Docs.rs
rust-htslib-0.48.0
rust-htslib 0.48.0
Docs.rs crate page
MIT
Links
Repository
crates.io
Source
Owners
github:rust-bio:owners
christopher-schroeder
Dependencies
bio-types >=0.9
normal
byteorder ^1.3
normal
custom_derive ^0.1
normal
derive-new ^0.7
normal
hts-sys ^2.1.4
normal
ieee754 ^0.2
normal
lazy_static ^1.4
normal
libc ^0.2
normal
libz-sys >=1.1.15
normal
linear-map ^1.2
normal
newtype_derive ^0.1
normal
regex ^1.3
normal
serde ^1
normal
optional
serde_bytes ^0.11
normal
optional
thiserror ^2
normal
url ^2.1
normal
bincode ^1.2
dev
pretty_assertions ^1.4
dev
serde_json ^1.0
dev
tempfile ^3.1.0
dev
Versions
54.86%
of the crate is documented
Platform
i686-unknown-linux-gnu
x86_64-unknown-linux-gnu
Feature flags
Rust
About docs.rs
Privacy policy
Rust website
The Book
Standard Library API Reference
Rust by Example
The Cargo Guide
Clippy Documentation
rust_
htslib
0.48.0
Module htslib
Module Items
Structs
Constants
Statics
Functions
Type Aliases
Unions
In crate rust_
htslib
rust_htslib
Module
htslib
Copy item path
Source
Expand description
Re-export hts-sys htslib bindings
Structs
§
BGZF
_G_
fpos64_
t
_G_
fpos_
t
_IO_
FILE
_IO_
codecvt
_IO_
marker
_IO_
wide_
data
__
Bindgen
Bitfield
Unit
__
atomic_
wide_
counter__
bindgen_
ty_
1
__
fsid_
t
__
locale_
data
__
locale_
struct
__
mbstate_
t
__
once_
flag
__
pthread_
cond_
s
__
pthread_
internal_
list
__
pthread_
internal_
slist
__
pthread_
mutex_
s
__
pthread_
rwlock_
arch_
t
__
sigset_
t
__
va_
list_
tag
bam1_
core_
t
bam1_t
bam_
mplp_
s
bam_
pileup1_
t
bam_
plp_
s
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_
region_
t
bcf_
sr_
regions_
t
bcf_
sr_
t
bcf_
srs_
t
bcf_
variant_
t
bgzf_
cache_
t
bgzf_
mtaux_
t
bgzidx_
t
cram_
block
cram_
block_
compression_
hdr
cram_
block_
slice_
hdr
cram_
cid2ds_
t
cram_
codec
cram_
container
cram_fd
cram_
file_
def
cram_
method_
details
cram_
metrics
cram_
slice
div_t
drand48_
data
errmod_
t
faidx_t
fd_set
hFILE
htsFile
htsFormat
htsFormat__
bindgen_
ty_
1
htsThread
Pool
hts_
base_
mod
hts_
base_
mod_
state
hts_
filter_
t
hts_
idx_
t
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
random_
data
refs_t
sam_
hdr_
t
sam_
hrecs_
t
tbx_
conf_
t
tbx_t
timespec
timeval
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_
FREA
D1
BAM_
FREA
D2
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
EHWPOISON
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_
FEATURE_
BZIP2
HTS_
FEATURE_
CC
HTS_
FEATURE_
CFLAGS
HTS_
FEATURE_
CONFIGURE
HTS_
FEATURE_
CPPFLAGS
HTS_
FEATURE_
GCS
HTS_
FEATURE_
HTSCODECS
HTS_
FEATURE_
LDFLAGS
HTS_
FEATURE_
LIBCURL
HTS_
FEATURE_
LIBDEFLATE
HTS_
FEATURE_
LZMA
HTS_
FEATURE_
PLUGINS
HTS_
FEATURE_
S3
HTS_
FMT_
BAI
HTS_
FMT_
CRAI
HTS_
FMT_
CSI
HTS_
FMT_
FAI
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_
MOD_
REPORT_
UNCHECKED
HTS_
MOD_
UNCHECKED
HTS_
MOD_
UNKNOWN
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_
LEAS
T8_
MAX
INT_
LEAS
T8_
MIN
INT_
LEAS
T16_
MAX
INT_
LEAS
T16_
MIN
INT_
LEAS
T32_
MAX
INT_
LEAS
T32_
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
PRIXFAS
T8
PRIXFAS
T16
PRIXFAS
T32
PRIXFAS
T64
PRIXLEAS
T8
PRIXLEAS
T16
PRIXLEAS
T32
PRIXLEAS
T64
PRIXMAX
PRIXPTR
PRId8
PRId16
PRId32
PRId64
PRIdFAS
T8
PRIdFAS
T16
PRIdFAS
T32
PRIdFAS
T64
PRIdLEAS
T8
PRIdLEAS
T16
PRIdLEAS
T32
PRIdLEAS
T64
PRIdMAX
PRIdPTR
PRIhts_
pos
PRIi8
PRIi16
PRIi32
PRIi64
PRIiFAS
T8
PRIiFAS
T16
PRIiFAS
T32
PRIiFAS
T64
PRIiLEAS
T8
PRIiLEAS
T16
PRIiLEAS
T32
PRIiLEAS
T64
PRIiMAX
PRIiPTR
PRIo8
PRIo16
PRIo32
PRIo64
PRIoFAS
T8
PRIoFAS
T16
PRIoFAS
T32
PRIoFAS
T64
PRIoLEAS
T8
PRIoLEAS
T16
PRIoLEAS
T32
PRIoLEAS
T64
PRIoMAX
PRIoPTR
PRIu8
PRIu16
PRIu32
PRIu64
PRIuFAS
T8
PRIuFAS
T16
PRIuFAS
T32
PRIuFAS
T64
PRIuLEAS
T8
PRIuLEAS
T16
PRIuLEAS
T32
PRIuLEAS
T64
PRIuMAX
PRIuPTR
PRIx8
PRIx16
PRIx32
PRIx64
PRIxFAS
T8
PRIxFAS
T16
PRIxFAS
T32
PRIxFAS
T64
PRIxLEAS
T8
PRIxLEAS
T16
PRIxLEAS
T32
PRIxLEAS
T64
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
SCNdFAS
T8
SCNdFAS
T16
SCNdFAS
T32
SCNdFAS
T64
SCNdLEAS
T8
SCNdLEAS
T16
SCNdLEAS
T32
SCNdLEAS
T64
SCNdMAX
SCNdPTR
SCNi8
SCNi16
SCNi32
SCNi64
SCNiFAS
T8
SCNiFAS
T16
SCNiFAS
T32
SCNiFAS
T64
SCNiLEAS
T8
SCNiLEAS
T16
SCNiLEAS
T32
SCNiLEAS
T64
SCNiMAX
SCNiPTR
SCNo8
SCNo16
SCNo32
SCNo64
SCNoFAS
T8
SCNoFAS
T16
SCNoFAS
T32
SCNoFAS
T64
SCNoLEAS
T8
SCNoLEAS
T16
SCNoLEAS
T32
SCNoLEAS
T64
SCNoMAX
SCNoPTR
SCNu8
SCNu16
SCNu32
SCNu64
SCNuFAS
T8
SCNuFAS
T16
SCNuFAS
T32
SCNuFAS
T64
SCNuLEAS
T8
SCNuLEAS
T16
SCNuLEAS
T32
SCNuLEAS
T64
SCNuMAX
SCNuPTR
SCNx8
SCNx16
SCNx32
SCNx64
SCNxFAS
T8
SCNxFAS
T16
SCNxFAS
T32
SCNxFAS
T64
SCNxLEAS
T8
SCNxLEAS
T16
SCNxLEAS
T32
SCNxLEAS
T64
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_
LEAS
T8_
MAX
UINT_
LEAS
T16_
MAX
UINT_
LEAS
T32_
MAX
VCF_ANY
VCF_BND
VCF_DEL
VCF_
INDEL
VCF_INS
VCF_MNP
VCF_
OTHER
VCF_
OVERLAP
VCF_REF
VCF_SNP
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_
ENDIANNESS_
H
_BITS_
ENDIAN_
H
_BITS_
ERRNO_
H
_BITS_
POSI
X1_
LIM_
H
_BITS_
POSI
X2_
LIM_
H
_BITS_
PTHREADTYPES_
ARCH_
H
_BITS_
PTHREADTYPES_
COMMON_
H
_BITS_
STDINT_
INTN_
H
_BITS_
STDINT_
UINTN_
H
_BITS_
STDIO_
LIM_
H
_BITS_
TIME64_
H
_BITS_
TYPESIZES_
H
_BITS_
TYPES_
H
_BITS_
TYPES_
LOCALE_
T_
H
_BITS_
TYPES___
LOCALE_
T_
H
_BITS_
UINTN_
IDENTITY_
H
_BITS_
WCHAR_
H
_DEFAULT_
SOURCE
_ENDIAN_
H
_ERRNO_
H
_FEATURES_
H
_INTTYPES_
H
_IOFBF
_IOLBF
_IONBF
_IO_
EOF_
SEEN
_IO_
ERR_
SEEN
_IO_
USER_
LOCK
_LIBC_
LIMITS_
H_
_POSI
X2_
BC_
BASE_
MAX
_POSI
X2_
BC_
DIM_
MAX
_POSI
X2_
BC_
SCALE_
MAX
_POSI
X2_
BC_
STRING_
MAX
_POSI
X2_
CHARCLASS_
NAME_
MAX
_POSI
X2_
COLL_
WEIGHTS_
MAX
_POSI
X2_
EXPR_
NEST_
MAX
_POSI
X2_
LINE_
MAX
_POSI
X2_
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
_STDC_
PREDEF_
H
_STDINT_
H
_STDIO_
H
_STDLIB_
H
_STRINGS_
H
_STRING_
H
_STRUCT_
TIMESPEC
_SYS_
CDEFS_
H
_SYS_
SELECT_
H
_SYS_
TYPES_
H
_THREAD_
MUTEX_
INTERNAL_
H
_THREAD_
SHARED_
TYPES_
H
__
BIG_
ENDIAN
__
BIT_
TYPES_
DEFINED__
__
BYTE_
ORDER
__
FD_
SETSIZE
__
FILE_
defined
__
FLOAT_
WORD_
ORDER
__
GLIBC_
MINOR__
__
GLIBC_
USE_
DEPRECATED_
GETS
__
GLIBC_
USE_
DEPRECATED_
SCANF
__
GLIBC_
USE_
IEC_
60559_
BFP_
EXT
__
GLIBC_
USE_
IEC_
60559_
BFP_
EXT_
C2X
__
GLIBC_
USE_
IEC_
60559_
EXT
__
GLIBC_
USE_
IEC_
60559_
FUNCS_
EXT
__
GLIBC_
USE_
IEC_
60559_
FUNCS_
EXT_
C2X
__
GLIBC_
USE_
IEC_
60559_
TYPES_
EXT
__
GLIBC_
USE_
ISOC2X
__
GLIBC_
USE_
LIB_
EXT2
__
GLIBC__
__
GNUC_
VA_
LIST
__
GNU_
LIBRARY__
__
HAVE_
DISTINCT_
FLOA
T16
__
HAVE_
DISTINCT_
FLOA
T32
__
HAVE_
DISTINCT_
FLOA
T64
__
HAVE_
DISTINCT_
FLOA
T32X
__
HAVE_
DISTINCT_
FLOA
T64X
__
HAVE_
DISTINCT_
FLOA
T128
__
HAVE_
DISTINCT_
FLOA
T128X
__
HAVE_
FLOA
T16
__
HAVE_
FLOA
T32
__
HAVE_
FLOA
T64
__
HAVE_
FLOA
T32X
__
HAVE_
FLOA
T64X
__
HAVE_
FLOA
T64X_
LONG_
DOUBLE
__
HAVE_
FLOA
T128
__
HAVE_
FLOA
T128X
__
HAVE_
FLOATN_
NOT_
TYPEDEF
__
HAVE_
GENERIC_
SELECTION
__
INO_
T_
MATCHES_
INO64_
T
__
KERNEL_
OLD_
TIMEVAL_
MATCHES_
TIMEVA
L64
__
LDOUBLE_
REDIRECTS_
TO_
FLOA
T128_
ABI
__
LITTLE_
ENDIAN
__
OFF_
T_
MATCHES_
OFF64_
T
__
PDP_
ENDIAN
__
PRI64_
PREFIX
__
PRIPTR_
PREFIX
__
PTHREAD_
MUTEX_
HAVE_
PREV
__
RLIM_
T_
MATCHES_
RLIM64_
T
__
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
__
STATFS_
MATCHES_
STATF
S64
__
STDC_
IEC_
559_
COMPLEX__
__
STDC_
IEC_
559__
__
STDC_
IEC_
60559_
BFP__
__
STDC_
IEC_
60559_
COMPLEX__
__
STDC_
ISO_
10646__
__
SYSCALL_
WORDSIZE
__
TIMESIZE
__
USE_
ATFILE
__
USE_
FORTIFY_
LEVEL
__
USE_
ISOC11
__
USE_
ISOC95
__
USE_
ISOC99
__
USE_
MISC
__
USE_
POSIX
__
USE_
POSI
X2
__
USE_
POSI
X199309
__
USE_
POSI
X199506
__
USE_
POSIX_
IMPLICITLY
__
USE_
XOPE
N2K
__
USE_
XOPE
N2K8
__WALL
__
WCLONE
__
WCOREFLAG
__
WNOTHREAD
__
WORDSIZE
__
WORDSIZE_
TIME64_
COMPA
T32
__
W_
CONTINUED
____
FILE_
defined
_____
fpos64_
t_
defined
_____
fpos_
t_
defined
____
gwchar_
t_
defined
____
mbstate_
t_
defined
__
clock_
t_
defined
__
clockid_
t_
defined
__
glibc_
c99_
flexarr_
available
__
have_
pthread_
attr_
t
__
ldiv_
t_
defined
__
lldiv_
t_
defined
__
sigset_
t_
defined
__
struct_
FILE_
defined
__
time_
t_
defined
__
timer_
t_
defined
__
timeval_
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_
noidx_
error
bcf_
sr_
error_
not_
bgzf
bcf_
sr_
error_
open_
failed
bcf_
sr_
error_
vcf_
parse_
error
bcf_
sr_
opt_
t_
BCF_
SR_
ALLOW_
NO_
IDX
bcf_
sr_
opt_
t_
BCF_
SR_
PAIR_
LOGIC
bcf_
sr_
opt_
t_
BCF_
SR_
REGIONS_
OVERLAP
bcf_
sr_
opt_
t_
BCF_
SR_
REQUIRE_
IDX
bcf_
sr_
opt_
t_
BCF_
SR_
TARGETS_
OVERLAP
bcf_
str_
missing
bcf_
str_
vector_
end
bcf_
variant_
match_
bcf_
match_
exact
bcf_
variant_
match_
bcf_
match_
overlap
bcf_
variant_
match_
bcf_
match_
subset
cram_
block_
method_
CRAM_
COMP_
ARITH
cram_
block_
method_
CRAM_
COMP_
BZIP2
cram_
block_
method_
CRAM_
COMP_
FQZ
cram_
block_
method_
CRAM_
COMP_
GZIP
cram_
block_
method_
CRAM_
COMP_
LZMA
cram_
block_
method_
CRAM_
COMP_
RANS4x8
cram_
block_
method_
CRAM_
COMP_
RANS
Nx16
cram_
block_
method_
CRAM_
COMP_
RAW
cram_
block_
method_
CRAM_
COMP_
TOK3
cram_
block_
method_
CRAM_
COMP_
UNKNOWN
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
htsCompression_
razf_
compression
htsCompression_
xz_
compression
htsCompression_
zstd_
compression
htsExact
Format_
bai
htsExact
Format_
bam
htsExact
Format_
bcf
htsExact
Format_
bed
htsExact
Format_
binary_
format
htsExact
Format_
crai
htsExact
Format_
cram
htsExact
Format_
csi
htsExact
Format_
d4_
format
htsExact
Format_
empty_
format
htsExact
Format_
fai_
format
htsExact
Format_
fasta_
format
htsExact
Format_
fastq_
format
htsExact
Format_
format_
maximum
htsExact
Format_
fqi_
format
htsExact
Format_
gzi
htsExact
Format_
hts_
crypt4gh_
format
htsExact
Format_
htsget
htsExact
Format_
json
htsExact
Format_
sam
htsExact
Format_
tbi
htsExact
Format_
text_
format
htsExact
Format_
unknown_
format
htsExact
Format_
vcf
htsFormat
Category_
category_
maximum
htsFormat
Category_
index_
file
htsFormat
Category_
region_
list
htsFormat
Category_
sequence_
data
htsFormat
Category_
unknown_
category
htsFormat
Category_
variant_
data
htsLog
Level_
HTS_
LOG_
DEBUG
htsLog
Level_
HTS_
LOG_
ERROR
htsLog
Level_
HTS_
LOG_
INFO
htsLog
Level_
HTS_
LOG_
OFF
htsLog
Level_
HTS_
LOG_
TRACE
htsLog
Level_
HTS_
LOG_
WARNING
htsRealn
Flags_
BAQ_
APPLY
htsRealn
Flags_
BAQ_
AUTO
htsRealn
Flags_
BAQ_
EXTEND
htsRealn
Flags_
BAQ_
GENAPSYS
htsRealn
Flags_
BAQ_
ILLUMINA
htsRealn
Flags_
BAQ_
ONT
htsRealn
Flags_
BAQ_
PACBIO
htsRealn
Flags_
BAQ_
PACBIOCCS
htsRealn
Flags_
BAQ_
REDO
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_
POS_
DELTA
hts_
fmt_
option_
CRAM_
OPT_
PREFIX
hts_
fmt_
option_
CRAM_
OPT_
RANGE
hts_
fmt_
option_
CRAM_
OPT_
RANGE_
NOSEEK
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_
ARITH
hts_
fmt_
option_
CRAM_
OPT_
USE_
BZIP2
hts_
fmt_
option_
CRAM_
OPT_
USE_
FQZ
hts_
fmt_
option_
CRAM_
OPT_
USE_
LZMA
hts_
fmt_
option_
CRAM_
OPT_
USE_
RANS
hts_
fmt_
option_
CRAM_
OPT_
USE_
TOK
hts_
fmt_
option_
CRAM_
OPT_
VERBOSITY
hts_
fmt_
option_
CRAM_
OPT_
VERSION
hts_
fmt_
option_
FASTQ_
OPT_
AUX
hts_
fmt_
option_
FASTQ_
OPT_
BARCODE
hts_
fmt_
option_
FASTQ_
OPT_
CASAVA
hts_
fmt_
option_
FASTQ_
OPT_
NAME2
hts_
fmt_
option_
FASTQ_
OPT_
RNUM
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_
FILTER
hts_
fmt_
option_
HTS_
OPT_
NTHREADS
hts_
fmt_
option_
HTS_
OPT_
PROFILE
hts_
fmt_
option_
HTS_
OPT_
THREAD_
POOL
hts_
profile_
option_
HTS_
PROFILE_
ARCHIVE
hts_
profile_
option_
HTS_
PROFILE_
FAST
hts_
profile_
option_
HTS_
PROFILE_
NORMAL
hts_
profile_
option_
HTS_
PROFILE_
SMALL
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
§
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
tbx_
conf_
bed
tbx_
conf_
gff
tbx_
conf_
psltbl
tbx_
conf_
sam
tbx_
conf_
vcf
Functions
§
_Exit
⚠
__
assert
⚠
__
assert_
fail
⚠
__
assert_
perror_
fail
⚠
__
ctype_
get_
mb_
cur_
max
⚠
__
errno_
location
⚠
__
getdelim
⚠
__
memcmpeq
⚠
__
overflow
⚠
__
stpcpy
⚠
__
stpncpy
⚠
__
strtok_
r
⚠
__uflow
⚠
a64l
⚠
abort
⚠
abs
⚠
aligned_
alloc
⚠
alloca
⚠
at_
quick_
exit
⚠
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_
first
⚠
bam_
aux_
get
⚠
bam_
aux_
next
⚠
bam_
aux_
remove
⚠
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_
queryi
⚠
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_
parse_
basemod2
⚠
bam_
parse_
cigar
⚠
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_
insertion_
mod
⚠
bam_
plp_
next
⚠
bam_
plp_
push
⚠
bam_
plp_
reset
⚠
bam_
plp_
set_
maxcnt
⚠
bam_
read1
⚠
bam_
set1
⚠
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_
has_
variant_
type
⚠
bcf_
has_
variant_
types
⚠
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_
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_
variant_
length
⚠
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
⚠
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_
method
⚠
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_
cid2ds_
free
⚠
cram_
cid2ds_
query
⚠
cram_
close
⚠
cram_
codec_
describe
⚠
cram_
codec_
get_
content_
ids
⚠
cram_
compress_
block
⚠
cram_
compress_
block2
⚠
cram_
container_
get_
landmarks
⚠
cram_
container_
get_
length
⚠
cram_
container_
get_
num_
bases
⚠
cram_
container_
get_
num_
blocks
⚠
cram_
container_
get_
num_
records
⚠
cram_
container_
is_
empty
⚠
cram_
container_
set_
landmarks
⚠
cram_
container_
set_
length
⚠
cram_
container_
set_
num_
blocks
⚠
cram_
container_
size
⚠
cram_
copy_
slice
⚠
cram_
decode_
compression_
header
⚠
cram_
decode_
slice_
header
⚠
cram_
describe_
encodings
⚠
cram_
dopen
⚠
cram_
eof
⚠
cram_
expand_
method
⚠
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_
compression_
header
⚠
cram_
free_
container
⚠
cram_
free_
slice_
header
⚠
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_
slice_
hdr_
get_
coords
⚠
cram_
slice_
hdr_
get_
embed_
ref_
id
⚠
cram_
slice_
hdr_
get_
num_
blocks
⚠
cram_
store_
container
⚠
cram_
transcode_
rg
⚠
cram_
uncompress_
block
⚠
cram_
update_
cid2ds_
map
⚠
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
⚠
explicit_
bzero
⚠
fai_
adjust_
region
⚠
fai_
build
⚠
fai_
build3
⚠
fai_
destroy
⚠
fai_
fetch
⚠
fai_
fetch64
⚠
fai_
fetchqual
⚠
fai_
fetchqual64
⚠
fai_
line_
length
⚠
fai_
load
⚠
fai_
load3
⚠
fai_
load3_
format
⚠
fai_
load_
format
⚠
fai_
parse_
region
⚠
fai_
path
⚠
fai_
set_
cache_
size
⚠
fai_
thread_
pool
⚠
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
⚠
faidx_
seq_
len64
⚠
fclose
⚠
fcvt
⚠
fcvt_r
⚠
fdopen
⚠
feof
⚠
feof_
unlocked
⚠
ferror
⚠
ferror_
unlocked
⚠
fflush
⚠
fflush_
unlocked
⚠
ffs
⚠
ffsl
⚠
ffsll
⚠
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
⚠
getsubopt
⚠
getw
⚠
hrec_
add_
idx
⚠
hts_
base_
mod_
state_
alloc
⚠
hts_
base_
mod_
state_
free
⚠
hts_
check_
EOF
⚠
hts_
close
⚠
hts_
detect_
format
⚠
hts_
detect_
format2
⚠
hts_
feature_
string
⚠
hts_
features
⚠
hts_
file_
type
⚠
hts_
flush
⚠
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_
nseq
⚠
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_
lib_
shutdown
⚠
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_
filter_
expression
⚠
hts_
set_
log_
level
⚠
hts_
set_
opt
⚠
hts_
set_
thread_
pool
⚠
hts_
set_
threads
⚠
hts_
test_
feature
⚠
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_
is_
shutdown
⚠
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
⚠
quick_
exit
⚠
rand
⚠
rand_r
⚠
random
⚠
random_
r
⚠
realloc
⚠
reallocarray
⚠
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_
cigar
⚠
sam_
parse_
region
⚠
sam_
passes_
filter
⚠
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
⚠
strcasecmp_
l
⚠
strcat
⚠
strchr
⚠
strcmp
⚠
strcoll
⚠
strcoll_
l
⚠
strcpy
⚠
strcspn
⚠
strdup
⚠
strerror
⚠
strerror_
l
⚠
strerror_
r
⚠
stringify_
argv
⚠
strlen
⚠
strncasecmp
⚠
strncasecmp_
l
⚠
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_
open_
mode
⚠
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
_Float32
_Float64
_Float32x
_Float64x
_IO_
lock_
t
__FILE
__
blkcnt64_
t
__
blkcnt_
t
__
blksize_
t
__
builtin_
va_
list
__
caddr_
t
__
clock_
t
__
clockid_
t
__
compar_
fn_
t
__
daddr_
t
__dev_t
__
fd_
mask
__
fpos64_
t
__
fpos_
t
__
fsblkcnt64_
t
__
fsblkcnt_
t
__
fsfilcnt64_
t
__
fsfilcnt_
t
__
fsword_
t
__gid_t
__
gnuc_
va_
list
__
gwchar_
t
__id_t
__
ino64_
t
__ino_t
__
int8_
t
__
int16_
t
__
int32_
t
__
int64_
t
__
int_
least8_
t
__
int_
least16_
t
__
int_
least32_
t
__
int_
least64_
t
__
intmax_
t
__
intptr_
t
__key_t
__
locale_
t
__
loff_
t
__
mode_
t
__
nlink_
t
__
off64_
t
__off_t
__pid_t
__
pthread_
list_
t
__
pthread_
slist_
t
__
quad_
t
__
rlim64_
t
__
rlim_
t
__
sig_
atomic_
t
__
socklen_
t
__
ssize_
t
__
suseconds64_
t
__
suseconds_
t
__
syscall_
slong_
t
__
syscall_
ulong_
t
__
thrd_
t
__
time_
t
__
timer_
t
__tss_t
__
u_
char
__u_int
__
u_
long
__
u_
quad_
t
__
u_
short
__uid_t
__
uint8_
t
__
uint16_
t
__
uint32_
t
__
uint64_
t
__
uint_
least8_
t
__
uint_
least16_
t
__
uint_
least32_
t
__
uint_
least64_
t
__
uintmax_
t
__
useconds_
t
bam_
hdr_
t
bam_
mplp_
t
bam_
plp_
auto_
f
bam_
plp_
t
bcf_
sr_
error
bcf_
sr_
opt_
t
bcf_
variant_
match
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
fd_mask
fpos_t
fsblkcnt_
t
fsfilcnt_
t
fsid_t
gid_t
htsCompression
htsExact
Format
htsFormat
Category
htsLog
Level
htsRealn
Flags
hts_
fmt_
option
hts_
id2name_
f
hts_
itr_
multi_
query_
func
hts_
itr_
multi_
t
hts_
itr_
query_
func
hts_
name2id_
f
hts_
pair32_
t
hts_
pos_
t
hts_
profile_
option
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
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
§
__
atomic_
wide_
counter
__
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