Module rust_htslib::htslib

This module exposes the raw Htslib bindings.

Structs

BGZF
SAM_hdr
_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
__fsid_t
__hts_idx_t
__kstring_t
__locale_data
__locale_struct
__mbstate_t
__pthread_cond_s
__pthread_cond_s__bindgen_ty_1__bindgen_ty_1
__pthread_cond_s__bindgen_ty_2__bindgen_ty_1
__pthread_internal_list
__pthread_mutex_s
__pthread_rwlock_arch_t
__sigset_t
__va_list_tag
_bcf_sr_regions_t
_region_t
aux_key_t
bam1_core_t
bam1_t
bam_hdr_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
gzFile_s
gz_header_s
hFILE
htsFile
htsFormat
htsFormat__bindgen_ty_1
htsThreadPool
hts_itr_multi_t
hts_itr_t
hts_itr_t__bindgen_ty_1
hts_md5_context
hts_opt
hts_pair32_t
hts_pair64_t
hts_pair64_max_t
hts_reglist_t
hts_tpool
internal_state
kbitset_iter_t
kbitset_t
ks_tokaux_t
ldiv_t
lldiv_t
probaln_par_t
random_data
refs_t
tbx_conf_t
tbx_t
timespec
timeval
variant_t
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
BCF1_DIRTY_ID
BCF1_DIRTY_ALS
BCF1_DIRTY_FLT
BCF1_DIRTY_INF
BCF_BT_CHAR
BCF_BT_FLOAT
BCF_BT_INT8
BCF_BT_INT16
BCF_BT_INT32
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_REAL
BCF_HT_STR
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
EOF
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
F_LOCK
F_OK
F_TEST
F_TLOCK
F_ULOCK
GT_HAPL_A
GT_HAPL_R
GT_HET_AA
GT_HET_RA
GT_HOM_AA
GT_HOM_RR
GT_UNKN
HOST_NAME_MAX
HTS_ALLOW_UNALIGNED
HTS_FMT_BAI
HTS_FMT_CRAI
HTS_FMT_CSI
HTS_FMT_TBI
HTS_IDX_NOCOOR
HTS_IDX_NONE
HTS_IDX_REST
HTS_IDX_START
HTS_PARSE_THOUSANDS_SEP
INT8_MIN
INT8_MAX
INT16_MIN
INT16_MAX
INT32_MIN
INT32_MAX
INTPTR_MAX
INTPTR_MIN
INT_FAST8_MIN
INT_FAST8_MAX
INT_FAST16_MIN
INT_FAST16_MAX
INT_FAST32_MIN
INT_FAST32_MAX
INT_LEAST8_MIN
INT_LEAST8_MAX
INT_LEAST16_MIN
INT_LEAST16_MAX
INT_LEAST32_MIN
INT_LEAST32_MAX
LINE_MAX
LINK_MAX
LITTLE_ENDIAN
LOGIN_NAME_MAX
L_INCR
L_SET
L_XTND
L_ctermid
L_tmpnam
MAX_CANON
MAX_INPUT
MAX_MEM_LEVEL
MAX_WBITS
MB_LEN_MAX
MQ_PRIO_MAX
NAME_MAX
NGROUPS_MAX
NR_OPEN
PATH_MAX
PDP_ENDIAN
PIPE_BUF
PTHREAD_DESTRUCTOR_ITERATIONS
PTHREAD_KEYS_MAX
PTHREAD_STACK_MIN
PTRDIFF_MAX
PTRDIFF_MIN
P_tmpdir
RAND_MAX
RE_DUP_MAX
RTSIG_MAX
R_OK
SAM_FORMAT_VERSION
SEEK_CUR
SEEK_END
SEEK_SET
SEM_VALUE_MAX
SIG_ATOMIC_MAX
SIG_ATOMIC_MIN
SIZE_MAX
STDERR_FILENO
STDIN_FILENO
STDOUT_FILENO
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_REF
VCF_SNP
WCONTINUED
WEXITED
WINT_MAX
WINT_MIN
WNOHANG
WNOWAIT
WSTOPPED
WUNTRACED
W_OK
XATTR_LIST_MAX
XATTR_NAME_MAX
XATTR_SIZE_MAX
X_OK
ZLIB_VERNUM
ZLIB_VERSION
ZLIB_VER_MAJOR
ZLIB_VER_MINOR
ZLIB_VER_REVISION
ZLIB_VER_SUBREVISION
Z_ASCII
Z_BEST_COMPRESSION
Z_BEST_SPEED
Z_BINARY
Z_BLOCK
Z_BUF_ERROR
Z_DATA_ERROR
Z_DEFAULT_COMPRESSION
Z_DEFAULT_STRATEGY
Z_DEFLATED
Z_ERRNO
Z_FILTERED
Z_FINISH
Z_FIXED
Z_FULL_FLUSH
Z_HUFFMAN_ONLY
Z_MEM_ERROR
Z_NEED_DICT
Z_NO_COMPRESSION
Z_NO_FLUSH
Z_NULL
Z_OK
Z_PARTIAL_FLUSH
Z_RLE
Z_STREAM_END
Z_STREAM_ERROR
Z_SYNC_FLUSH
Z_TEXT
Z_TREES
Z_UNKNOWN
Z_VERSION_ERROR
_ALLOCA_H
_ASSERT_H
_ATFILE_SOURCE
_BITS_BYTESWAP_H
_BITS_G_CONFIG_H
_BITS_LIBIO_H
_BITS_POSIX1_LIM_H
_BITS_POSIX2_LIM_H
_BITS_POSIX_OPT_H
_BITS_PTHREADTYPES_ARCH_H
_BITS_PTHREADTYPES_COMMON_H
_BITS_STDINT_INTN_H
_BITS_STDINT_UINTN_H
_BITS_STDIO_LIM_H
_BITS_SYSMACROS_H
_BITS_TYPESIZES_H
_BITS_TYPES_H
_BITS_TYPES_LOCALE_T_H
_BITS_TYPES___LOCALE_T_H
_BITS_UINTN_IDENTITY_H
_BITS_WCHAR_H
_CS_GNU_LIBC_VERSION
_CS_GNU_LIBPTHREAD_VERSION
_CS_LFS64_CFLAGS
_CS_LFS64_LDFLAGS
_CS_LFS64_LIBS
_CS_LFS64_LINTFLAGS
_CS_LFS_CFLAGS
_CS_LFS_LDFLAGS
_CS_LFS_LIBS
_CS_LFS_LINTFLAGS
_CS_PATH
_CS_POSIX_V6_LPBIG_OFFBIG_CFLAGS
_CS_POSIX_V6_LPBIG_OFFBIG_LDFLAGS
_CS_POSIX_V6_LPBIG_OFFBIG_LIBS
_CS_POSIX_V6_LPBIG_OFFBIG_LINTFLAGS
_CS_POSIX_V7_LPBIG_OFFBIG_CFLAGS
_CS_POSIX_V7_LPBIG_OFFBIG_LDFLAGS
_CS_POSIX_V7_LPBIG_OFFBIG_LIBS
_CS_POSIX_V7_LPBIG_OFFBIG_LINTFLAGS
_CS_POSIX_V6_ILP32_OFFBIG_CFLAGS
_CS_POSIX_V6_ILP32_OFFBIG_LDFLAGS
_CS_POSIX_V6_ILP32_OFFBIG_LIBS
_CS_POSIX_V6_ILP32_OFFBIG_LINTFLAGS
_CS_POSIX_V6_ILP32_OFF32_CFLAGS
_CS_POSIX_V6_ILP32_OFF32_LDFLAGS
_CS_POSIX_V6_ILP32_OFF32_LIBS
_CS_POSIX_V6_ILP32_OFF32_LINTFLAGS
_CS_POSIX_V6_LP64_OFF64_CFLAGS
_CS_POSIX_V6_LP64_OFF64_LDFLAGS
_CS_POSIX_V6_LP64_OFF64_LIBS
_CS_POSIX_V6_LP64_OFF64_LINTFLAGS
_CS_POSIX_V7_ILP32_OFFBIG_CFLAGS
_CS_POSIX_V7_ILP32_OFFBIG_LDFLAGS
_CS_POSIX_V7_ILP32_OFFBIG_LIBS
_CS_POSIX_V7_ILP32_OFFBIG_LINTFLAGS
_CS_POSIX_V7_ILP32_OFF32_CFLAGS
_CS_POSIX_V7_ILP32_OFF32_LDFLAGS
_CS_POSIX_V7_ILP32_OFF32_LIBS
_CS_POSIX_V7_ILP32_OFF32_LINTFLAGS
_CS_POSIX_V7_LP64_OFF64_CFLAGS
_CS_POSIX_V7_LP64_OFF64_LDFLAGS
_CS_POSIX_V7_LP64_OFF64_LIBS
_CS_POSIX_V7_LP64_OFF64_LINTFLAGS
_CS_V5_WIDTH_RESTRICTED_ENVS
_CS_V6_WIDTH_RESTRICTED_ENVS
_CS_V6_ENV
_CS_V7_WIDTH_RESTRICTED_ENVS
_CS_V7_ENV
_CS_XBS5_LPBIG_OFFBIG_CFLAGS
_CS_XBS5_LPBIG_OFFBIG_LDFLAGS
_CS_XBS5_LPBIG_OFFBIG_LIBS
_CS_XBS5_LPBIG_OFFBIG_LINTFLAGS
_CS_XBS5_ILP32_OFFBIG_CFLAGS
_CS_XBS5_ILP32_OFFBIG_LDFLAGS
_CS_XBS5_ILP32_OFFBIG_LIBS
_CS_XBS5_ILP32_OFFBIG_LINTFLAGS
_CS_XBS5_ILP32_OFF32_CFLAGS
_CS_XBS5_ILP32_OFF32_LDFLAGS
_CS_XBS5_ILP32_OFF32_LIBS
_CS_XBS5_ILP32_OFF32_LINTFLAGS
_CS_XBS5_LP64_OFF64_CFLAGS
_CS_XBS5_LP64_OFF64_LDFLAGS
_CS_XBS5_LP64_OFF64_LIBS
_CS_XBS5_LP64_OFF64_LINTFLAGS
_DEFAULT_SOURCE
_ENDIAN_H
_FEATURES_H
_GETOPT_CORE_H
_GETOPT_POSIX_H
_G_BUFSIZ
_G_HAVE_MMAP
_G_HAVE_MREMAP
_G_IO_IO_FILE_VERSION
_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_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
_LFS64_ASYNCHRONOUS_IO
_LFS64_LARGEFILE
_LFS64_STDIO
_LFS_ASYNCHRONOUS_IO
_LFS_LARGEFILE
_LIBC_LIMITS_H_
_OLD_STDIO_MAGIC
_PC_2_SYMLINKS
_PC_ALLOC_SIZE_MIN
_PC_ASYNC_IO
_PC_CHOWN_RESTRICTED
_PC_FILESIZEBITS
_PC_LINK_MAX
_PC_MAX_CANON
_PC_MAX_INPUT
_PC_NAME_MAX
_PC_NO_TRUNC
_PC_PATH_MAX
_PC_PIPE_BUF
_PC_PRIO_IO
_PC_REC_INCR_XFER_SIZE
_PC_REC_MAX_XFER_SIZE
_PC_REC_MIN_XFER_SIZE
_PC_REC_XFER_ALIGN
_PC_SOCK_MAXBUF
_PC_SYMLINK_MAX
_PC_SYNC_IO
_PC_VDISABLE
_POSIX2_BC_BASE_MAX
_POSIX2_BC_DIM_MAX
_POSIX2_BC_SCALE_MAX
_POSIX2_BC_STRING_MAX
_POSIX2_COLL_WEIGHTS_MAX
_POSIX2_EXPR_NEST_MAX
_POSIX2_LINE_MAX
_POSIX2_RE_DUP_MAX
_POSIX2_CHARCLASS_NAME_MAX
_POSIX2_VERSION
_POSIX2_C_VERSION
_POSIX2_C_BIND
_POSIX2_C_DEV
_POSIX2_SW_DEV
_POSIX2_LOCALEDEF
_POSIX2_CHAR_TERM
_POSIX_ADVISORY_INFO
_POSIX_AIO_LISTIO_MAX
_POSIX_AIO_MAX
_POSIX_ARG_MAX
_POSIX_ASYNCHRONOUS_IO
_POSIX_ASYNC_IO
_POSIX_BARRIERS
_POSIX_CHILD_MAX
_POSIX_CHOWN_RESTRICTED
_POSIX_CLOCKRES_MIN
_POSIX_CLOCK_SELECTION
_POSIX_CPUTIME
_POSIX_C_SOURCE
_POSIX_DELAYTIMER_MAX
_POSIX_FSYNC
_POSIX_HOST_NAME_MAX
_POSIX_IPV6
_POSIX_JOB_CONTROL
_POSIX_LINK_MAX
_POSIX_LOGIN_NAME_MAX
_POSIX_MAPPED_FILES
_POSIX_MAX_CANON
_POSIX_MAX_INPUT
_POSIX_MEMLOCK
_POSIX_MEMLOCK_RANGE
_POSIX_MEMORY_PROTECTION
_POSIX_MESSAGE_PASSING
_POSIX_MONOTONIC_CLOCK
_POSIX_MQ_OPEN_MAX
_POSIX_MQ_PRIO_MAX
_POSIX_NAME_MAX
_POSIX_NGROUPS_MAX
_POSIX_NO_TRUNC
_POSIX_OPEN_MAX
_POSIX_PATH_MAX
_POSIX_PIPE_BUF
_POSIX_PRIORITIZED_IO
_POSIX_PRIORITY_SCHEDULING
_POSIX_RAW_SOCKETS
_POSIX_READER_WRITER_LOCKS
_POSIX_REALTIME_SIGNALS
_POSIX_REENTRANT_FUNCTIONS
_POSIX_REGEXP
_POSIX_RE_DUP_MAX
_POSIX_RTSIG_MAX
_POSIX_SAVED_IDS
_POSIX_SEMAPHORES
_POSIX_SEM_NSEMS_MAX
_POSIX_SEM_VALUE_MAX
_POSIX_SHARED_MEMORY_OBJECTS
_POSIX_SHELL
_POSIX_SIGQUEUE_MAX
_POSIX_SOURCE
_POSIX_SPAWN
_POSIX_SPIN_LOCKS
_POSIX_SPORADIC_SERVER
_POSIX_SSIZE_MAX
_POSIX_STREAM_MAX
_POSIX_SYMLINK_MAX
_POSIX_SYMLOOP_MAX
_POSIX_SYNCHRONIZED_IO
_POSIX_THREADS
_POSIX_THREAD_ATTR_STACKADDR
_POSIX_THREAD_ATTR_STACKSIZE
_POSIX_THREAD_CPUTIME
_POSIX_THREAD_DESTRUCTOR_ITERATIONS
_POSIX_THREAD_KEYS_MAX
_POSIX_THREAD_PRIORITY_SCHEDULING
_POSIX_THREAD_PRIO_INHERIT
_POSIX_THREAD_PRIO_PROTECT
_POSIX_THREAD_PROCESS_SHARED
_POSIX_THREAD_ROBUST_PRIO_INHERIT
_POSIX_THREAD_ROBUST_PRIO_PROTECT
_POSIX_THREAD_SAFE_FUNCTIONS
_POSIX_THREAD_SPORADIC_SERVER
_POSIX_THREAD_THREADS_MAX
_POSIX_TIMEOUTS
_POSIX_TIMERS
_POSIX_TIMER_MAX
_POSIX_TRACE
_POSIX_TRACE_EVENT_FILTER
_POSIX_TRACE_INHERIT
_POSIX_TRACE_LOG
_POSIX_TTY_NAME_MAX
_POSIX_TYPED_MEMORY_OBJECTS
_POSIX_TZNAME_MAX
_POSIX_V6_LPBIG_OFFBIG
_POSIX_V7_LPBIG_OFFBIG
_POSIX_V6_LP64_OFF64
_POSIX_V7_LP64_OFF64
_POSIX_VDISABLE
_POSIX_VERSION
_SC_2_VERSION
_SC_2_C_BIND
_SC_2_C_DEV
_SC_2_FORT_DEV
_SC_2_FORT_RUN
_SC_2_SW_DEV
_SC_2_LOCALEDEF
_SC_2_CHAR_TERM
_SC_2_C_VERSION
_SC_2_UPE
_SC_2_PBS
_SC_2_PBS_ACCOUNTING
_SC_2_PBS_LOCATE
_SC_2_PBS_MESSAGE
_SC_2_PBS_TRACK
_SC_2_PBS_CHECKPOINT
_SC_ADVISORY_INFO
_SC_AIO_LISTIO_MAX
_SC_AIO_MAX
_SC_AIO_PRIO_DELTA_MAX
_SC_ARG_MAX
_SC_ASYNCHRONOUS_IO
_SC_ATEXIT_MAX
_SC_AVPHYS_PAGES
_SC_BARRIERS
_SC_BASE
_SC_BC_BASE_MAX
_SC_BC_DIM_MAX
_SC_BC_SCALE_MAX
_SC_BC_STRING_MAX
_SC_CHARCLASS_NAME_MAX
_SC_CHAR_BIT
_SC_CHAR_MAX
_SC_CHAR_MIN
_SC_CHILD_MAX
_SC_CLK_TCK
_SC_CLOCK_SELECTION
_SC_COLL_WEIGHTS_MAX
_SC_CPUTIME
_SC_C_LANG_SUPPORT
_SC_C_LANG_SUPPORT_R
_SC_DELAYTIMER_MAX
_SC_DEVICE_IO
_SC_DEVICE_SPECIFIC
_SC_DEVICE_SPECIFIC_R
_SC_EQUIV_CLASS_MAX
_SC_EXPR_NEST_MAX
_SC_FD_MGMT
_SC_FIFO
_SC_FILE_ATTRIBUTES
_SC_FILE_LOCKING
_SC_FILE_SYSTEM
_SC_FSYNC
_SC_GETGR_R_SIZE_MAX
_SC_GETPW_R_SIZE_MAX
_SC_HOST_NAME_MAX
_SC_INT_MAX
_SC_INT_MIN
_SC_IOV_MAX
_SC_IPV6
_SC_JOB_CONTROL
_SC_LEVEL1_ICACHE_SIZE
_SC_LEVEL1_ICACHE_ASSOC
_SC_LEVEL1_ICACHE_LINESIZE
_SC_LEVEL1_DCACHE_SIZE
_SC_LEVEL1_DCACHE_ASSOC
_SC_LEVEL1_DCACHE_LINESIZE
_SC_LEVEL2_CACHE_SIZE
_SC_LEVEL2_CACHE_ASSOC
_SC_LEVEL2_CACHE_LINESIZE
_SC_LEVEL3_CACHE_SIZE
_SC_LEVEL3_CACHE_ASSOC
_SC_LEVEL3_CACHE_LINESIZE
_SC_LEVEL4_CACHE_SIZE
_SC_LEVEL4_CACHE_ASSOC
_SC_LEVEL4_CACHE_LINESIZE
_SC_LINE_MAX
_SC_LOGIN_NAME_MAX
_SC_LONG_BIT
_SC_MAPPED_FILES
_SC_MB_LEN_MAX
_SC_MEMLOCK
_SC_MEMLOCK_RANGE
_SC_MEMORY_PROTECTION
_SC_MESSAGE_PASSING
_SC_MONOTONIC_CLOCK
_SC_MQ_OPEN_MAX
_SC_MQ_PRIO_MAX
_SC_MULTI_PROCESS
_SC_NETWORKING
_SC_NGROUPS_MAX
_SC_NL_ARGMAX
_SC_NL_LANGMAX
_SC_NL_MSGMAX
_SC_NL_NMAX
_SC_NL_SETMAX
_SC_NL_TEXTMAX
_SC_NPROCESSORS_CONF
_SC_NPROCESSORS_ONLN
_SC_NZERO
_SC_OPEN_MAX
_SC_PAGESIZE
_SC_PASS_MAX
_SC_PHYS_PAGES
_SC_PII
_SC_PII_INTERNET
_SC_PII_INTERNET_DGRAM
_SC_PII_INTERNET_STREAM
_SC_PII_OSI
_SC_PII_OSI_CLTS
_SC_PII_OSI_COTS
_SC_PII_OSI_M
_SC_PII_SOCKET
_SC_PII_XTI
_SC_PIPE
_SC_POLL
_SC_PRIORITIZED_IO
_SC_PRIORITY_SCHEDULING
_SC_RAW_SOCKETS
_SC_READER_WRITER_LOCKS
_SC_REALTIME_SIGNALS
_SC_REGEXP
_SC_REGEX_VERSION
_SC_RE_DUP_MAX
_SC_RTSIG_MAX
_SC_SAVED_IDS
_SC_SCHAR_MAX
_SC_SCHAR_MIN
_SC_SELECT
_SC_SEMAPHORES
_SC_SEM_NSEMS_MAX
_SC_SEM_VALUE_MAX
_SC_SHARED_MEMORY_OBJECTS
_SC_SHELL
_SC_SHRT_MAX
_SC_SHRT_MIN
_SC_SIGNALS
_SC_SIGQUEUE_MAX
_SC_SINGLE_PROCESS
_SC_SPAWN
_SC_SPIN_LOCKS
_SC_SPORADIC_SERVER
_SC_SSIZE_MAX
_SC_SS_REPL_MAX
_SC_STREAMS
_SC_STREAM_MAX
_SC_SYMLOOP_MAX
_SC_SYNCHRONIZED_IO
_SC_SYSTEM_DATABASE
_SC_SYSTEM_DATABASE_R
_SC_THREADS
_SC_THREAD_ATTR_STACKADDR
_SC_THREAD_ATTR_STACKSIZE
_SC_THREAD_CPUTIME
_SC_THREAD_DESTRUCTOR_ITERATIONS
_SC_THREAD_KEYS_MAX
_SC_THREAD_PRIORITY_SCHEDULING
_SC_THREAD_PRIO_INHERIT
_SC_THREAD_PRIO_PROTECT
_SC_THREAD_PROCESS_SHARED
_SC_THREAD_ROBUST_PRIO_INHERIT
_SC_THREAD_ROBUST_PRIO_PROTECT
_SC_THREAD_SAFE_FUNCTIONS
_SC_THREAD_SPORADIC_SERVER
_SC_THREAD_STACK_MIN
_SC_THREAD_THREADS_MAX
_SC_TIMEOUTS
_SC_TIMERS
_SC_TIMER_MAX
_SC_TRACE
_SC_TRACE_EVENT_FILTER
_SC_TRACE_EVENT_NAME_MAX
_SC_TRACE_INHERIT
_SC_TRACE_LOG
_SC_TRACE_NAME_MAX
_SC_TRACE_SYS_MAX
_SC_TRACE_USER_EVENT_MAX
_SC_TTY_NAME_MAX
_SC_TYPED_MEMORY_OBJECTS
_SC_TZNAME_MAX
_SC_T_IOV_MAX
_SC_UCHAR_MAX
_SC_UINT_MAX
_SC_UIO_MAXIOV
_SC_ULONG_MAX
_SC_USER_GROUPS
_SC_USER_GROUPS_R
_SC_USHRT_MAX
_SC_V6_LPBIG_OFFBIG
_SC_V7_LPBIG_OFFBIG
_SC_V6_ILP32_OFFBIG
_SC_V6_ILP32_OFF32
_SC_V6_LP64_OFF64
_SC_V7_ILP32_OFFBIG
_SC_V7_ILP32_OFF32
_SC_V7_LP64_OFF64
_SC_VERSION
_SC_WORD_BIT
_SC_XBS5_LPBIG_OFFBIG
_SC_XBS5_ILP32_OFFBIG
_SC_XBS5_ILP32_OFF32
_SC_XBS5_LP64_OFF64
_SC_XOPEN_CRYPT
_SC_XOPEN_ENH_I18N
_SC_XOPEN_LEGACY
_SC_XOPEN_REALTIME
_SC_XOPEN_REALTIME_THREADS
_SC_XOPEN_SHM
_SC_XOPEN_STREAMS
_SC_XOPEN_UNIX
_SC_XOPEN_VERSION
_SC_XOPEN_XCU_VERSION
_SC_XOPEN_XPG2
_SC_XOPEN_XPG3
_SC_XOPEN_XPG4
_STDC_PREDEF_H
_STDINT_H
_STDIO_H
_STDLIB_H
_STRINGS_H
_STRING_H
_SYS_CDEFS_H
_SYS_SELECT_H
_SYS_SYSMACROS_H
_SYS_TYPES_H
_THREAD_SHARED_TYPES_H
_UNISTD_H
_XBS5_LPBIG_OFFBIG
_XBS5_LP64_OFF64
_XOPEN_CRYPT
_XOPEN_ENH_I18N
_XOPEN_LEGACY
_XOPEN_REALTIME
_XOPEN_REALTIME_THREADS
_XOPEN_SHM
_XOPEN_UNIX
_XOPEN_VERSION
_XOPEN_XCU_VERSION
_XOPEN_XPG2
_XOPEN_XPG3
_XOPEN_XPG4
__BIG_ENDIAN
__BIT_TYPES_DEFINED__
__BYTE_ORDER
__ENUM_IDTYPE_T
__FD_SETSIZE
__FD_ZERO_STOS
__FILE_defined
__FLOAT_WORD_ORDER
__GLIBC_MINOR__
__GLIBC_USE_DEPRECATED_GETS
__GLIBC_USE_IEC_60559_BFP_EXT
__GLIBC_USE_IEC_60559_FUNCS_EXT
__GLIBC_USE_IEC_60559_TYPES_EXT
__GLIBC_USE_LIB_EXT2
__GLIBC__
__GNUC_VA_LIST
__GNU_LIBRARY__
__HAVE_DISTINCT_FLOAT16
__HAVE_DISTINCT_FLOAT32
__HAVE_DISTINCT_FLOAT32X
__HAVE_DISTINCT_FLOAT64
__HAVE_DISTINCT_FLOAT64X
__HAVE_DISTINCT_FLOAT128
__HAVE_DISTINCT_FLOAT128X
__HAVE_FLOAT16
__HAVE_FLOAT32
__HAVE_FLOAT32X
__HAVE_FLOAT64X
__HAVE_FLOAT64X_LONG_DOUBLE
__HAVE_FLOAT64
__HAVE_FLOAT128
__HAVE_FLOAT128X
__HAVE_FLOATN_NOT_TYPEDEF
__HAVE_GENERIC_SELECTION
__ILP32_OFFBIG_CFLAGS
__ILP32_OFFBIG_LDFLAGS
__ILP32_OFF32_CFLAGS
__ILP32_OFF32_LDFLAGS
__INO_T_MATCHES_INO64_T
__LITTLE_ENDIAN
__LP64_OFF64_CFLAGS
__LP64_OFF64_LDFLAGS
__OFF_T_MATCHES_OFF64_T
__PDP_ENDIAN
__POSIX2_THIS_VERSION
__PTHREAD_MUTEX_HAVE_PREV
__PTHREAD_MUTEX_LOCK_ELISION
__PTHREAD_MUTEX_NUSERS_AFTER_KIND
__PTHREAD_MUTEX_USE_UNION
__PTHREAD_RWLOCK_INT_FLAGS_SHARED
__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
__STDC_IEC_559__
__STDC_IEC_559_COMPLEX__
__STDC_ISO_10646__
__STDC_NO_THREADS__
__SYSCALL_WORDSIZE
__USE_ATFILE
__USE_FORTIFY_LEVEL
__USE_ISOC11
__USE_ISOC95
__USE_ISOC99
__USE_MISC
__USE_POSIX
__USE_POSIX2
__USE_POSIX199309
__USE_POSIX199506
__USE_POSIX_IMPLICITLY
__USE_XOPEN2K
__USE_XOPEN2K8
__WALL
__WCLONE
__WCOREFLAG
__WNOTHREAD
__WORDSIZE
__WORDSIZE_TIME64_COMPAT32
__W_CONTINUED
____FILE_defined
____mbstate_t_defined
__clock_t_defined
__clockid_t_defined
__codecvt_result___codecvt_error
__codecvt_result___codecvt_noconv
__codecvt_result___codecvt_ok
__codecvt_result___codecvt_partial
__glibc_c99_flexarr_available
__have_pthread_attr_t
__ldiv_t_defined
__lldiv_t_defined
__sigset_t_defined
__time_t_defined
__timer_t_defined
__timespec_defined
__timeval_defined
bcf_gt_missing
bcf_int8_vector_end
bcf_int8_missing
bcf_int16_vector_end
bcf_int16_missing
bcf_int32_vector_end
bcf_int32_missing
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_BZIP2
cram_block_method_ERROR
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
htsCompression_bgzf
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_format_maximum
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
idtype_t_P_ALL
idtype_t_P_PGID
idtype_t_P_PID
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_stdin_
_IO_2_1_stdout_
_IO_2_1_stderr_
__environ
bcf_float_missing
bcf_float_vector_end
bcf_type_shift
hts_verbose
optarg
opterr
optind
optopt
seq_nt16_table
seq_nt16_str
seq_nt16_int
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⚠
__ctype_get_mb_cur_max⚠
__getdelim⚠
__getpgid⚠
__overflow⚠
__stpcpy⚠
__stpncpy⚠
__strtok_r⚠
__uflow⚠
__underflow⚠
_exit⚠
a64l⚠
abort⚠
abs⚠
access⚠
acct⚠
adler32⚠
adler32_z⚠
adler32_combine⚠
alarm⚠
aligned_alloc⚠
alloca⚠
at_quick_exit⚠
atexit⚠
atof⚠
atoi⚠
atol⚠
atoll⚠
bam_aux2i⚠
bam_aux2f⚠
bam_aux2A⚠
bam_aux2Z⚠
bam_auxB2i⚠
bam_auxB2f⚠
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_destroy⚠
bam_hdr_dup⚠
bam_hdr_init⚠
bam_hdr_read⚠
bam_hdr_write⚠
bam_init1⚠
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_plp_auto⚠
bam_plp_constructor⚠
bam_plp_destroy⚠
bam_plp_destructor⚠
bam_plp_init⚠
bam_plp_next⚠
bam_plp_push⚠
bam_plp_reset⚠
bam_plp_set_maxcnt⚠
bam_read1⚠
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_index_build⚠
bcf_index_build2⚠
bcf_index_build3⚠
bcf_index_load2⚠
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_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⚠
brk⚠
bsearch⚠
bzero⚠
calloc⚠
chdir⚠
chown⚠
chroot⚠
clearenv⚠
clearerr⚠
clearerr_unlocked⚠
close⚠
compress⚠
compress2⚠
compressBound⚠
confstr⚠
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⚠
crc32⚠
crc32_z⚠
crc32_combine⚠
ctermid⚠
daemon⚠
deflate⚠
deflateBound⚠
deflateCopy⚠
deflateEnd⚠
deflateGetDictionary⚠
deflateInit2_⚠
deflateInit_⚠
deflateParams⚠
deflatePending⚠
deflatePrime⚠
deflateReset⚠
deflateResetKeep⚠
deflateSetDictionary⚠
deflateSetHeader⚠
deflateTune⚠
div⚠
dprintf⚠
drand48⚠
drand48_r⚠
dup⚠
dup2⚠
ecvt⚠
ecvt_r⚠
endusershell⚠
erand48⚠
erand48_r⚠
errmod_cal⚠
errmod_destroy⚠
errmod_init⚠
execl⚠
execle⚠
execlp⚠
execv⚠
execve⚠
execvp⚠
exit⚠
explicit_bzero⚠
faccessat⚠
fchdir⚠
fchown⚠
fchownat⚠
fclose⚠
fcvt⚠
fcvt_r⚠
fdatasync⚠
fdopen⚠
feof⚠
feof_unlocked⚠
ferror⚠
ferror_unlocked⚠
fexecve⚠
fflush⚠
fflush_unlocked⚠
ffs⚠
ffsl⚠
ffsll⚠
fgetc⚠
fgetc_unlocked⚠
fgetpos⚠
fgets⚠
fileno⚠
fileno_unlocked⚠
flockfile⚠
fmemopen⚠
fopen⚠
fork⚠
fpathconf⚠
fprintf⚠
fputc⚠
fputc_unlocked⚠
fputs⚠
fread⚠
fread_unlocked⚠
free⚠
freopen⚠
fscanf⚠
fscanf1⚠
fseek⚠
fseeko⚠
fsetpos⚠
fsync⚠
ftell⚠
ftello⚠
ftruncate⚠
ftrylockfile⚠
funlockfile⚠
fwrite⚠
fwrite_unlocked⚠
gcvt⚠
get_crc_table⚠
getc⚠
getc_unlocked⚠
getchar⚠
getchar_unlocked⚠
getcwd⚠
getdelim⚠
getdomainname⚠
getdtablesize⚠
getegid⚠
getentropy⚠
getenv⚠
geteuid⚠
getgid⚠
getgroups⚠
gethostid⚠
gethostname⚠
getline⚠
getloadavg⚠
getlogin⚠
getlogin_r⚠
getopt⚠
getpagesize⚠
getpass⚠
getpgid⚠
getpgrp⚠
getpid⚠
getppid⚠
getsid⚠
getsubopt⚠
getuid⚠
getusershell⚠
getw⚠
getwd⚠
gnu_dev_major⚠
gnu_dev_makedev⚠
gnu_dev_minor⚠
gzbuffer⚠
gzclearerr⚠
gzclose⚠
gzclose_r⚠
gzclose_w⚠
gzdirect⚠
gzdopen⚠
gzeof⚠
gzerror⚠
gzflush⚠
gzfread⚠
gzfwrite⚠
gzgetc⚠
gzgetc_⚠
gzgets⚠
gzoffset⚠
gzopen⚠
gzprintf⚠
gzputc⚠
gzputs⚠
gzread⚠
gzrewind⚠
gzseek⚠
gzsetparams⚠
gztell⚠
gzungetc⚠
gzvprintf⚠
gzwrite⚠
hrec_add_idx⚠
hts_check_EOF⚠
hts_close⚠
hts_detect_format⚠
hts_file_type⚠
hts_format_description⚠
hts_format_file_extension⚠
hts_get_bgzfp⚠
hts_get_format⚠
hts_get_log_level⚠
hts_getline⚠
hts_hopen⚠
hts_idx_destroy⚠
hts_idx_finish⚠
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_push⚠
hts_idx_save⚠
hts_idx_save_as⚠
hts_idx_seqnames⚠
hts_idx_set_meta⚠
hts_itr_destroy⚠
hts_itr_multi_bam⚠
hts_itr_multi_cram⚠
hts_itr_multi_destroy⚠
hts_itr_multi_next⚠
hts_itr_next⚠
hts_itr_query⚠
hts_itr_querys⚠
hts_itr_regions⚠
hts_log⚠
hts_md5_init⚠
hts_md5_update⚠
hts_md5_final⚠
hts_md5_reset⚠
hts_md5_hex⚠
hts_md5_destroy⚠
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_readlines⚠
hts_readlist⚠
hts_reglist_free⚠
hts_set_cache_size⚠
hts_set_fai_filename⚠
hts_set_log_level⚠
hts_set_opt⚠
hts_set_thread_pool⚠
hts_set_threads⚠
hts_version⚠
index⚠
inflate⚠
inflateBack⚠
inflateBackEnd⚠
inflateBackInit_⚠
inflateCodesUsed⚠
inflateCopy⚠
inflateEnd⚠
inflateGetDictionary⚠
inflateGetHeader⚠
inflateInit2_⚠
inflateInit_⚠
inflateMark⚠
inflatePrime⚠
inflateReset⚠
inflateReset2⚠
inflateResetKeep⚠
inflateSetDictionary⚠
inflateSync⚠
inflateSyncPoint⚠
inflateUndermine⚠
inflateValidate⚠
initstate⚠
initstate_r⚠
int32_put_blk⚠
isatty⚠
jrand48⚠
jrand48_r⚠
kbs_destroy⚠
kbs_init⚠
kbs_init2⚠
kbs_insert⚠
kgetline⚠
kmemmem⚠
kputd⚠
ksplit_core⚠
ksprintf⚠
kstrnstr⚠
kstrstr⚠
kstrtok⚠
kvsprintf⚠
l64a⚠
labs⚠
lchown⚠
lcong48⚠
lcong48_r⚠
ldiv⚠
link⚠
linkat⚠
llabs⚠
lldiv⚠
lockf⚠
lrand48⚠
lrand48_r⚠
lseek⚠
malloc⚠
mblen⚠
mbstowcs⚠
mbtowc⚠
memccpy⚠
memchr⚠
memcmp⚠
memcpy⚠
memmove⚠
memset⚠
mkdtemp⚠
mkstemp⚠
mkstemps⚠
mktemp⚠
mrand48⚠
mrand48_r⚠
nice⚠
nrand48⚠
nrand48_r⚠
on_exit⚠
open_memstream⚠
pathconf⚠
pause⚠
pclose⚠
perror⚠
pipe⚠
popen⚠
posix_memalign⚠
pread⚠
printf⚠
probaln_glocal⚠
profil⚠
pselect⚠
putc⚠
putc_unlocked⚠
putchar⚠
putchar_unlocked⚠
putenv⚠
puts⚠
putw⚠
pwrite⚠
qecvt⚠
qecvt_r⚠
qfcvt⚠
qfcvt_r⚠
qgcvt⚠
qsort⚠
quick_exit⚠
rand⚠
rand_r⚠
random⚠
random_r⚠
read⚠
readlink⚠
readlinkat⚠
realloc⚠
realpath⚠
remove⚠
rename⚠
renameat⚠
revoke⚠
rewind⚠
rindex⚠
rmdir⚠
rpmatch⚠
sam_cap_mapq⚠
sam_format1⚠
sam_hdr_add_PG⚠
sam_hdr_change_HD⚠
sam_hdr_free⚠
sam_hdr_length⚠
sam_hdr_parse⚠
sam_hdr_parse_⚠
sam_hdr_read⚠
sam_hdr_str⚠
sam_hdr_write⚠
sam_index_build⚠
sam_index_build2⚠
sam_index_build3⚠
sam_index_load⚠
sam_index_load2⚠
sam_itr_queryi⚠
sam_itr_querys⚠
sam_itr_regions⚠
sam_open_mode⚠
sam_open_mode_opts⚠
sam_parse1⚠
sam_prob_realn⚠
sam_read1⚠
sam_write1⚠
sbrk⚠
scanf⚠
scanf1⚠
seed48⚠
seed48_r⚠
select⚠
setbuf⚠
setbuffer⚠
setdomainname⚠
setegid⚠
setenv⚠
seteuid⚠
setgid⚠
sethostid⚠
sethostname⚠
setlinebuf⚠
setlogin⚠
setpgid⚠
setpgrp⚠
setregid⚠
setreuid⚠
setsid⚠
setstate⚠
setstate_r⚠
setuid⚠
setusershell⚠
setvbuf⚠
sleep⚠
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⚠
strtok⚠
strtok_r⚠
strtol⚠
strtoll⚠
strtoq⚠
strtoul⚠
strtoull⚠
strtouq⚠
strxfrm⚠
strxfrm_l⚠
symlink⚠
symlinkat⚠
sync⚠
syscall⚠
sysconf⚠
system⚠
tbx_destroy⚠
tbx_index⚠
tbx_index_build⚠
tbx_index_build2⚠
tbx_index_build3⚠
tbx_index_load⚠
tbx_index_load2⚠
tbx_name2id⚠
tbx_readrec⚠
tbx_seqnames⚠
tcgetpgrp⚠
tcsetpgrp⚠
tempnam⚠
tmpfile⚠
tmpnam⚠
tmpnam_r⚠
truncate⚠
ttyname⚠
ttyname_r⚠
ttyslot⚠
ualarm⚠
uncompress⚠
uncompress2⚠
ungetc⚠
unlink⚠
unlinkat⚠
unsetenv⚠
usleep⚠
valloc⚠
vcf_format⚠
vcf_hdr_read⚠
vcf_hdr_write⚠
vcf_parse⚠
vcf_read⚠
vcf_write⚠
vdprintf⚠
vfork⚠
vfprintf⚠
vfscanf⚠
vfscanf1⚠
vhangup⚠
vprintf⚠
vscanf⚠
vscanf1⚠
vsnprintf⚠
vsprintf⚠
vsscanf⚠
vsscanf1⚠
wcstombs⚠
wctomb⚠
write⚠
zError⚠
zlibCompileFlags⚠
zlibVersion⚠

Type Definitions

Byte
Bytef
FILE
_Float32
_Float32x
_Float64
_Float64x
_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
__fsword_t
__gid_t
__gnuc_va_list
__id_t
__ino64_t
__ino_t
__int8_t
__int16_t
__int32_t
__int64_t
__intmax_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
__quad_t
__rlim64_t
__rlim_t
__sig_atomic_t
__socklen_t
__ssize_t
__suseconds_t
__syscall_slong_t
__syscall_ulong_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
__uintmax_t
__useconds_t
_bindgen_ty_1
_bindgen_ty_2
_bindgen_ty_3
alloc_func
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
charf
clock_t
clockid_t
cram_block_method
cram_content_type
daddr_t
dev_t
fd_mask
fpos_t
free_func
fsblkcnt_t
fsfilcnt_t
fsid_t
gid_t
gzFile
gz_header
gz_headerp
htsCompression
htsExactFormat
htsFormatCategory
htsLogLevel
hts_fmt_option
hts_id2name_f
hts_idx_t
hts_itr_multi_query_func
hts_itr_query_func
hts_name2id_f
hts_readrec_func
hts_seek_func
hts_tell_func
id_t
idtype_t
in_func
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
intf
intmax_t
key_t
kgets_func
kstring_t
locale_t
loff_t
mode_t
nlink_t
off_t
out_func
pid_t
pthread_key_t
pthread_once_t
pthread_spinlock_t
pthread_t
quad_t
register_t
samFile
sam_fields
sigset_t
socklen_t
suseconds_t
time_t
timer_t
uInt
uIntf
uLong
uLongf
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
useconds_t
ushort
va_list
vcfFile
voidp
voidpc
voidpf
wchar_t
z_crc_t
z_size_t
z_stream
z_streamp

Unions

__mbstate_t__bindgen_ty_1
__pthread_cond_s__bindgen_ty_1
__pthread_cond_s__bindgen_ty_2
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