List of all items
Structs
- BGZF
- _G_fpos64_t
- _G_fpos_t
- _IO_FILE
- _IO_FILE_plus
- _IO_jump_t
- _IO_marker
- __BindgenBitfieldUnit
- __bam_mplp_t
- __bam_plp_t
- __bgzidx_t
- __faidx_t
- __fsid_t
- __hts_idx_t
- __locale_data
- __locale_struct
- __mbstate_t
- __pthread_internal_list
- __sigset_t
- __va_list_tag
- _bcf_sr_regions_t
- _region_t
- aux_key_t
- bam1_core_t
- bam1_t
- bam_pileup1_t
- bcf1_t
- bcf_dec_t
- bcf_fmt_t
- bcf_hdr_t
- bcf_hrec_t
- bcf_idinfo_t
- bcf_idpair_t
- bcf_info_t
- bcf_sr_t
- bcf_srs_t
- bgzf_cache_t
- bgzf_mtaux_t
- cram_block
- cram_block_compression_hdr
- cram_block_slice_hdr
- cram_container
- cram_fd
- cram_file_def
- cram_metrics
- cram_slice
- div_t
- drand48_data
- errmod_t
- fd_set
- hFILE
- htsFile
- htsFormat
- htsFormat__bindgen_ty_1
- htsThreadPool
- hts_base_mod
- hts_base_mod_state
- hts_itr_t
- hts_itr_t__bindgen_ty_1
- hts_md5_context
- hts_opt
- hts_pair64_max_t
- hts_pair64_t
- hts_pair_pos_t
- hts_reglist_t
- hts_tpool
- hts_tpool_process
- hts_tpool_result
- imaxdiv_t
- kbitset_iter_t
- kbitset_t
- ks_tokaux_t
- kstring_t
- ldiv_t
- lldiv_t
- probaln_par_t
- pthread_cond_t__bindgen_ty_1
- pthread_mutex_t___pthread_mutex_s
- pthread_rwlock_t__bindgen_ty_1
- random_data
- refs_t
- sam_hdr_t
- sam_hrecs_t
- tbx_conf_t
- tbx_t
- timespec
- timeval
- variant_t
- wait__bindgen_ty_1
- wait__bindgen_ty_2
- z_stream_s
Unions
- __WAIT_STATUS
- __mbstate_t__bindgen_ty_1
- bam_pileup_cd
- bcf_info_t__bindgen_ty_1
- htsFile__bindgen_ty_1
- hts_opt__bindgen_ty_1
- pthread_attr_t
- pthread_barrier_t
- pthread_barrierattr_t
- pthread_cond_t
- pthread_condattr_t
- pthread_mutex_t
- pthread_mutexattr_t
- pthread_rwlock_t
- pthread_rwlockattr_t
- wait
Functions
- _Exit
- _IO_feof
- _IO_ferror
- _IO_flockfile
- _IO_free_backup_area
- _IO_ftrylockfile
- _IO_funlockfile
- _IO_getc
- _IO_padn
- _IO_peekc_locked
- _IO_putc
- _IO_seekoff
- _IO_seekpos
- _IO_sgetn
- _IO_vfprintf
- _IO_vfscanf
- __assert
- __assert_fail
- __assert_perror_fail
- __bzero
- __ctype_get_mb_cur_max
- __errno_location
- __getdelim
- __overflow
- __secure_getenv
- __stpcpy
- __stpncpy
- __strtok_r
- __uflow
- __underflow
- a64l
- abort
- abs
- alloca
- atexit
- atof
- atoi
- atol
- atoll
- 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_copy1
- bam_destroy1
- bam_dup1
- bam_endpos
- bam_flag2str
- bam_hdr_read
- bam_hdr_write
- bam_init1
- bam_mods_at_next_pos
- bam_mods_at_qpos
- bam_mods_query_type
- bam_mods_recorded
- 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_next_basemod
- bam_parse_basemod
- 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_set_qname
- bam_str2flag
- bam_write1
- bcf_add_filter
- bcf_add_id
- bcf_calc_ac
- bcf_clear
- bcf_copy
- bcf_destroy
- bcf_dup
- bcf_empty
- bcf_enc_vchar
- bcf_enc_vfloat
- bcf_enc_vint
- bcf_fmt_array
- bcf_fmt_sized_array
- bcf_get_fmt
- bcf_get_fmt_id
- bcf_get_format_string
- bcf_get_format_values
- bcf_get_info
- bcf_get_info_id
- bcf_get_info_values
- bcf_get_variant_type
- bcf_get_variant_types
- bcf_gt_type
- bcf_has_filter
- bcf_hdr_add_hrec
- bcf_hdr_add_sample
- bcf_hdr_append
- bcf_hdr_combine
- bcf_hdr_destroy
- bcf_hdr_dup
- bcf_hdr_fmt_text
- bcf_hdr_format
- bcf_hdr_get_hrec
- bcf_hdr_get_version
- bcf_hdr_id2int
- bcf_hdr_init
- bcf_hdr_merge
- bcf_hdr_parse
- bcf_hdr_parse_line
- bcf_hdr_printf
- bcf_hdr_read
- bcf_hdr_remove
- bcf_hdr_seqnames
- bcf_hdr_set
- bcf_hdr_set_samples
- bcf_hdr_set_version
- bcf_hdr_subset
- bcf_hdr_sync
- bcf_hdr_write
- bcf_hrec_add_key
- bcf_hrec_destroy
- bcf_hrec_dup
- bcf_hrec_find_key
- bcf_hrec_format
- bcf_hrec_set_val
- bcf_idx_init
- bcf_idx_save
- bcf_index_build
- bcf_index_build2
- bcf_index_build3
- bcf_index_load2
- bcf_index_load3
- bcf_init
- bcf_is_snp
- bcf_read
- bcf_readrec
- bcf_remove_allele_set
- bcf_remove_alleles
- bcf_remove_filter
- bcf_sr_add_reader
- bcf_sr_destroy
- bcf_sr_destroy_threads
- bcf_sr_init
- bcf_sr_next_line
- bcf_sr_regions_destroy
- bcf_sr_regions_flush
- bcf_sr_regions_init
- bcf_sr_regions_next
- bcf_sr_regions_overlap
- bcf_sr_regions_seek
- bcf_sr_remove_reader
- bcf_sr_seek
- bcf_sr_set_opt
- bcf_sr_set_regions
- bcf_sr_set_samples
- bcf_sr_set_targets
- bcf_sr_set_threads
- bcf_sr_strerror
- bcf_subset
- bcf_subset_format
- bcf_translate
- bcf_trim_alleles
- bcf_unpack
- bcf_update_alleles
- bcf_update_alleles_str
- bcf_update_filter
- bcf_update_format
- bcf_update_format_string
- bcf_update_id
- bcf_update_info
- bcf_write
- bcmp
- bcopy
- bgzf_block_write
- bgzf_check_EOF
- bgzf_close
- bgzf_compress
- bgzf_compression
- bgzf_dopen
- bgzf_flush
- bgzf_flush_try
- bgzf_getc
- bgzf_getline
- bgzf_hopen
- bgzf_index_build_init
- bgzf_index_dump
- bgzf_index_dump_hfile
- bgzf_index_load
- bgzf_index_load_hfile
- bgzf_is_bgzf
- bgzf_mt
- bgzf_open
- bgzf_peek
- bgzf_raw_read
- bgzf_raw_write
- bgzf_read
- bgzf_read_block
- bgzf_seek
- bgzf_set_cache_size
- bgzf_thread_pool
- bgzf_useek
- bgzf_utell
- bgzf_write
- bsearch
- bzero
- calloc
- cfree
- clearenv
- clearerr
- clearerr_unlocked
- cram_block_append
- cram_block_get_comp_size
- cram_block_get_content_id
- cram_block_get_content_type
- cram_block_get_crc32
- cram_block_get_data
- cram_block_get_offset
- cram_block_get_uncomp_size
- cram_block_set_comp_size
- cram_block_set_content_id
- cram_block_set_crc32
- cram_block_set_data
- cram_block_set_offset
- cram_block_set_uncomp_size
- cram_block_size
- cram_block_update_size
- cram_check_EOF
- cram_close
- cram_compress_block
- cram_container_get_landmarks
- cram_container_get_length
- cram_container_get_num_blocks
- cram_container_is_empty
- cram_container_set_landmarks
- cram_container_set_length
- cram_container_set_num_blocks
- cram_container_size
- cram_copy_slice
- cram_dopen
- cram_eof
- cram_fd_get_fp
- cram_fd_get_header
- cram_fd_get_version
- cram_fd_set_fp
- cram_fd_set_header
- cram_fd_set_version
- cram_flush
- cram_free_block
- cram_free_container
- cram_get_refs
- cram_major_vers
- cram_minor_vers
- cram_new_block
- cram_new_container
- cram_open
- cram_read_block
- cram_read_container
- cram_seek
- cram_set_header
- cram_set_option
- cram_set_voption
- cram_store_container
- cram_transcode_rg
- cram_uncompress_block
- cram_write_block
- cram_write_container
- ctermid
- div
- dprintf
- drand48
- drand48_r
- ecvt
- ecvt_r
- erand48
- erand48_r
- errmod_cal
- errmod_destroy
- errmod_init
- exit
- fai_build
- fai_build3
- fai_destroy
- fai_fetch
- fai_fetch64
- fai_fetchqual
- fai_fetchqual64
- fai_load
- fai_load3
- fai_load3_format
- fai_load_format
- fai_parse_region
- fai_set_cache_size
- faidx_fetch_nseq
- faidx_fetch_qual
- faidx_fetch_qual64
- faidx_fetch_seq
- faidx_fetch_seq64
- faidx_has_seq
- faidx_iseq
- faidx_nseq
- faidx_seq_len
- fclose
- fcvt
- fcvt_r
- fdopen
- feof
- feof_unlocked
- ferror
- ferror_unlocked
- fflush
- fflush_unlocked
- ffs
- fgetc
- fgetc_unlocked
- fgetpos
- fgets
- fileno
- fileno_unlocked
- flockfile
- fmemopen
- fopen
- fprintf
- fputc
- fputc_unlocked
- fputs
- fread
- fread_unlocked
- free
- freopen
- fscanf
- fscanf1
- fseek
- fseeko
- fsetpos
- ftell
- ftello
- ftrylockfile
- funlockfile
- fwrite
- fwrite_unlocked
- gcvt
- getc
- getc_unlocked
- getchar
- getchar_unlocked
- getdelim
- getenv
- getline
- getloadavg
- gets
- getsubopt
- getw
- gnu_dev_major
- gnu_dev_makedev
- gnu_dev_minor
- hrec_add_idx
- hts_base_mod_state_alloc
- hts_base_mod_state_free
- hts_check_EOF
- hts_close
- hts_detect_format
- hts_file_type
- hts_format_description
- hts_format_file_extension
- hts_free
- hts_get_bgzfp
- hts_get_format
- hts_get_log_level
- hts_getline
- hts_hopen
- hts_idx_destroy
- hts_idx_finish
- hts_idx_fmt
- hts_idx_get_meta
- hts_idx_get_n_no_coor
- hts_idx_get_stat
- hts_idx_init
- hts_idx_load
- hts_idx_load2
- hts_idx_load3
- hts_idx_push
- hts_idx_save
- hts_idx_save_as
- hts_idx_seqnames
- hts_idx_set_meta
- hts_idx_tbi_name
- hts_itr_destroy
- hts_itr_multi_bam
- hts_itr_multi_cram
- hts_itr_multi_next
- hts_itr_next
- hts_itr_query
- hts_itr_querys
- hts_itr_regions
- hts_log
- hts_md5_destroy
- hts_md5_final
- hts_md5_hex
- hts_md5_init
- hts_md5_reset
- hts_md5_update
- hts_open
- hts_open_format
- hts_opt_add
- hts_opt_apply
- hts_opt_free
- hts_parse_decimal
- hts_parse_format
- hts_parse_opt_list
- hts_parse_reg
- hts_parse_reg64
- hts_parse_region
- hts_readlines
- hts_readlist
- hts_reglist_create
- hts_reglist_free
- hts_resize_array_
- hts_set_cache_size
- hts_set_fai_filename
- hts_set_log_level
- hts_set_opt
- hts_set_thread_pool
- hts_set_threads
- hts_tpool_delete_result
- hts_tpool_destroy
- hts_tpool_dispatch
- hts_tpool_dispatch2
- hts_tpool_dispatch3
- hts_tpool_init
- hts_tpool_kill
- hts_tpool_next_result
- hts_tpool_next_result_wait
- hts_tpool_process_attach
- hts_tpool_process_destroy
- hts_tpool_process_detach
- hts_tpool_process_empty
- hts_tpool_process_flush
- hts_tpool_process_init
- hts_tpool_process_len
- hts_tpool_process_qsize
- hts_tpool_process_ref_decr
- hts_tpool_process_ref_incr
- hts_tpool_process_reset
- hts_tpool_process_shutdown
- hts_tpool_process_sz
- hts_tpool_result_data
- hts_tpool_size
- hts_tpool_wake_dispatch
- hts_version
- imaxabs
- imaxdiv
- index
- initstate
- initstate_r
- int32_put_blk
- jrand48
- jrand48_r
- kbs_destroy
- kbs_init
- kbs_init2
- kbs_insert
- kgetline
- kgetline2
- kmemmem
- kputd
- ksplit_core
- ksprintf
- kstrnstr
- kstrstr
- kstrtok
- kvsprintf
- l64a
- labs
- lcong48
- lcong48_r
- ldiv
- llabs
- lldiv
- lrand48
- lrand48_r
- malloc
- mblen
- mbstowcs
- mbtowc
- memccpy
- memchr
- memcmp
- memcpy
- memmove
- memset
- mkdtemp
- mkstemp
- mkstemps
- mktemp
- mrand48
- mrand48_r
- nrand48
- nrand48_r
- on_exit
- open_memstream
- pclose
- perror
- popen
- posix_memalign
- printf
- probaln_glocal
- pselect
- putc
- putc_unlocked
- putchar
- putchar_unlocked
- putenv
- puts
- putw
- qecvt
- qecvt_r
- qfcvt
- qfcvt_r
- qgcvt
- qsort
- rand
- rand_r
- random
- random_r
- realloc
- realpath
- remove
- rename
- renameat
- rewind
- rindex
- rpmatch
- 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_line_id
- sam_hdr_find_line_pos
- 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_id
- sam_hdr_str
- sam_hdr_tid2len
- sam_hdr_tid2name
- 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_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
- scanf
- scanf1
- seed48
- seed48_r
- select
- setbuf
- setbuffer
- setenv
- setlinebuf
- setstate
- setstate_r
- setvbuf
- snprintf
- sprintf
- srand
- srand48
- srand48_r
- srandom
- srandom_r
- sscanf
- sscanf1
- stpcpy
- stpncpy
- strcasecmp
- strcat
- strchr
- strcmp
- strcoll
- strcoll_l
- strcpy
- strcspn
- strdup
- strerror
- strerror_l
- strerror_r
- stringify_argv
- strlen
- strncasecmp
- strncat
- strncmp
- strncpy
- strndup
- strnlen
- strpbrk
- strrchr
- strsep
- strsignal
- strspn
- strstr
- strtod
- strtof
- strtoimax
- strtok
- strtok_r
- strtol
- strtoll
- strtoq
- strtoul
- strtoull
- strtoumax
- strtouq
- strxfrm
- strxfrm_l
- system
- tbx_destroy
- tbx_index
- tbx_index_build
- tbx_index_build2
- tbx_index_build3
- tbx_index_load
- tbx_index_load2
- tbx_index_load3
- tbx_name2id
- tbx_readrec
- tbx_seqnames
- tempnam
- tmpfile
- tmpnam
- tmpnam_r
- ungetc
- unsetenv
- valloc
- vcf_format
- vcf_hdr_read
- vcf_hdr_write
- vcf_parse
- vcf_read
- vcf_write
- vcf_write_line
- vdprintf
- vfprintf
- vfscanf
- vfscanf1
- vprintf
- vscanf
- vscanf1
- vsnprintf
- vsprintf
- vsscanf
- vsscanf1
- wcstoimax
- wcstombs
- wcstoumax
- wctomb
Type Aliases
- FILE
- SAM_hdr
- _G_int16_t
- _G_int32_t
- _G_uint16_t
- _G_uint32_t
- _IO_lock_t
- __FILE
- __blkcnt64_t
- __blkcnt_t
- __blksize_t
- __builtin_va_list
- __caddr_t
- __clock_t
- __clockid_t
- __codecvt_result
- __compar_fn_t
- __daddr_t
- __dev_t
- __fd_mask
- __fsblkcnt64_t
- __fsblkcnt_t
- __fsfilcnt64_t
- __fsfilcnt_t
- __gid_t
- __gnuc_va_list
- __gwchar_t
- __id_t
- __ino64_t
- __ino_t
- __int16_t
- __int32_t
- __int64_t
- __int8_t
- __intptr_t
- __io_close_fn
- __io_read_fn
- __io_seek_fn
- __io_write_fn
- __key_t
- __locale_t
- __loff_t
- __mode_t
- __nlink_t
- __off64_t
- __off_t
- __pid_t
- __pthread_list_t
- __qaddr_t
- __quad_t
- __rlim64_t
- __rlim_t
- __sig_atomic_t
- __socklen_t
- __ssize_t
- __suseconds_t
- __swblk_t
- __time_t
- __timer_t
- __u_char
- __u_int
- __u_long
- __u_quad_t
- __u_short
- __uid_t
- __uint16_t
- __uint32_t
- __uint64_t
- __uint8_t
- __useconds_t
- bam_hdr_t
- bam_mplp_t
- bam_plp_auto_f
- bam_plp_t
- bcf_sr_error
- bcf_sr_opt_t
- bcf_sr_regions_t
- bgzidx_t
- blkcnt_t
- blksize_t
- caddr_t
- clock_t
- clockid_t
- cram_block_method
- cram_content_type
- daddr_t
- dev_t
- fai_format_options
- fai_load_options
- faidx_t
- fd_mask
- fpos_t
- fsblkcnt_t
- fsfilcnt_t
- fsid_t
- gid_t
- htsCompression
- htsExactFormat
- htsFormatCategory
- htsLogLevel
- hts_fmt_option
- hts_id2name_f
- hts_idx_t
- hts_itr_multi_query_func
- hts_itr_multi_t
- hts_itr_query_func
- hts_name2id_f
- hts_pair32_t
- hts_pos_t
- hts_readrec_func
- hts_seek_func
- hts_tell_func
- id_t
- ino_t
- int_fast16_t
- int_fast32_t
- int_fast64_t
- int_fast8_t
- int_least16_t
- int_least32_t
- int_least64_t
- int_least8_t
- intmax_t
- key_t
- kgets_func
- kgets_func2
- locale_t
- loff_t
- mode_t
- nlink_t
- off_t
- pid_t
- pthread_key_t
- pthread_once_t
- pthread_spinlock_t
- pthread_t
- quad_t
- register_t
- samFile
- sam_fields
- sigset_t
- size_t
- ssize_t
- suseconds_t
- time_t
- timer_t
- u_char
- u_int
- u_int16_t
- u_int32_t
- u_int64_t
- u_int8_t
- u_long
- u_quad_t
- u_short
- uid_t
- uint
- uint16_u
- uint32_u
- uint64_u
- uint_fast16_t
- uint_fast32_t
- uint_fast64_t
- uint_fast8_t
- uint_least16_t
- uint_least32_t
- uint_least64_t
- uint_least8_t
- uintmax_t
- ulong
- ushort
- va_list
- vcfFile
- wchar_t
Statics
- _IO_2_1_stderr_
- _IO_2_1_stdin_
- _IO_2_1_stdout_
- bam_cigar_table
- bcf_float_missing
- bcf_float_vector_end
- bcf_type_shift
- hts_verbose
- seq_nt16_int
- seq_nt16_str
- seq_nt16_table
- stderr
- stdin
- stdout
- sys_errlist
- sys_nerr
- tbx_conf_bed
- tbx_conf_gff
- tbx_conf_psltbl
- tbx_conf_sam
- tbx_conf_vcf
Constants
- AIO_PRIO_DELTA_MAX
- ARG_MAX
- 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
- BCF1_DIRTY_ALS
- BCF1_DIRTY_FLT
- BCF1_DIRTY_ID
- BCF1_DIRTY_INF
- BCF_BT_CHAR
- BCF_BT_FLOAT
- BCF_BT_INT16
- BCF_BT_INT32
- BCF_BT_INT64
- BCF_BT_INT8
- BCF_BT_NULL
- BCF_DT_CTG
- BCF_DT_ID
- BCF_DT_SAMPLE
- BCF_ERR_CHAR
- BCF_ERR_CTG_INVALID
- BCF_ERR_CTG_UNDEF
- BCF_ERR_LIMITS
- BCF_ERR_NCOLS
- BCF_ERR_TAG_INVALID
- BCF_ERR_TAG_UNDEF
- BCF_HL_CTG
- BCF_HL_FLT
- BCF_HL_FMT
- BCF_HL_GEN
- BCF_HL_INFO
- BCF_HL_STR
- BCF_HT_FLAG
- BCF_HT_INT
- BCF_HT_LONG
- BCF_HT_REAL
- BCF_HT_STR
- BCF_MAX_BT_INT16
- BCF_MAX_BT_INT32
- BCF_MAX_BT_INT8
- BCF_MIN_BT_INT16
- BCF_MIN_BT_INT32
- BCF_MIN_BT_INT8
- BCF_SR_PAIR_ANY
- BCF_SR_PAIR_BOTH
- BCF_SR_PAIR_BOTH_REF
- BCF_SR_PAIR_EXACT
- BCF_SR_PAIR_INDELS
- BCF_SR_PAIR_INDEL_REF
- BCF_SR_PAIR_SNPS
- BCF_SR_PAIR_SNP_REF
- BCF_SR_PAIR_SOME
- BCF_UN_ALL
- BCF_UN_FLT
- BCF_UN_FMT
- BCF_UN_IND
- BCF_UN_INFO
- BCF_UN_SHR
- BCF_UN_STR
- BCF_VL_A
- BCF_VL_FIXED
- BCF_VL_G
- BCF_VL_R
- BCF_VL_VAR
- BC_BASE_MAX
- BC_DIM_MAX
- BC_SCALE_MAX
- BC_STRING_MAX
- BGZF_BLOCK_SIZE
- BGZF_ERR_CRC
- BGZF_ERR_HEADER
- BGZF_ERR_IO
- BGZF_ERR_MISUSE
- BGZF_ERR_MT
- BGZF_ERR_ZLIB
- BGZF_MAX_BLOCK_SIZE
- BIG_ENDIAN
- BUFSIZ
- BYTE_ORDER
- CHARCLASS_NAME_MAX
- COLLAPSE_ANY
- COLLAPSE_BOTH
- COLLAPSE_INDELS
- COLLAPSE_NONE
- COLLAPSE_SNPS
- COLLAPSE_SOME
- COLL_WEIGHTS_MAX
- DELAYTIMER_MAX
- E2BIG
- EACCES
- EADDRINUSE
- EADDRNOTAVAIL
- EADV
- EAFNOSUPPORT
- EAGAIN
- EALREADY
- EBADE
- EBADF
- EBADFD
- EBADMSG
- EBADR
- EBADRQC
- EBADSLT
- EBFONT
- EBUSY
- ECANCELED
- ECHILD
- ECHRNG
- ECOMM
- ECONNABORTED
- ECONNREFUSED
- ECONNRESET
- EDEADLK
- EDEADLOCK
- EDESTADDRREQ
- EDOM
- EDOTDOT
- EDQUOT
- EEXIST
- EFAULT
- EFBIG
- EHOSTDOWN
- EHOSTUNREACH
- EIDRM
- EILSEQ
- EINPROGRESS
- EINTR
- EINVAL
- EIO
- EISCONN
- EISDIR
- EISNAM
- EKEYEXPIRED
- EKEYREJECTED
- EKEYREVOKED
- EL2HLT
- EL2NSYNC
- EL3HLT
- EL3RST
- ELIBACC
- ELIBBAD
- ELIBEXEC
- ELIBMAX
- ELIBSCN
- ELNRNG
- ELOOP
- EMEDIUMTYPE
- EMFILE
- EMLINK
- EMSGSIZE
- EMULTIHOP
- ENAMETOOLONG
- ENAVAIL
- ENETDOWN
- ENETRESET
- ENETUNREACH
- ENFILE
- ENOANO
- ENOBUFS
- ENOCSI
- ENODATA
- ENODEV
- ENOENT
- ENOEXEC
- ENOKEY
- ENOLCK
- ENOLINK
- ENOMEDIUM
- ENOMEM
- ENOMSG
- ENONET
- ENOPKG
- ENOPROTOOPT
- ENOSPC
- ENOSR
- ENOSTR
- ENOSYS
- ENOTBLK
- ENOTCONN
- ENOTDIR
- ENOTEMPTY
- ENOTNAM
- ENOTRECOVERABLE
- ENOTSOCK
- ENOTSUP
- ENOTTY
- ENOTUNIQ
- ENXIO
- EOF
- EOPNOTSUPP
- EOVERFLOW
- EOWNERDEAD
- EPERM
- EPFNOSUPPORT
- EPIPE
- EPROTO
- EPROTONOSUPPORT
- EPROTOTYPE
- ERANGE
- EREMCHG
- EREMOTE
- EREMOTEIO
- ERESTART
- ERFKILL
- EROFS
- ESHUTDOWN
- ESOCKTNOSUPPORT
- ESPIPE
- ESRCH
- ESRMNT
- ESTALE
- ESTRPIPE
- ETIME
- ETIMEDOUT
- ETOOMANYREFS
- ETXTBSY
- EUCLEAN
- EUNATCH
- EUSERS
- EWOULDBLOCK
- EXDEV
- EXFULL
- EXIT_FAILURE
- EXIT_SUCCESS
- EXPR_NEST_MAX
- FD_SETSIZE
- FILENAME_MAX
- FOPEN_MAX
- FT_BCF
- FT_BCF_GZ
- FT_GZ
- FT_STDIN
- FT_UNKN
- FT_VCF
- FT_VCF_GZ
- GT_HAPL_A
- GT_HAPL_R
- GT_HET_AA
- GT_HET_RA
- GT_HOM_AA
- GT_HOM_RR
- GT_UNKN
- HAVE___BUILTIN_CLZ
- HOST_NAME_MAX
- HTS_ALLOW_UNALIGNED
- HTS_FMT_BAI
- HTS_FMT_CRAI
- HTS_FMT_CSI
- HTS_FMT_TBI
- HTS_IDX_DELIM
- HTS_IDX_NOCOOR
- HTS_IDX_NONE
- HTS_IDX_REST
- HTS_IDX_SAVE_REMOTE
- HTS_IDX_SILENT_FAIL
- HTS_IDX_START
- HTS_PARSE_LIST
- HTS_PARSE_ONE_COORD
- HTS_PARSE_THOUSANDS_SEP
- HTS_PATH_SEPARATOR_CHAR
- HTS_PATH_SEPARATOR_STR
- HTS_RESIZE_CLEAR
- HTS_VERSION
- INT16_MAX
- INT16_MIN
- INT32_MAX
- INT32_MIN
- INT8_MAX
- INT8_MIN
- INTPTR_MAX
- INTPTR_MIN
- INT_FAST16_MAX
- INT_FAST16_MIN
- INT_FAST32_MAX
- INT_FAST32_MIN
- INT_FAST8_MAX
- INT_FAST8_MIN
- INT_LEAST16_MAX
- INT_LEAST16_MIN
- INT_LEAST32_MAX
- INT_LEAST32_MIN
- INT_LEAST8_MAX
- INT_LEAST8_MIN
- LINE_MAX
- LINK_MAX
- LITTLE_ENDIAN
- LOGIN_NAME_MAX
- L_ctermid
- L_tmpnam
- MAX_CANON
- MAX_INPUT
- MB_LEN_MAX
- MQ_PRIO_MAX
- NAME_MAX
- NGROUPS_MAX
- NR_OPEN
- PATH_MAX
- PDP_ENDIAN
- PIPE_BUF
- PRIX16
- PRIX32
- PRIX64
- PRIX8
- PRIXFAST16
- PRIXFAST32
- PRIXFAST64
- PRIXFAST8
- PRIXLEAST16
- PRIXLEAST32
- PRIXLEAST64
- PRIXLEAST8
- PRIXMAX
- PRIXPTR
- PRId16
- PRId32
- PRId64
- PRId8
- PRIdFAST16
- PRIdFAST32
- PRIdFAST64
- PRIdFAST8
- PRIdLEAST16
- PRIdLEAST32
- PRIdLEAST64
- PRIdLEAST8
- PRIdMAX
- PRIdPTR
- PRIhts_pos
- PRIi16
- PRIi32
- PRIi64
- PRIi8
- PRIiFAST16
- PRIiFAST32
- PRIiFAST64
- PRIiFAST8
- PRIiLEAST16
- PRIiLEAST32
- PRIiLEAST64
- PRIiLEAST8
- PRIiMAX
- PRIiPTR
- PRIo16
- PRIo32
- PRIo64
- PRIo8
- PRIoFAST16
- PRIoFAST32
- PRIoFAST64
- PRIoFAST8
- PRIoLEAST16
- PRIoLEAST32
- PRIoLEAST64
- PRIoLEAST8
- PRIoMAX
- PRIoPTR
- PRIu16
- PRIu32
- PRIu64
- PRIu8
- PRIuFAST16
- PRIuFAST32
- PRIuFAST64
- PRIuFAST8
- PRIuLEAST16
- PRIuLEAST32
- PRIuLEAST64
- PRIuLEAST8
- PRIuMAX
- PRIuPTR
- PRIx16
- PRIx32
- PRIx64
- PRIx8
- PRIxFAST16
- PRIxFAST32
- PRIxFAST64
- PRIxFAST8
- PRIxLEAST16
- PRIxLEAST32
- PRIxLEAST64
- PRIxLEAST8
- PRIxMAX
- PRIxPTR
- PTHREAD_DESTRUCTOR_ITERATIONS
- PTHREAD_KEYS_MAX
- PTHREAD_STACK_MIN
- PTRDIFF_MAX
- PTRDIFF_MIN
- P_tmpdir
- RAND_MAX
- RE_DUP_MAX
- RTSIG_MAX
- SAM_FORMAT_VERSION
- SCNd16
- SCNd32
- SCNd64
- SCNd8
- SCNdFAST16
- SCNdFAST32
- SCNdFAST64
- SCNdFAST8
- SCNdLEAST16
- SCNdLEAST32
- SCNdLEAST64
- SCNdLEAST8
- SCNdMAX
- SCNdPTR
- SCNi16
- SCNi32
- SCNi64
- SCNi8
- SCNiFAST16
- SCNiFAST32
- SCNiFAST64
- SCNiFAST8
- SCNiLEAST16
- SCNiLEAST32
- SCNiLEAST64
- SCNiLEAST8
- SCNiMAX
- SCNiPTR
- SCNo16
- SCNo32
- SCNo64
- SCNo8
- SCNoFAST16
- SCNoFAST32
- SCNoFAST64
- SCNoFAST8
- SCNoLEAST16
- SCNoLEAST32
- SCNoLEAST64
- SCNoLEAST8
- SCNoMAX
- SCNoPTR
- SCNu16
- SCNu32
- SCNu64
- SCNu8
- SCNuFAST16
- SCNuFAST32
- SCNuFAST64
- SCNuFAST8
- SCNuLEAST16
- SCNuLEAST32
- SCNuLEAST64
- SCNuLEAST8
- SCNuMAX
- SCNuPTR
- SCNx16
- SCNx32
- SCNx64
- SCNx8
- SCNxFAST16
- SCNxFAST32
- SCNxFAST64
- SCNxFAST8
- SCNxLEAST16
- SCNxLEAST32
- SCNxLEAST64
- SCNxLEAST8
- SCNxMAX
- SCNxPTR
- SEEK_CUR
- SEEK_END
- SEEK_SET
- SEM_VALUE_MAX
- SIG_ATOMIC_MAX
- SIG_ATOMIC_MIN
- SIZE_MAX
- TBX_GENERIC
- TBX_MAX_SHIFT
- TBX_SAM
- TBX_UCSC
- TBX_VCF
- TMP_MAX
- TTY_NAME_MAX
- UINT16_MAX
- UINT32_MAX
- UINT8_MAX
- UINTPTR_MAX
- UINT_FAST16_MAX
- UINT_FAST32_MAX
- UINT_FAST8_MAX
- UINT_LEAST16_MAX
- UINT_LEAST32_MAX
- UINT_LEAST8_MAX
- VCF_BND
- VCF_INDEL
- VCF_MNP
- VCF_OTHER
- VCF_OVERLAP
- VCF_REF
- VCF_SNP
- WCHAR_MAX
- WCHAR_MIN
- WCONTINUED
- WEXITED
- WINT_MAX
- WINT_MIN
- WNOHANG
- WNOWAIT
- WSTOPPED
- WUNTRACED
- XATTR_LIST_MAX
- XATTR_NAME_MAX
- XATTR_SIZE_MAX
- _ALLOCA_H
- _ASSERT_H
- _ATFILE_SOURCE
- _BITS_BYTESWAP_H
- _BITS_POSIX1_LIM_H
- _BITS_POSIX2_LIM_H
- _BITS_PTHREADTYPES_H
- _BITS_TYPESIZES_H
- _BITS_TYPES_H
- _BITS_WCHAR_H
- _BSD_SOURCE
- _ENDIAN_H
- _ERRNO_H
- _FEATURES_H
- _G_BUFSIZ
- _G_HAVE_ATEXIT
- _G_HAVE_BOOL
- _G_HAVE_IO_FILE_OPEN
- _G_HAVE_IO_GETLINE_INFO
- _G_HAVE_LONG_DOUBLE_IO
- _G_HAVE_MMAP
- _G_HAVE_MREMAP
- _G_HAVE_PRINTF_FP
- _G_HAVE_SYS_CDEFS
- _G_HAVE_SYS_WAIT
- _G_IO_IO_FILE_VERSION
- _G_NAMES_HAVE_UNDERSCORE
- _G_NEED_STDARG_H
- _G_USING_THUNKS
- _G_VTABLE_LABEL_HAS_LENGTH
- _G_VTABLE_LABEL_PREFIX
- _G_config_h
- _INTTYPES_H
- _IOFBF
- _IOLBF
- _IONBF
- _IOS_APPEND
- _IOS_ATEND
- _IOS_BIN
- _IOS_INPUT
- _IOS_NOCREATE
- _IOS_NOREPLACE
- _IOS_OUTPUT
- _IOS_TRUNC
- _IO_BAD_SEEN
- _IO_BOOLALPHA
- _IO_BUFSIZ
- _IO_CURRENTLY_PUTTING
- _IO_DEC
- _IO_DELETE_DONT_CLOSE
- _IO_DONT_CLOSE
- _IO_EOF_SEEN
- _IO_ERR_SEEN
- _IO_FIXED
- _IO_FLAGS2_MMAP
- _IO_FLAGS2_NOTCANCEL
- _IO_FLAGS2_USER_WBUF
- _IO_HAVE_SYS_WAIT
- _IO_HEX
- _IO_INTERNAL
- _IO_IN_BACKUP
- _IO_IS_APPENDING
- _IO_IS_FILEBUF
- _IO_LEFT
- _IO_LINE_BUF
- _IO_LINKED
- _IO_MAGIC
- _IO_MAGIC_MASK
- _IO_NO_READS
- _IO_NO_WRITES
- _IO_OCT
- _IO_RIGHT
- _IO_SCIENTIFIC
- _IO_SHOWBASE
- _IO_SHOWPOINT
- _IO_SHOWPOS
- _IO_SKIPWS
- _IO_STDIO
- _IO_TIED_PUT_GET
- _IO_UNBUFFERED
- _IO_UNIFIED_JUMPTABLES
- _IO_UNITBUF
- _IO_UPPERCASE
- _IO_USER_BUF
- _IO_USER_LOCK
- _LIBC_LIMITS_H_
- _OLD_STDIO_MAGIC
- _POSIX2_BC_BASE_MAX
- _POSIX2_BC_DIM_MAX
- _POSIX2_BC_SCALE_MAX
- _POSIX2_BC_STRING_MAX
- _POSIX2_CHARCLASS_NAME_MAX
- _POSIX2_COLL_WEIGHTS_MAX
- _POSIX2_EXPR_NEST_MAX
- _POSIX2_LINE_MAX
- _POSIX2_RE_DUP_MAX
- _POSIX_AIO_LISTIO_MAX
- _POSIX_AIO_MAX
- _POSIX_ARG_MAX
- _POSIX_CHILD_MAX
- _POSIX_CLOCKRES_MIN
- _POSIX_C_SOURCE
- _POSIX_DELAYTIMER_MAX
- _POSIX_HOST_NAME_MAX
- _POSIX_LINK_MAX
- _POSIX_LOGIN_NAME_MAX
- _POSIX_MAX_CANON
- _POSIX_MAX_INPUT
- _POSIX_MQ_OPEN_MAX
- _POSIX_MQ_PRIO_MAX
- _POSIX_NAME_MAX
- _POSIX_NGROUPS_MAX
- _POSIX_OPEN_MAX
- _POSIX_PATH_MAX
- _POSIX_PIPE_BUF
- _POSIX_RE_DUP_MAX
- _POSIX_RTSIG_MAX
- _POSIX_SEM_NSEMS_MAX
- _POSIX_SEM_VALUE_MAX
- _POSIX_SIGQUEUE_MAX
- _POSIX_SOURCE
- _POSIX_SSIZE_MAX
- _POSIX_STREAM_MAX
- _POSIX_SYMLINK_MAX
- _POSIX_SYMLOOP_MAX
- _POSIX_THREAD_DESTRUCTOR_ITERATIONS
- _POSIX_THREAD_KEYS_MAX
- _POSIX_THREAD_THREADS_MAX
- _POSIX_TIMER_MAX
- _POSIX_TTY_NAME_MAX
- _POSIX_TZNAME_MAX
- _SIGSET_H_types
- _STDINT_H
- _STDIO_H
- _STDLIB_H
- _STRING_H
- _STRUCT_TIMEVAL
- _SVID_SOURCE
- _SYS_CDEFS_H
- _SYS_SELECT_H
- _SYS_SYSMACROS_H
- _SYS_TYPES_H
- _XLOCALE_H
- __BIG_ENDIAN
- __BIT_TYPES_DEFINED__
- __BYTE_ORDER
- __FD_SETSIZE
- __FD_ZERO_STOS
- __FILE_defined
- __FLOAT_WORD_ORDER
- __GLIBC_HAVE_LONG_LONG
- __GLIBC_MINOR__
- __GLIBC__
- __GNUC_VA_LIST
- __GNU_LIBRARY__
- __LITTLE_ENDIAN
- __PDP_ENDIAN
- __PRI64_PREFIX
- __PRIPTR_PREFIX
- __PTHREAD_MUTEX_HAVE_PREV
- __SIZEOF_PTHREAD_ATTR_T
- __SIZEOF_PTHREAD_BARRIERATTR_T
- __SIZEOF_PTHREAD_BARRIER_T
- __SIZEOF_PTHREAD_CONDATTR_T
- __SIZEOF_PTHREAD_COND_T
- __SIZEOF_PTHREAD_MUTEXATTR_T
- __SIZEOF_PTHREAD_MUTEX_T
- __SIZEOF_PTHREAD_RWLOCKATTR_T
- __SIZEOF_PTHREAD_RWLOCK_T
- __STDC_IEC_559_COMPLEX__
- __STDC_IEC_559__
- __STDC_ISO_10646__
- __USE_ANSI
- __USE_ATFILE
- __USE_BSD
- __USE_FORTIFY_LEVEL
- __USE_ISOC95
- __USE_ISOC99
- __USE_MISC
- __USE_POSIX
- __USE_POSIX199309
- __USE_POSIX199506
- __USE_POSIX2
- __USE_POSIX_IMPLICITLY
- __USE_SVID
- __USE_XOPEN2K
- __USE_XOPEN2K8
- __WALL
- __WCHAR_MAX
- __WCHAR_MIN
- __WCLONE
- __WCOREFLAG
- __WNOTHREAD
- __WORDSIZE
- __WORDSIZE_COMPAT32
- __W_CONTINUED
- ____FILE_defined
- ____gwchar_t_defined
- __clock_t_defined
- __clockid_t_defined
- __codecvt_result___codecvt_error
- __codecvt_result___codecvt_noconv
- __codecvt_result___codecvt_ok
- __codecvt_result___codecvt_partial
- __ldiv_t_defined
- __lldiv_t_defined
- __mbstate_t_defined
- __time_t_defined
- __timer_t_defined
- __timespec_defined
- bcf_gt_missing
- bcf_int16_missing
- bcf_int16_vector_end
- bcf_int32_missing
- bcf_int32_vector_end
- bcf_int64_missing
- bcf_int64_vector_end
- bcf_int8_missing
- bcf_int8_vector_end
- bcf_sr_error_api_usage_error
- bcf_sr_error_bcf_read_error
- bcf_sr_error_file_type_error
- bcf_sr_error_header_error
- bcf_sr_error_idx_load_failed
- bcf_sr_error_no_eof
- bcf_sr_error_no_memory
- bcf_sr_error_not_bgzf
- bcf_sr_error_open_failed
- bcf_sr_error_vcf_parse_error
- bcf_sr_opt_t_BCF_SR_PAIR_LOGIC
- bcf_sr_opt_t_BCF_SR_REQUIRE_IDX
- bcf_str_missing
- bcf_str_vector_end
- cram_block_method_BM_ERROR
- cram_block_method_BZIP2
- cram_block_method_GZIP
- cram_block_method_GZIP_RLE
- cram_block_method_LZMA
- cram_block_method_RANS
- cram_block_method_RANS0
- cram_block_method_RANS1
- cram_block_method_RAW
- cram_content_type_COMPRESSION_HEADER
- cram_content_type_CORE
- cram_content_type_CT_ERROR
- cram_content_type_EXTERNAL
- cram_content_type_FILE_HEADER
- cram_content_type_MAPPED_SLICE
- cram_content_type_UNMAPPED_SLICE
- fai_format_options_FAI_FASTA
- fai_format_options_FAI_FASTQ
- fai_format_options_FAI_NONE
- fai_load_options_FAI_CREATE
- htsCompression_bgzf
- htsCompression_bzip2_compression
- htsCompression_compression_maximum
- htsCompression_custom
- htsCompression_gzip
- htsCompression_no_compression
- htsExactFormat_bai
- htsExactFormat_bam
- htsExactFormat_bcf
- htsExactFormat_bed
- htsExactFormat_binary_format
- htsExactFormat_crai
- htsExactFormat_cram
- htsExactFormat_csi
- htsExactFormat_empty_format
- htsExactFormat_fai_format
- htsExactFormat_fasta_format
- htsExactFormat_fastq_format
- htsExactFormat_format_maximum
- htsExactFormat_fqi_format
- htsExactFormat_gzi
- htsExactFormat_htsget
- htsExactFormat_json
- htsExactFormat_sam
- htsExactFormat_tbi
- htsExactFormat_text_format
- htsExactFormat_unknown_format
- htsExactFormat_vcf
- htsFormatCategory_category_maximum
- htsFormatCategory_index_file
- htsFormatCategory_region_list
- htsFormatCategory_sequence_data
- htsFormatCategory_unknown_category
- htsFormatCategory_variant_data
- htsLogLevel_HTS_LOG_DEBUG
- htsLogLevel_HTS_LOG_ERROR
- htsLogLevel_HTS_LOG_INFO
- htsLogLevel_HTS_LOG_OFF
- htsLogLevel_HTS_LOG_TRACE
- htsLogLevel_HTS_LOG_WARNING
- hts_fmt_option_CRAM_OPT_BASES_PER_SLICE
- hts_fmt_option_CRAM_OPT_DECODE_MD
- hts_fmt_option_CRAM_OPT_EMBED_REF
- hts_fmt_option_CRAM_OPT_IGNORE_MD5
- hts_fmt_option_CRAM_OPT_LOSSY_NAMES
- hts_fmt_option_CRAM_OPT_MULTI_SEQ_PER_SLICE
- hts_fmt_option_CRAM_OPT_NO_REF
- hts_fmt_option_CRAM_OPT_NTHREADS
- hts_fmt_option_CRAM_OPT_PREFIX
- hts_fmt_option_CRAM_OPT_RANGE
- hts_fmt_option_CRAM_OPT_REFERENCE
- hts_fmt_option_CRAM_OPT_REQUIRED_FIELDS
- hts_fmt_option_CRAM_OPT_SEQS_PER_SLICE
- hts_fmt_option_CRAM_OPT_SHARED_REF
- hts_fmt_option_CRAM_OPT_SLICES_PER_CONTAINER
- hts_fmt_option_CRAM_OPT_STORE_MD
- hts_fmt_option_CRAM_OPT_STORE_NM
- hts_fmt_option_CRAM_OPT_THREAD_POOL
- hts_fmt_option_CRAM_OPT_USE_BZIP2
- hts_fmt_option_CRAM_OPT_USE_LZMA
- hts_fmt_option_CRAM_OPT_USE_RANS
- hts_fmt_option_CRAM_OPT_VERBOSITY
- hts_fmt_option_CRAM_OPT_VERSION
- hts_fmt_option_HTS_OPT_BLOCK_SIZE
- hts_fmt_option_HTS_OPT_CACHE_SIZE
- hts_fmt_option_HTS_OPT_COMPRESSION_LEVEL
- hts_fmt_option_HTS_OPT_NTHREADS
- hts_fmt_option_HTS_OPT_THREAD_POOL
- sam_fields_SAM_AUX
- sam_fields_SAM_CIGAR
- sam_fields_SAM_FLAG
- sam_fields_SAM_MAPQ
- sam_fields_SAM_PNEXT
- sam_fields_SAM_POS
- sam_fields_SAM_QNAME
- sam_fields_SAM_QUAL
- sam_fields_SAM_RGAUX
- sam_fields_SAM_RNAME
- sam_fields_SAM_RNEXT
- sam_fields_SAM_SEQ
- sam_fields_SAM_TLEN