
BAM_CIGAR_SHIFT
BAM_CIGAR_STR
BAM_CIGAR_TYPE
BAM_CINS
BAM_CMATCH
BAM_CPAD
BAM_CREF_SKIP
BAM_CSOFT_CLIP
BAM_FDUP
BAM_FMREVERSE
BAM_FMUNMAP
BAM_FPAIRED
BAM_FPROPER_PAIR
BAM_FQCFAIL
BAM_FREAD1
BAM_FREAD2
BAM_FREVERSE
BAM_FSECONDARY
BAM_FSUPPLEMENTARY
BAM_FUNMAP
BAM_USER_OWNS_DATA
BAM_USER_OWNS_STRUCT
SAM_FORMAT_VERSION
static variables
bam_cigar_table
structs
__bam_mplp_t
__bam_plp_t
bam1_core_t
bam1_t
bam_pileup1_t
sam_hdr_t
sam_hrecs_t
unions
bam_pileup_cd
** SAM I/O ***