Crate hts_sys

This module exposes the raw Htslib bindings.

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_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

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_INT8
BCF_BT_INT16
BCF_BT_INT32
BCF_BT_INT64
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_INT8
BCF_MAX_BT_INT16
BCF_MAX_BT_INT32
BCF_MIN_BT_INT8
BCF_MIN_BT_INT16
BCF_MIN_BT_INT32
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
INT8_MAX
INT8_MIN
INT16_MAX
INT16_MIN
INT32_MAX
INT32_MIN
INTPTR_MAX
INTPTR_MIN
INT_FAST8_MAX
INT_FAST8_MIN
INT_FAST16_MAX
INT_FAST16_MIN
INT_FAST32_MAX
INT_FAST32_MIN
INT_LEAST8_MAX
INT_LEAST8_MIN
INT_LEAST16_MAX
INT_LEAST16_MIN
INT_LEAST32_MAX
INT_LEAST32_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
PRIX8
PRIX16
PRIX32
PRIX64
PRIXFAST8
PRIXFAST16
PRIXFAST32
PRIXFAST64
PRIXLEAST8
PRIXLEAST16
PRIXLEAST32
PRIXLEAST64
PRIXMAX
PRIXPTR
PRId8
PRId16
PRId32
PRId64
PRIdFAST8
PRIdFAST16
PRIdFAST32
PRIdFAST64
PRIdLEAST8
PRIdLEAST16
PRIdLEAST32
PRIdLEAST64
PRIdMAX
PRIdPTR
PRIhts_pos
PRIi8
PRIi16
PRIi32
PRIi64
PRIiFAST8
PRIiFAST16
PRIiFAST32
PRIiFAST64
PRIiLEAST8
PRIiLEAST16
PRIiLEAST32
PRIiLEAST64
PRIiMAX
PRIiPTR
PRIo8
PRIo16
PRIo32
PRIo64
PRIoFAST8
PRIoFAST16
PRIoFAST32
PRIoFAST64
PRIoLEAST8
PRIoLEAST16
PRIoLEAST32
PRIoLEAST64
PRIoMAX
PRIoPTR
PRIu8
PRIu16
PRIu32
PRIu64
PRIuFAST8
PRIuFAST16
PRIuFAST32
PRIuFAST64
PRIuLEAST8
PRIuLEAST16
PRIuLEAST32
PRIuLEAST64
PRIuMAX
PRIuPTR
PRIx8
PRIx16
PRIx32
PRIx64
PRIxFAST8
PRIxFAST16
PRIxFAST32
PRIxFAST64
PRIxLEAST8
PRIxLEAST16
PRIxLEAST32
PRIxLEAST64
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
SCNd8
SCNd16
SCNd32
SCNd64
SCNdFAST8
SCNdFAST16
SCNdFAST32
SCNdFAST64
SCNdLEAST8
SCNdLEAST16
SCNdLEAST32
SCNdLEAST64
SCNdMAX
SCNdPTR
SCNi8
SCNi16
SCNi32
SCNi64
SCNiFAST8
SCNiFAST16
SCNiFAST32
SCNiFAST64
SCNiLEAST8
SCNiLEAST16
SCNiLEAST32
SCNiLEAST64
SCNiMAX
SCNiPTR
SCNo8
SCNo16
SCNo32
SCNo64
SCNoFAST8
SCNoFAST16
SCNoFAST32
SCNoFAST64
SCNoLEAST8
SCNoLEAST16
SCNoLEAST32
SCNoLEAST64
SCNoMAX
SCNoPTR
SCNu8
SCNu16
SCNu32
SCNu64
SCNuFAST8
SCNuFAST16
SCNuFAST32
SCNuFAST64
SCNuLEAST8
SCNuLEAST16
SCNuLEAST32
SCNuLEAST64
SCNuMAX
SCNuPTR
SCNx8
SCNx16
SCNx32
SCNx64
SCNxFAST8
SCNxFAST16
SCNxFAST32
SCNxFAST64
SCNxLEAST8
SCNxLEAST16
SCNxLEAST32
SCNxLEAST64
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
UINT8_MAX
UINT16_MAX
UINT32_MAX
UINTPTR_MAX
UINT_FAST8_MAX
UINT_FAST16_MAX
UINT_FAST32_MAX
UINT_LEAST8_MAX
UINT_LEAST16_MAX
UINT_LEAST32_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_POSIX2
__USE_POSIX199309
__USE_POSIX199506
__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_int8_missing
bcf_int8_vector_end
bcf_int16_missing
bcf_int16_vector_end
bcf_int32_missing
bcf_int32_vector_end
bcf_int64_missing
bcf_int64_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

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

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_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_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_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 Definitions

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
__int8_t
__int16_t
__int32_t
__int64_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
__uint8_t
__uint16_t
__uint32_t
__uint64_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_fast8_t
int_fast16_t
int_fast32_t
int_fast64_t
int_least8_t
int_least16_t
int_least32_t
int_least64_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_int8_t
u_int16_t
u_int32_t
u_int64_t
u_long
u_quad_t
u_short
uid_t
uint
uint16_u
uint32_u
uint64_u
uint_fast8_t
uint_fast16_t
uint_fast32_t
uint_fast64_t
uint_least8_t
uint_least16_t
uint_least32_t
uint_least64_t
uintmax_t
ulong
ushort
va_list
vcfFile
wchar_t

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