/* automatically generated by rust-bindgen 0.55.1 */ #[repr(C)] #[derive(Copy, Clone, Debug, Default, Eq, Hash, Ord, PartialEq, PartialOrd)] pub struct __BindgenBitfieldUnit { storage: Storage, align: [Align; 0], } impl __BindgenBitfieldUnit { #[inline] pub const fn new(storage: Storage) -> Self { Self { storage, align: [] } } } impl __BindgenBitfieldUnit where Storage: AsRef<[u8]> + AsMut<[u8]>, { #[inline] pub fn get_bit(&self, index: usize) -> bool { debug_assert!(index / 8 < self.storage.as_ref().len()); let byte_index = index / 8; let byte = self.storage.as_ref()[byte_index]; let bit_index = if cfg!(target_endian = "big") { 7 - (index % 8) } else { index % 8 }; let mask = 1 << bit_index; byte & mask == mask } #[inline] pub fn set_bit(&mut self, index: usize, val: bool) { debug_assert!(index / 8 < self.storage.as_ref().len()); let byte_index = index / 8; let byte = &mut self.storage.as_mut()[byte_index]; let bit_index = if cfg!(target_endian = "big") { 7 - (index % 8) } else { index % 8 }; let mask = 1 << bit_index; if val { *byte |= mask; } else { *byte &= !mask; } } #[inline] pub fn get(&self, bit_offset: usize, bit_width: u8) -> u64 { debug_assert!(bit_width <= 64); debug_assert!(bit_offset / 8 < self.storage.as_ref().len()); debug_assert!((bit_offset + (bit_width as usize)) / 8 <= self.storage.as_ref().len()); let mut val = 0; for i in 0..(bit_width as usize) { if self.get_bit(i + bit_offset) { let index = if cfg!(target_endian = "big") { bit_width as usize - 1 - i } else { i }; val |= 1 << index; } } val } #[inline] pub fn set(&mut self, bit_offset: usize, bit_width: u8, val: u64) { debug_assert!(bit_width <= 64); debug_assert!(bit_offset / 8 < self.storage.as_ref().len()); debug_assert!((bit_offset + (bit_width as usize)) / 8 <= self.storage.as_ref().len()); for i in 0..(bit_width as usize) { let mask = 1 << i; let val_bit_is_set = val & mask == mask; let index = if cfg!(target_endian = "big") { bit_width as usize - 1 - i } else { i }; self.set_bit(index + bit_offset, val_bit_is_set); } } } pub const _STDINT_H: u32 = 1; pub const _FEATURES_H: u32 = 1; pub const _DEFAULT_SOURCE: u32 = 1; pub const __GLIBC_USE_ISOC2X: u32 = 0; pub const __USE_ISOC11: u32 = 1; pub const __USE_ISOC99: u32 = 1; pub const __USE_ISOC95: u32 = 1; pub const __USE_POSIX_IMPLICITLY: u32 = 1; pub const _POSIX_SOURCE: u32 = 1; pub const _POSIX_C_SOURCE: u32 = 200809; pub const __USE_POSIX: u32 = 1; pub const __USE_POSIX2: u32 = 1; pub const __USE_POSIX199309: u32 = 1; pub const __USE_POSIX199506: u32 = 1; pub const __USE_XOPEN2K: u32 = 1; pub const __USE_XOPEN2K8: u32 = 1; pub const _ATFILE_SOURCE: u32 = 1; pub const __USE_MISC: u32 = 1; pub const __USE_ATFILE: u32 = 1; pub const __USE_FORTIFY_LEVEL: u32 = 0; pub const __GLIBC_USE_DEPRECATED_GETS: u32 = 0; pub const __GLIBC_USE_DEPRECATED_SCANF: u32 = 0; pub const _STDC_PREDEF_H: u32 = 1; pub const __STDC_IEC_559__: u32 = 1; pub const __STDC_IEC_559_COMPLEX__: u32 = 1; pub const __STDC_ISO_10646__: u32 = 201706; pub const __GNU_LIBRARY__: u32 = 6; pub const __GLIBC__: u32 = 2; pub const __GLIBC_MINOR__: u32 = 31; pub const _SYS_CDEFS_H: u32 = 1; pub const __glibc_c99_flexarr_available: u32 = 1; pub const __WORDSIZE: u32 = 64; pub const __WORDSIZE_TIME64_COMPAT32: u32 = 1; pub const __SYSCALL_WORDSIZE: u32 = 64; pub const __LONG_DOUBLE_USES_FLOAT128: u32 = 0; pub const __HAVE_GENERIC_SELECTION: u32 = 1; pub const __GLIBC_USE_LIB_EXT2: u32 = 0; pub const __GLIBC_USE_IEC_60559_BFP_EXT: u32 = 0; pub const __GLIBC_USE_IEC_60559_BFP_EXT_C2X: u32 = 0; pub const __GLIBC_USE_IEC_60559_FUNCS_EXT: u32 = 0; pub const __GLIBC_USE_IEC_60559_FUNCS_EXT_C2X: u32 = 0; pub const __GLIBC_USE_IEC_60559_TYPES_EXT: u32 = 0; pub const _BITS_TYPES_H: u32 = 1; pub const __TIMESIZE: u32 = 64; pub const _BITS_TYPESIZES_H: u32 = 1; pub const __OFF_T_MATCHES_OFF64_T: u32 = 1; pub const __INO_T_MATCHES_INO64_T: u32 = 1; pub const __RLIM_T_MATCHES_RLIM64_T: u32 = 1; pub const __STATFS_MATCHES_STATFS64: u32 = 1; pub const __FD_SETSIZE: u32 = 1024; pub const _BITS_TIME64_H: u32 = 1; pub const _BITS_WCHAR_H: u32 = 1; pub const _BITS_STDINT_INTN_H: u32 = 1; pub const _BITS_STDINT_UINTN_H: u32 = 1; pub const INT8_MIN: i32 = -128; pub const INT16_MIN: i32 = -32768; pub const INT32_MIN: i32 = -2147483648; pub const INT8_MAX: u32 = 127; pub const INT16_MAX: u32 = 32767; pub const INT32_MAX: u32 = 2147483647; pub const UINT8_MAX: u32 = 255; pub const UINT16_MAX: u32 = 65535; pub const UINT32_MAX: u32 = 4294967295; pub const INT_LEAST8_MIN: i32 = -128; pub const INT_LEAST16_MIN: i32 = -32768; pub const INT_LEAST32_MIN: i32 = -2147483648; pub const INT_LEAST8_MAX: u32 = 127; pub const INT_LEAST16_MAX: u32 = 32767; pub const INT_LEAST32_MAX: u32 = 2147483647; pub const UINT_LEAST8_MAX: u32 = 255; pub const UINT_LEAST16_MAX: u32 = 65535; pub const UINT_LEAST32_MAX: u32 = 4294967295; pub const INT_FAST8_MIN: i32 = -128; pub const INT_FAST16_MIN: i64 = -9223372036854775808; pub const INT_FAST32_MIN: i64 = -9223372036854775808; pub const INT_FAST8_MAX: u32 = 127; pub const INT_FAST16_MAX: u64 = 9223372036854775807; pub const INT_FAST32_MAX: u64 = 9223372036854775807; pub const UINT_FAST8_MAX: u32 = 255; pub const UINT_FAST16_MAX: i32 = -1; pub const UINT_FAST32_MAX: i32 = -1; pub const INTPTR_MIN: i64 = -9223372036854775808; pub const INTPTR_MAX: u64 = 9223372036854775807; pub const UINTPTR_MAX: i32 = -1; pub const PTRDIFF_MIN: i64 = -9223372036854775808; pub const PTRDIFF_MAX: u64 = 9223372036854775807; pub const SIG_ATOMIC_MIN: i32 = -2147483648; pub const SIG_ATOMIC_MAX: u32 = 2147483647; pub const SIZE_MAX: i32 = -1; pub const WINT_MIN: u32 = 0; pub const WINT_MAX: u32 = 4294967295; pub const _INTTYPES_H: u32 = 1; pub const ____gwchar_t_defined: u32 = 1; pub const __PRI64_PREFIX: &'static [u8; 2usize] = b"l\0"; pub const __PRIPTR_PREFIX: &'static [u8; 2usize] = b"l\0"; pub const PRId8: &'static [u8; 2usize] = b"d\0"; pub const PRId16: &'static [u8; 2usize] = b"d\0"; pub const PRId32: &'static [u8; 2usize] = b"d\0"; pub const PRId64: &'static [u8; 3usize] = b"ld\0"; pub const PRIdLEAST8: &'static [u8; 2usize] = b"d\0"; pub const PRIdLEAST16: &'static [u8; 2usize] = b"d\0"; pub const PRIdLEAST32: &'static [u8; 2usize] = b"d\0"; pub const PRIdLEAST64: &'static [u8; 3usize] = b"ld\0"; pub const PRIdFAST8: &'static [u8; 2usize] = b"d\0"; pub const PRIdFAST16: &'static [u8; 3usize] = b"ld\0"; pub const PRIdFAST32: &'static [u8; 3usize] = b"ld\0"; pub const PRIdFAST64: &'static [u8; 3usize] = b"ld\0"; pub const PRIi8: &'static [u8; 2usize] = b"i\0"; pub const PRIi16: &'static [u8; 2usize] = b"i\0"; pub const PRIi32: &'static [u8; 2usize] = b"i\0"; pub const PRIi64: &'static [u8; 3usize] = b"li\0"; pub const PRIiLEAST8: &'static [u8; 2usize] = b"i\0"; pub const PRIiLEAST16: &'static [u8; 2usize] = b"i\0"; pub const PRIiLEAST32: &'static [u8; 2usize] = b"i\0"; pub const PRIiLEAST64: &'static [u8; 3usize] = b"li\0"; pub const PRIiFAST8: &'static [u8; 2usize] = b"i\0"; pub const PRIiFAST16: &'static [u8; 3usize] = b"li\0"; pub const PRIiFAST32: &'static [u8; 3usize] = b"li\0"; pub const PRIiFAST64: &'static [u8; 3usize] = b"li\0"; pub const PRIo8: &'static [u8; 2usize] = b"o\0"; pub const PRIo16: &'static [u8; 2usize] = b"o\0"; pub const PRIo32: &'static [u8; 2usize] = b"o\0"; pub const PRIo64: &'static [u8; 3usize] = b"lo\0"; pub const PRIoLEAST8: &'static [u8; 2usize] = b"o\0"; pub const PRIoLEAST16: &'static [u8; 2usize] = b"o\0"; pub const PRIoLEAST32: &'static [u8; 2usize] = b"o\0"; pub const PRIoLEAST64: &'static [u8; 3usize] = b"lo\0"; pub const PRIoFAST8: &'static [u8; 2usize] = b"o\0"; pub const PRIoFAST16: &'static [u8; 3usize] = b"lo\0"; pub const PRIoFAST32: &'static [u8; 3usize] = b"lo\0"; pub const PRIoFAST64: &'static [u8; 3usize] = b"lo\0"; pub const PRIu8: &'static [u8; 2usize] = b"u\0"; pub const PRIu16: &'static [u8; 2usize] = b"u\0"; pub const PRIu32: &'static [u8; 2usize] = b"u\0"; pub const PRIu64: &'static [u8; 3usize] = b"lu\0"; pub const PRIuLEAST8: &'static [u8; 2usize] = b"u\0"; pub const PRIuLEAST16: &'static [u8; 2usize] = b"u\0"; pub const PRIuLEAST32: &'static [u8; 2usize] = b"u\0"; pub const PRIuLEAST64: &'static [u8; 3usize] = b"lu\0"; pub const PRIuFAST8: &'static [u8; 2usize] = b"u\0"; pub const PRIuFAST16: &'static [u8; 3usize] = b"lu\0"; pub const PRIuFAST32: &'static [u8; 3usize] = b"lu\0"; pub const PRIuFAST64: &'static [u8; 3usize] = b"lu\0"; pub const PRIx8: &'static [u8; 2usize] = b"x\0"; pub const PRIx16: &'static [u8; 2usize] = b"x\0"; pub const PRIx32: &'static [u8; 2usize] = b"x\0"; pub const PRIx64: &'static [u8; 3usize] = b"lx\0"; pub const PRIxLEAST8: &'static [u8; 2usize] = b"x\0"; pub const PRIxLEAST16: &'static [u8; 2usize] = b"x\0"; pub const PRIxLEAST32: &'static [u8; 2usize] = b"x\0"; pub const PRIxLEAST64: &'static [u8; 3usize] = b"lx\0"; pub const PRIxFAST8: &'static [u8; 2usize] = b"x\0"; pub const PRIxFAST16: &'static [u8; 3usize] = b"lx\0"; pub const PRIxFAST32: &'static [u8; 3usize] = b"lx\0"; pub const PRIxFAST64: &'static [u8; 3usize] = b"lx\0"; pub const PRIX8: &'static [u8; 2usize] = b"X\0"; pub const PRIX16: &'static [u8; 2usize] = b"X\0"; pub const PRIX32: &'static [u8; 2usize] = b"X\0"; pub const PRIX64: &'static [u8; 3usize] = b"lX\0"; pub const PRIXLEAST8: &'static [u8; 2usize] = b"X\0"; pub const PRIXLEAST16: &'static [u8; 2usize] = b"X\0"; pub const PRIXLEAST32: &'static [u8; 2usize] = b"X\0"; pub const PRIXLEAST64: &'static [u8; 3usize] = b"lX\0"; pub const PRIXFAST8: &'static [u8; 2usize] = b"X\0"; pub const PRIXFAST16: &'static [u8; 3usize] = b"lX\0"; pub const PRIXFAST32: &'static [u8; 3usize] = b"lX\0"; pub const PRIXFAST64: &'static [u8; 3usize] = b"lX\0"; pub const PRIdMAX: &'static [u8; 3usize] = b"ld\0"; pub const PRIiMAX: &'static [u8; 3usize] = b"li\0"; pub const PRIoMAX: &'static [u8; 3usize] = b"lo\0"; pub const PRIuMAX: &'static [u8; 3usize] = b"lu\0"; pub const PRIxMAX: &'static [u8; 3usize] = b"lx\0"; pub const PRIXMAX: &'static [u8; 3usize] = b"lX\0"; pub const PRIdPTR: &'static [u8; 3usize] = b"ld\0"; pub const PRIiPTR: &'static [u8; 3usize] = b"li\0"; pub const PRIoPTR: &'static [u8; 3usize] = b"lo\0"; pub const PRIuPTR: &'static [u8; 3usize] = b"lu\0"; pub const PRIxPTR: &'static [u8; 3usize] = b"lx\0"; pub const PRIXPTR: &'static [u8; 3usize] = b"lX\0"; pub const SCNd8: &'static [u8; 4usize] = b"hhd\0"; pub const SCNd16: &'static [u8; 3usize] = b"hd\0"; pub const SCNd32: &'static [u8; 2usize] = b"d\0"; pub const SCNd64: &'static [u8; 3usize] = b"ld\0"; pub const SCNdLEAST8: &'static [u8; 4usize] = b"hhd\0"; pub const SCNdLEAST16: &'static [u8; 3usize] = b"hd\0"; pub const SCNdLEAST32: &'static [u8; 2usize] = b"d\0"; pub const SCNdLEAST64: &'static [u8; 3usize] = b"ld\0"; pub const SCNdFAST8: &'static [u8; 4usize] = b"hhd\0"; pub const SCNdFAST16: &'static [u8; 3usize] = b"ld\0"; pub const SCNdFAST32: &'static [u8; 3usize] = b"ld\0"; pub const SCNdFAST64: &'static [u8; 3usize] = b"ld\0"; pub const SCNi8: &'static [u8; 4usize] = b"hhi\0"; pub const SCNi16: &'static [u8; 3usize] = b"hi\0"; pub const SCNi32: &'static [u8; 2usize] = b"i\0"; pub const SCNi64: &'static [u8; 3usize] = b"li\0"; pub const SCNiLEAST8: &'static [u8; 4usize] = b"hhi\0"; pub const SCNiLEAST16: &'static [u8; 3usize] = b"hi\0"; pub const SCNiLEAST32: &'static [u8; 2usize] = b"i\0"; pub const SCNiLEAST64: &'static [u8; 3usize] = b"li\0"; pub const SCNiFAST8: &'static [u8; 4usize] = b"hhi\0"; pub const SCNiFAST16: &'static [u8; 3usize] = b"li\0"; pub const SCNiFAST32: &'static [u8; 3usize] = b"li\0"; pub const SCNiFAST64: &'static [u8; 3usize] = b"li\0"; pub const SCNu8: &'static [u8; 4usize] = b"hhu\0"; pub const SCNu16: &'static [u8; 3usize] = b"hu\0"; pub const SCNu32: &'static [u8; 2usize] = b"u\0"; pub const SCNu64: &'static [u8; 3usize] = b"lu\0"; pub const SCNuLEAST8: &'static [u8; 4usize] = b"hhu\0"; pub const SCNuLEAST16: &'static [u8; 3usize] = b"hu\0"; pub const SCNuLEAST32: &'static [u8; 2usize] = b"u\0"; pub const SCNuLEAST64: &'static [u8; 3usize] = b"lu\0"; pub const SCNuFAST8: &'static [u8; 4usize] = b"hhu\0"; pub const SCNuFAST16: &'static [u8; 3usize] = b"lu\0"; pub const SCNuFAST32: &'static [u8; 3usize] = b"lu\0"; pub const SCNuFAST64: &'static [u8; 3usize] = b"lu\0"; pub const SCNo8: &'static [u8; 4usize] = b"hho\0"; pub const SCNo16: &'static [u8; 3usize] = b"ho\0"; pub const SCNo32: &'static [u8; 2usize] = b"o\0"; pub const SCNo64: &'static [u8; 3usize] = b"lo\0"; pub const SCNoLEAST8: &'static [u8; 4usize] = b"hho\0"; pub const SCNoLEAST16: &'static [u8; 3usize] = b"ho\0"; pub const SCNoLEAST32: &'static [u8; 2usize] = b"o\0"; pub const SCNoLEAST64: &'static [u8; 3usize] = b"lo\0"; pub const SCNoFAST8: &'static [u8; 4usize] = b"hho\0"; pub const SCNoFAST16: &'static [u8; 3usize] = b"lo\0"; pub const SCNoFAST32: &'static [u8; 3usize] = b"lo\0"; pub const SCNoFAST64: &'static [u8; 3usize] = b"lo\0"; pub const SCNx8: &'static [u8; 4usize] = b"hhx\0"; pub const SCNx16: &'static [u8; 3usize] = b"hx\0"; pub const SCNx32: &'static [u8; 2usize] = b"x\0"; pub const SCNx64: &'static [u8; 3usize] = b"lx\0"; pub const SCNxLEAST8: &'static [u8; 4usize] = b"hhx\0"; pub const SCNxLEAST16: &'static [u8; 3usize] = b"hx\0"; pub const SCNxLEAST32: &'static [u8; 2usize] = b"x\0"; pub const SCNxLEAST64: &'static [u8; 3usize] = b"lx\0"; pub const SCNxFAST8: &'static [u8; 4usize] = b"hhx\0"; pub const SCNxFAST16: &'static [u8; 3usize] = b"lx\0"; pub const SCNxFAST32: &'static [u8; 3usize] = b"lx\0"; pub const SCNxFAST64: &'static [u8; 3usize] = b"lx\0"; pub const SCNdMAX: &'static [u8; 3usize] = b"ld\0"; pub const SCNiMAX: &'static [u8; 3usize] = b"li\0"; pub const SCNoMAX: &'static [u8; 3usize] = b"lo\0"; pub const SCNuMAX: &'static [u8; 3usize] = b"lu\0"; pub const SCNxMAX: &'static [u8; 3usize] = b"lx\0"; pub const SCNdPTR: &'static [u8; 3usize] = b"ld\0"; pub const SCNiPTR: &'static [u8; 3usize] = b"li\0"; pub const SCNoPTR: &'static [u8; 3usize] = b"lo\0"; pub const SCNuPTR: &'static [u8; 3usize] = b"lu\0"; pub const SCNxPTR: &'static [u8; 3usize] = b"lx\0"; pub const _STDIO_H: u32 = 1; pub const __GNUC_VA_LIST: u32 = 1; pub const _____fpos_t_defined: u32 = 1; pub const ____mbstate_t_defined: u32 = 1; pub const _____fpos64_t_defined: u32 = 1; pub const ____FILE_defined: u32 = 1; pub const __FILE_defined: u32 = 1; pub const __struct_FILE_defined: u32 = 1; pub const _IO_EOF_SEEN: u32 = 16; pub const _IO_ERR_SEEN: u32 = 32; pub const _IO_USER_LOCK: u32 = 32768; pub const _IOFBF: u32 = 0; pub const _IOLBF: u32 = 1; pub const _IONBF: u32 = 2; pub const BUFSIZ: u32 = 8192; pub const EOF: i32 = -1; pub const SEEK_SET: u32 = 0; pub const SEEK_CUR: u32 = 1; pub const SEEK_END: u32 = 2; pub const P_tmpdir: &'static [u8; 5usize] = b"/tmp\0"; pub const _BITS_STDIO_LIM_H: u32 = 1; pub const L_tmpnam: u32 = 20; pub const TMP_MAX: u32 = 238328; pub const FILENAME_MAX: u32 = 4096; pub const L_ctermid: u32 = 9; pub const FOPEN_MAX: u32 = 16; pub const HTS_PATH_SEPARATOR_CHAR: u8 = 58u8; pub const HTS_PATH_SEPARATOR_STR: &'static [u8; 2usize] = b":\0"; pub const HTS_RESIZE_CLEAR: u32 = 1; pub const HTS_IDX_DELIM: &'static [u8; 8usize] = b"##idx##\0"; pub const HTS_VERSION: u32 = 101002; pub const HTS_IDX_NOCOOR: i32 = -2; pub const HTS_IDX_START: i32 = -3; pub const HTS_IDX_REST: i32 = -4; pub const HTS_IDX_NONE: i32 = -5; pub const HTS_FMT_CSI: u32 = 0; pub const HTS_FMT_BAI: u32 = 1; pub const HTS_FMT_TBI: u32 = 2; pub const HTS_FMT_CRAI: u32 = 3; pub const PRIhts_pos: &'static [u8; 3usize] = b"ld\0"; pub const HTS_IDX_SAVE_REMOTE: u32 = 1; pub const HTS_IDX_SILENT_FAIL: u32 = 2; pub const HTS_PARSE_THOUSANDS_SEP: u32 = 1; pub const HTS_PARSE_ONE_COORD: u32 = 2; pub const HTS_PARSE_LIST: u32 = 4; pub const FT_UNKN: u32 = 0; pub const FT_GZ: u32 = 1; pub const FT_VCF: u32 = 2; pub const FT_VCF_GZ: u32 = 3; pub const FT_BCF: u32 = 4; pub const FT_BCF_GZ: u32 = 5; pub const FT_STDIN: u32 = 8; pub const SAM_FORMAT_VERSION: &'static [u8; 4usize] = b"1.6\0"; pub const BAM_CMATCH: u32 = 0; pub const BAM_CINS: u32 = 1; pub const BAM_CDEL: u32 = 2; pub const BAM_CREF_SKIP: u32 = 3; pub const BAM_CSOFT_CLIP: u32 = 4; pub const BAM_CHARD_CLIP: u32 = 5; pub const BAM_CPAD: u32 = 6; pub const BAM_CEQUAL: u32 = 7; pub const BAM_CDIFF: u32 = 8; pub const BAM_CBACK: u32 = 9; pub const BAM_CIGAR_STR: &'static [u8; 11usize] = b"MIDNSHP=XB\0"; pub const BAM_CIGAR_SHIFT: u32 = 4; pub const BAM_CIGAR_MASK: u32 = 15; pub const BAM_CIGAR_TYPE: u32 = 246183; pub const BAM_FPAIRED: u32 = 1; pub const BAM_FPROPER_PAIR: u32 = 2; pub const BAM_FUNMAP: u32 = 4; pub const BAM_FMUNMAP: u32 = 8; pub const BAM_FREVERSE: u32 = 16; pub const BAM_FMREVERSE: u32 = 32; pub const BAM_FREAD1: u32 = 64; pub const BAM_FREAD2: u32 = 128; pub const BAM_FSECONDARY: u32 = 256; pub const BAM_FQCFAIL: u32 = 512; pub const BAM_FDUP: u32 = 1024; pub const BAM_FSUPPLEMENTARY: u32 = 2048; pub const BAM_USER_OWNS_STRUCT: u32 = 1; pub const BAM_USER_OWNS_DATA: u32 = 2; pub const USE_SYSTEM_HTSLIB: u32 = 1; pub type __u_char = ::std::os::raw::c_uchar; pub type __u_short = ::std::os::raw::c_ushort; pub type __u_int = ::std::os::raw::c_uint; pub type __u_long = ::std::os::raw::c_ulong; pub type __int8_t = ::std::os::raw::c_schar; pub type __uint8_t = ::std::os::raw::c_uchar; pub type __int16_t = ::std::os::raw::c_short; pub type __uint16_t = ::std::os::raw::c_ushort; pub type __int32_t = ::std::os::raw::c_int; pub type __uint32_t = ::std::os::raw::c_uint; pub type __int64_t = ::std::os::raw::c_long; pub type __uint64_t = ::std::os::raw::c_ulong; pub type __int_least8_t = __int8_t; pub type __uint_least8_t = __uint8_t; pub type __int_least16_t = __int16_t; pub type __uint_least16_t = __uint16_t; pub type __int_least32_t = __int32_t; pub type __uint_least32_t = __uint32_t; pub type __int_least64_t = __int64_t; pub type __uint_least64_t = __uint64_t; pub type __quad_t = ::std::os::raw::c_long; pub type __u_quad_t = ::std::os::raw::c_ulong; pub type __intmax_t = ::std::os::raw::c_long; pub type __uintmax_t = ::std::os::raw::c_ulong; pub type __dev_t = ::std::os::raw::c_ulong; pub type __uid_t = ::std::os::raw::c_uint; pub type __gid_t = ::std::os::raw::c_uint; pub type __ino_t = ::std::os::raw::c_ulong; pub type __ino64_t = ::std::os::raw::c_ulong; pub type __mode_t = ::std::os::raw::c_uint; pub type __nlink_t = ::std::os::raw::c_ulong; pub type __off_t = ::std::os::raw::c_long; pub type __off64_t = ::std::os::raw::c_long; pub type __pid_t = ::std::os::raw::c_int; #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct __fsid_t { pub __val: [::std::os::raw::c_int; 2usize], } pub type __clock_t = ::std::os::raw::c_long; pub type __rlim_t = ::std::os::raw::c_ulong; pub type __rlim64_t = ::std::os::raw::c_ulong; pub type __id_t = ::std::os::raw::c_uint; pub type __time_t = ::std::os::raw::c_long; pub type __useconds_t = ::std::os::raw::c_uint; pub type __suseconds_t = ::std::os::raw::c_long; pub type __daddr_t = ::std::os::raw::c_int; pub type __key_t = ::std::os::raw::c_int; pub type __clockid_t = ::std::os::raw::c_int; pub type __timer_t = *mut ::std::os::raw::c_void; pub type __blksize_t = ::std::os::raw::c_long; pub type __blkcnt_t = ::std::os::raw::c_long; pub type __blkcnt64_t = ::std::os::raw::c_long; pub type __fsblkcnt_t = ::std::os::raw::c_ulong; pub type __fsblkcnt64_t = ::std::os::raw::c_ulong; pub type __fsfilcnt_t = ::std::os::raw::c_ulong; pub type __fsfilcnt64_t = ::std::os::raw::c_ulong; pub type __fsword_t = ::std::os::raw::c_long; pub type __ssize_t = ::std::os::raw::c_long; pub type __syscall_slong_t = ::std::os::raw::c_long; pub type __syscall_ulong_t = ::std::os::raw::c_ulong; pub type __loff_t = __off64_t; pub type __caddr_t = *mut ::std::os::raw::c_char; pub type __intptr_t = ::std::os::raw::c_long; pub type __socklen_t = ::std::os::raw::c_uint; pub type __sig_atomic_t = ::std::os::raw::c_int; pub type int_least8_t = __int_least8_t; pub type int_least16_t = __int_least16_t; pub type int_least32_t = __int_least32_t; pub type int_least64_t = __int_least64_t; pub type uint_least8_t = __uint_least8_t; pub type uint_least16_t = __uint_least16_t; pub type uint_least32_t = __uint_least32_t; pub type uint_least64_t = __uint_least64_t; pub type int_fast8_t = ::std::os::raw::c_schar; pub type int_fast16_t = ::std::os::raw::c_long; pub type int_fast32_t = ::std::os::raw::c_long; pub type int_fast64_t = ::std::os::raw::c_long; pub type uint_fast8_t = ::std::os::raw::c_uchar; pub type uint_fast16_t = ::std::os::raw::c_ulong; pub type uint_fast32_t = ::std::os::raw::c_ulong; pub type uint_fast64_t = ::std::os::raw::c_ulong; pub type intmax_t = __intmax_t; pub type uintmax_t = __uintmax_t; pub type size_t = ::std::os::raw::c_ulong; pub type wchar_t = ::std::os::raw::c_int; #[repr(C)] #[repr(align(16))] #[derive(Debug, Copy, Clone)] pub struct max_align_t { pub __clang_max_align_nonce1: ::std::os::raw::c_longlong, pub __bindgen_padding_0: u64, pub __clang_max_align_nonce2: u128, } pub type __gwchar_t = ::std::os::raw::c_int; #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct imaxdiv_t { pub quot: ::std::os::raw::c_long, pub rem: ::std::os::raw::c_long, } extern "C" { pub fn imaxabs(__n: intmax_t) -> intmax_t; } extern "C" { pub fn imaxdiv(__numer: intmax_t, __denom: intmax_t) -> imaxdiv_t; } extern "C" { pub fn strtoimax( __nptr: *const ::std::os::raw::c_char, __endptr: *mut *mut ::std::os::raw::c_char, __base: ::std::os::raw::c_int, ) -> intmax_t; } extern "C" { pub fn strtoumax( __nptr: *const ::std::os::raw::c_char, __endptr: *mut *mut ::std::os::raw::c_char, __base: ::std::os::raw::c_int, ) -> uintmax_t; } extern "C" { pub fn wcstoimax( __nptr: *const __gwchar_t, __endptr: *mut *mut __gwchar_t, __base: ::std::os::raw::c_int, ) -> intmax_t; } extern "C" { pub fn wcstoumax( __nptr: *const __gwchar_t, __endptr: *mut *mut __gwchar_t, __base: ::std::os::raw::c_int, ) -> uintmax_t; } pub type va_list = __builtin_va_list; pub type __gnuc_va_list = __builtin_va_list; #[repr(C)] #[derive(Copy, Clone)] pub struct __mbstate_t { pub __count: ::std::os::raw::c_int, pub __value: __mbstate_t__bindgen_ty_1, } #[repr(C)] #[derive(Copy, Clone)] pub union __mbstate_t__bindgen_ty_1 { pub __wch: ::std::os::raw::c_uint, pub __wchb: [::std::os::raw::c_char; 4usize], _bindgen_union_align: u32, } #[repr(C)] #[derive(Copy, Clone)] pub struct _G_fpos_t { pub __pos: __off_t, pub __state: __mbstate_t, } pub type __fpos_t = _G_fpos_t; #[repr(C)] #[derive(Copy, Clone)] pub struct _G_fpos64_t { pub __pos: __off64_t, pub __state: __mbstate_t, } pub type __fpos64_t = _G_fpos64_t; pub type __FILE = _IO_FILE; pub type FILE = _IO_FILE; #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct _IO_marker { _unused: [u8; 0], } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct _IO_codecvt { _unused: [u8; 0], } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct _IO_wide_data { _unused: [u8; 0], } pub type _IO_lock_t = ::std::os::raw::c_void; #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct _IO_FILE { pub _flags: ::std::os::raw::c_int, pub _IO_read_ptr: *mut ::std::os::raw::c_char, pub _IO_read_end: *mut ::std::os::raw::c_char, pub _IO_read_base: *mut ::std::os::raw::c_char, pub _IO_write_base: *mut ::std::os::raw::c_char, pub _IO_write_ptr: *mut ::std::os::raw::c_char, pub _IO_write_end: *mut ::std::os::raw::c_char, pub _IO_buf_base: *mut ::std::os::raw::c_char, pub _IO_buf_end: *mut ::std::os::raw::c_char, pub _IO_save_base: *mut ::std::os::raw::c_char, pub _IO_backup_base: *mut ::std::os::raw::c_char, pub _IO_save_end: *mut ::std::os::raw::c_char, pub _markers: *mut _IO_marker, pub _chain: *mut _IO_FILE, pub _fileno: ::std::os::raw::c_int, pub _flags2: ::std::os::raw::c_int, pub _old_offset: __off_t, pub _cur_column: ::std::os::raw::c_ushort, pub _vtable_offset: ::std::os::raw::c_schar, pub _shortbuf: [::std::os::raw::c_char; 1usize], pub _lock: *mut _IO_lock_t, pub _offset: __off64_t, pub _codecvt: *mut _IO_codecvt, pub _wide_data: *mut _IO_wide_data, pub _freeres_list: *mut _IO_FILE, pub _freeres_buf: *mut ::std::os::raw::c_void, pub __pad5: size_t, pub _mode: ::std::os::raw::c_int, pub _unused2: [::std::os::raw::c_char; 20usize], } pub type off_t = __off_t; pub type ssize_t = __ssize_t; pub type fpos_t = __fpos_t; extern "C" { pub static mut stdin: *mut FILE; } extern "C" { pub static mut stdout: *mut FILE; } extern "C" { pub static mut stderr: *mut FILE; } extern "C" { pub fn remove(__filename: *const ::std::os::raw::c_char) -> ::std::os::raw::c_int; } extern "C" { pub fn rename( __old: *const ::std::os::raw::c_char, __new: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn renameat( __oldfd: ::std::os::raw::c_int, __old: *const ::std::os::raw::c_char, __newfd: ::std::os::raw::c_int, __new: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn tmpfile() -> *mut FILE; } extern "C" { pub fn tmpnam(__s: *mut ::std::os::raw::c_char) -> *mut ::std::os::raw::c_char; } extern "C" { pub fn tmpnam_r(__s: *mut ::std::os::raw::c_char) -> *mut ::std::os::raw::c_char; } extern "C" { pub fn tempnam( __dir: *const ::std::os::raw::c_char, __pfx: *const ::std::os::raw::c_char, ) -> *mut ::std::os::raw::c_char; } extern "C" { pub fn fclose(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn fflush(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn fflush_unlocked(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn fopen( __filename: *const ::std::os::raw::c_char, __modes: *const ::std::os::raw::c_char, ) -> *mut FILE; } extern "C" { pub fn freopen( __filename: *const ::std::os::raw::c_char, __modes: *const ::std::os::raw::c_char, __stream: *mut FILE, ) -> *mut FILE; } extern "C" { pub fn fdopen(__fd: ::std::os::raw::c_int, __modes: *const ::std::os::raw::c_char) -> *mut FILE; } extern "C" { pub fn fmemopen( __s: *mut ::std::os::raw::c_void, __len: size_t, __modes: *const ::std::os::raw::c_char, ) -> *mut FILE; } extern "C" { pub fn open_memstream( __bufloc: *mut *mut ::std::os::raw::c_char, __sizeloc: *mut size_t, ) -> *mut FILE; } extern "C" { pub fn setbuf(__stream: *mut FILE, __buf: *mut ::std::os::raw::c_char); } extern "C" { pub fn setvbuf( __stream: *mut FILE, __buf: *mut ::std::os::raw::c_char, __modes: ::std::os::raw::c_int, __n: size_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn setbuffer(__stream: *mut FILE, __buf: *mut ::std::os::raw::c_char, __size: size_t); } extern "C" { pub fn setlinebuf(__stream: *mut FILE); } extern "C" { pub fn fprintf( __stream: *mut FILE, __format: *const ::std::os::raw::c_char, ... ) -> ::std::os::raw::c_int; } extern "C" { pub fn printf(__format: *const ::std::os::raw::c_char, ...) -> ::std::os::raw::c_int; } extern "C" { pub fn sprintf( __s: *mut ::std::os::raw::c_char, __format: *const ::std::os::raw::c_char, ... ) -> ::std::os::raw::c_int; } extern "C" { pub fn vfprintf( __s: *mut FILE, __format: *const ::std::os::raw::c_char, __arg: *mut __va_list_tag, ) -> ::std::os::raw::c_int; } extern "C" { pub fn vprintf( __format: *const ::std::os::raw::c_char, __arg: *mut __va_list_tag, ) -> ::std::os::raw::c_int; } extern "C" { pub fn vsprintf( __s: *mut ::std::os::raw::c_char, __format: *const ::std::os::raw::c_char, __arg: *mut __va_list_tag, ) -> ::std::os::raw::c_int; } extern "C" { pub fn snprintf( __s: *mut ::std::os::raw::c_char, __maxlen: ::std::os::raw::c_ulong, __format: *const ::std::os::raw::c_char, ... ) -> ::std::os::raw::c_int; } extern "C" { pub fn vsnprintf( __s: *mut ::std::os::raw::c_char, __maxlen: ::std::os::raw::c_ulong, __format: *const ::std::os::raw::c_char, __arg: *mut __va_list_tag, ) -> ::std::os::raw::c_int; } extern "C" { pub fn vdprintf( __fd: ::std::os::raw::c_int, __fmt: *const ::std::os::raw::c_char, __arg: *mut __va_list_tag, ) -> ::std::os::raw::c_int; } extern "C" { pub fn dprintf( __fd: ::std::os::raw::c_int, __fmt: *const ::std::os::raw::c_char, ... ) -> ::std::os::raw::c_int; } extern "C" { pub fn fscanf( __stream: *mut FILE, __format: *const ::std::os::raw::c_char, ... ) -> ::std::os::raw::c_int; } extern "C" { pub fn scanf(__format: *const ::std::os::raw::c_char, ...) -> ::std::os::raw::c_int; } extern "C" { pub fn sscanf( __s: *const ::std::os::raw::c_char, __format: *const ::std::os::raw::c_char, ... ) -> ::std::os::raw::c_int; } extern "C" { #[link_name = "\u{1}__isoc99_fscanf"] pub fn fscanf1( __stream: *mut FILE, __format: *const ::std::os::raw::c_char, ... ) -> ::std::os::raw::c_int; } extern "C" { #[link_name = "\u{1}__isoc99_scanf"] pub fn scanf1(__format: *const ::std::os::raw::c_char, ...) -> ::std::os::raw::c_int; } extern "C" { #[link_name = "\u{1}__isoc99_sscanf"] pub fn sscanf1( __s: *const ::std::os::raw::c_char, __format: *const ::std::os::raw::c_char, ... ) -> ::std::os::raw::c_int; } extern "C" { pub fn vfscanf( __s: *mut FILE, __format: *const ::std::os::raw::c_char, __arg: *mut __va_list_tag, ) -> ::std::os::raw::c_int; } extern "C" { pub fn vscanf( __format: *const ::std::os::raw::c_char, __arg: *mut __va_list_tag, ) -> ::std::os::raw::c_int; } extern "C" { pub fn vsscanf( __s: *const ::std::os::raw::c_char, __format: *const ::std::os::raw::c_char, __arg: *mut __va_list_tag, ) -> ::std::os::raw::c_int; } extern "C" { #[link_name = "\u{1}__isoc99_vfscanf"] pub fn vfscanf1( __s: *mut FILE, __format: *const ::std::os::raw::c_char, __arg: *mut __va_list_tag, ) -> ::std::os::raw::c_int; } extern "C" { #[link_name = "\u{1}__isoc99_vscanf"] pub fn vscanf1( __format: *const ::std::os::raw::c_char, __arg: *mut __va_list_tag, ) -> ::std::os::raw::c_int; } extern "C" { #[link_name = "\u{1}__isoc99_vsscanf"] pub fn vsscanf1( __s: *const ::std::os::raw::c_char, __format: *const ::std::os::raw::c_char, __arg: *mut __va_list_tag, ) -> ::std::os::raw::c_int; } extern "C" { pub fn fgetc(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn getc(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn getchar() -> ::std::os::raw::c_int; } extern "C" { pub fn getc_unlocked(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn getchar_unlocked() -> ::std::os::raw::c_int; } extern "C" { pub fn fgetc_unlocked(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn fputc(__c: ::std::os::raw::c_int, __stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn putc(__c: ::std::os::raw::c_int, __stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn putchar(__c: ::std::os::raw::c_int) -> ::std::os::raw::c_int; } extern "C" { pub fn fputc_unlocked(__c: ::std::os::raw::c_int, __stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn putc_unlocked(__c: ::std::os::raw::c_int, __stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn putchar_unlocked(__c: ::std::os::raw::c_int) -> ::std::os::raw::c_int; } extern "C" { pub fn getw(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn putw(__w: ::std::os::raw::c_int, __stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn fgets( __s: *mut ::std::os::raw::c_char, __n: ::std::os::raw::c_int, __stream: *mut FILE, ) -> *mut ::std::os::raw::c_char; } extern "C" { pub fn __getdelim( __lineptr: *mut *mut ::std::os::raw::c_char, __n: *mut size_t, __delimiter: ::std::os::raw::c_int, __stream: *mut FILE, ) -> __ssize_t; } extern "C" { pub fn getdelim( __lineptr: *mut *mut ::std::os::raw::c_char, __n: *mut size_t, __delimiter: ::std::os::raw::c_int, __stream: *mut FILE, ) -> __ssize_t; } extern "C" { pub fn getline( __lineptr: *mut *mut ::std::os::raw::c_char, __n: *mut size_t, __stream: *mut FILE, ) -> __ssize_t; } extern "C" { pub fn fputs(__s: *const ::std::os::raw::c_char, __stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn puts(__s: *const ::std::os::raw::c_char) -> ::std::os::raw::c_int; } extern "C" { pub fn ungetc(__c: ::std::os::raw::c_int, __stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn fread( __ptr: *mut ::std::os::raw::c_void, __size: ::std::os::raw::c_ulong, __n: ::std::os::raw::c_ulong, __stream: *mut FILE, ) -> ::std::os::raw::c_ulong; } extern "C" { pub fn fwrite( __ptr: *const ::std::os::raw::c_void, __size: ::std::os::raw::c_ulong, __n: ::std::os::raw::c_ulong, __s: *mut FILE, ) -> ::std::os::raw::c_ulong; } extern "C" { pub fn fread_unlocked( __ptr: *mut ::std::os::raw::c_void, __size: size_t, __n: size_t, __stream: *mut FILE, ) -> size_t; } extern "C" { pub fn fwrite_unlocked( __ptr: *const ::std::os::raw::c_void, __size: size_t, __n: size_t, __stream: *mut FILE, ) -> size_t; } extern "C" { pub fn fseek( __stream: *mut FILE, __off: ::std::os::raw::c_long, __whence: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn ftell(__stream: *mut FILE) -> ::std::os::raw::c_long; } extern "C" { pub fn rewind(__stream: *mut FILE); } extern "C" { pub fn fseeko( __stream: *mut FILE, __off: __off_t, __whence: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn ftello(__stream: *mut FILE) -> __off_t; } extern "C" { pub fn fgetpos(__stream: *mut FILE, __pos: *mut fpos_t) -> ::std::os::raw::c_int; } extern "C" { pub fn fsetpos(__stream: *mut FILE, __pos: *const fpos_t) -> ::std::os::raw::c_int; } extern "C" { pub fn clearerr(__stream: *mut FILE); } extern "C" { pub fn feof(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn ferror(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn clearerr_unlocked(__stream: *mut FILE); } extern "C" { pub fn feof_unlocked(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn ferror_unlocked(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn perror(__s: *const ::std::os::raw::c_char); } extern "C" { pub static mut sys_nerr: ::std::os::raw::c_int; } extern "C" { pub static mut sys_errlist: [*const ::std::os::raw::c_char; 0usize]; } extern "C" { pub fn fileno(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn fileno_unlocked(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn popen( __command: *const ::std::os::raw::c_char, __modes: *const ::std::os::raw::c_char, ) -> *mut FILE; } extern "C" { pub fn pclose(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn ctermid(__s: *mut ::std::os::raw::c_char) -> *mut ::std::os::raw::c_char; } extern "C" { pub fn flockfile(__stream: *mut FILE); } extern "C" { pub fn ftrylockfile(__stream: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn funlockfile(__stream: *mut FILE); } extern "C" { pub fn __uflow(arg1: *mut FILE) -> ::std::os::raw::c_int; } extern "C" { pub fn __overflow(arg1: *mut FILE, arg2: ::std::os::raw::c_int) -> ::std::os::raw::c_int; } pub const htsLogLevel_HTS_LOG_OFF: htsLogLevel = 0; pub const htsLogLevel_HTS_LOG_ERROR: htsLogLevel = 1; pub const htsLogLevel_HTS_LOG_WARNING: htsLogLevel = 3; pub const htsLogLevel_HTS_LOG_INFO: htsLogLevel = 4; pub const htsLogLevel_HTS_LOG_DEBUG: htsLogLevel = 5; pub const htsLogLevel_HTS_LOG_TRACE: htsLogLevel = 6; pub type htsLogLevel = ::std::os::raw::c_uint; extern "C" { pub fn hts_set_log_level(level: htsLogLevel); } extern "C" { pub fn hts_get_log_level() -> htsLogLevel; } extern "C" { pub static mut hts_verbose: ::std::os::raw::c_int; } extern "C" { pub fn hts_log( severity: htsLogLevel, context: *const ::std::os::raw::c_char, format: *const ::std::os::raw::c_char, ... ); } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct BGZF { _unused: [u8; 0], } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct cram_fd { _unused: [u8; 0], } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct hFILE { _unused: [u8; 0], } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct hts_tpool { _unused: [u8; 0], } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct kstring_t { pub l: size_t, pub m: size_t, pub s: *mut ::std::os::raw::c_char, } extern "C" { pub fn hts_resize_array_( arg1: size_t, arg2: size_t, arg3: size_t, arg4: *mut ::std::os::raw::c_void, arg5: *mut *mut ::std::os::raw::c_void, arg6: ::std::os::raw::c_int, arg7: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_free(ptr: *mut ::std::os::raw::c_void); } pub const htsFormatCategory_unknown_category: htsFormatCategory = 0; pub const htsFormatCategory_sequence_data: htsFormatCategory = 1; pub const htsFormatCategory_variant_data: htsFormatCategory = 2; pub const htsFormatCategory_index_file: htsFormatCategory = 3; pub const htsFormatCategory_region_list: htsFormatCategory = 4; pub const htsFormatCategory_category_maximum: htsFormatCategory = 32767; pub type htsFormatCategory = ::std::os::raw::c_uint; pub const htsExactFormat_unknown_format: htsExactFormat = 0; pub const htsExactFormat_binary_format: htsExactFormat = 1; pub const htsExactFormat_text_format: htsExactFormat = 2; pub const htsExactFormat_sam: htsExactFormat = 3; pub const htsExactFormat_bam: htsExactFormat = 4; pub const htsExactFormat_bai: htsExactFormat = 5; pub const htsExactFormat_cram: htsExactFormat = 6; pub const htsExactFormat_crai: htsExactFormat = 7; pub const htsExactFormat_vcf: htsExactFormat = 8; pub const htsExactFormat_bcf: htsExactFormat = 9; pub const htsExactFormat_csi: htsExactFormat = 10; pub const htsExactFormat_gzi: htsExactFormat = 11; pub const htsExactFormat_tbi: htsExactFormat = 12; pub const htsExactFormat_bed: htsExactFormat = 13; pub const htsExactFormat_htsget: htsExactFormat = 14; pub const htsExactFormat_json: htsExactFormat = 14; pub const htsExactFormat_empty_format: htsExactFormat = 15; pub const htsExactFormat_fasta_format: htsExactFormat = 16; pub const htsExactFormat_fastq_format: htsExactFormat = 17; pub const htsExactFormat_fai_format: htsExactFormat = 18; pub const htsExactFormat_fqi_format: htsExactFormat = 19; pub const htsExactFormat_format_maximum: htsExactFormat = 32767; pub type htsExactFormat = ::std::os::raw::c_uint; pub const htsCompression_no_compression: htsCompression = 0; pub const htsCompression_gzip: htsCompression = 1; pub const htsCompression_bgzf: htsCompression = 2; pub const htsCompression_custom: htsCompression = 3; pub const htsCompression_bzip2_compression: htsCompression = 4; pub const htsCompression_compression_maximum: htsCompression = 32767; pub type htsCompression = ::std::os::raw::c_uint; #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct htsFormat { pub category: htsFormatCategory, pub format: htsExactFormat, pub version: htsFormat__bindgen_ty_1, pub compression: htsCompression, pub compression_level: ::std::os::raw::c_short, pub specific: *mut ::std::os::raw::c_void, } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct htsFormat__bindgen_ty_1 { pub major: ::std::os::raw::c_short, pub minor: ::std::os::raw::c_short, } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct __hts_idx_t { _unused: [u8; 0], } pub type hts_idx_t = __hts_idx_t; #[repr(C)] #[derive(Copy, Clone)] pub struct htsFile { pub _bitfield_1: __BindgenBitfieldUnit<[u8; 4usize], u32>, pub lineno: i64, pub line: kstring_t, pub fn_: *mut ::std::os::raw::c_char, pub fn_aux: *mut ::std::os::raw::c_char, pub fp: htsFile__bindgen_ty_1, pub state: *mut ::std::os::raw::c_void, pub format: htsFormat, pub idx: *mut hts_idx_t, pub fnidx: *const ::std::os::raw::c_char, pub bam_header: *mut sam_hdr_t, } #[repr(C)] #[derive(Copy, Clone)] pub union htsFile__bindgen_ty_1 { pub bgzf: *mut BGZF, pub cram: *mut cram_fd, pub hfile: *mut hFILE, _bindgen_union_align: u64, } impl htsFile { #[inline] pub fn is_bin(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(0usize, 1u8) as u32) } } #[inline] pub fn set_is_bin(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(0usize, 1u8, val as u64) } } #[inline] pub fn is_write(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(1usize, 1u8) as u32) } } #[inline] pub fn set_is_write(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(1usize, 1u8, val as u64) } } #[inline] pub fn is_be(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(2usize, 1u8) as u32) } } #[inline] pub fn set_is_be(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(2usize, 1u8, val as u64) } } #[inline] pub fn is_cram(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(3usize, 1u8) as u32) } } #[inline] pub fn set_is_cram(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(3usize, 1u8, val as u64) } } #[inline] pub fn is_bgzf(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(4usize, 1u8) as u32) } } #[inline] pub fn set_is_bgzf(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(4usize, 1u8, val as u64) } } #[inline] pub fn dummy(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(5usize, 27u8) as u32) } } #[inline] pub fn set_dummy(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(5usize, 27u8, val as u64) } } #[inline] pub fn new_bitfield_1( is_bin: u32, is_write: u32, is_be: u32, is_cram: u32, is_bgzf: u32, dummy: u32, ) -> __BindgenBitfieldUnit<[u8; 4usize], u32> { let mut __bindgen_bitfield_unit: __BindgenBitfieldUnit<[u8; 4usize], u32> = Default::default(); __bindgen_bitfield_unit.set(0usize, 1u8, { let is_bin: u32 = unsafe { ::std::mem::transmute(is_bin) }; is_bin as u64 }); __bindgen_bitfield_unit.set(1usize, 1u8, { let is_write: u32 = unsafe { ::std::mem::transmute(is_write) }; is_write as u64 }); __bindgen_bitfield_unit.set(2usize, 1u8, { let is_be: u32 = unsafe { ::std::mem::transmute(is_be) }; is_be as u64 }); __bindgen_bitfield_unit.set(3usize, 1u8, { let is_cram: u32 = unsafe { ::std::mem::transmute(is_cram) }; is_cram as u64 }); __bindgen_bitfield_unit.set(4usize, 1u8, { let is_bgzf: u32 = unsafe { ::std::mem::transmute(is_bgzf) }; is_bgzf as u64 }); __bindgen_bitfield_unit.set(5usize, 27u8, { let dummy: u32 = unsafe { ::std::mem::transmute(dummy) }; dummy as u64 }); __bindgen_bitfield_unit } } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct htsThreadPool { pub pool: *mut hts_tpool, pub qsize: ::std::os::raw::c_int, } pub const sam_fields_SAM_QNAME: sam_fields = 1; pub const sam_fields_SAM_FLAG: sam_fields = 2; pub const sam_fields_SAM_RNAME: sam_fields = 4; pub const sam_fields_SAM_POS: sam_fields = 8; pub const sam_fields_SAM_MAPQ: sam_fields = 16; pub const sam_fields_SAM_CIGAR: sam_fields = 32; pub const sam_fields_SAM_RNEXT: sam_fields = 64; pub const sam_fields_SAM_PNEXT: sam_fields = 128; pub const sam_fields_SAM_TLEN: sam_fields = 256; pub const sam_fields_SAM_SEQ: sam_fields = 512; pub const sam_fields_SAM_QUAL: sam_fields = 1024; pub const sam_fields_SAM_AUX: sam_fields = 2048; pub const sam_fields_SAM_RGAUX: sam_fields = 4096; pub type sam_fields = ::std::os::raw::c_uint; pub const hts_fmt_option_CRAM_OPT_DECODE_MD: hts_fmt_option = 0; pub const hts_fmt_option_CRAM_OPT_PREFIX: hts_fmt_option = 1; pub const hts_fmt_option_CRAM_OPT_VERBOSITY: hts_fmt_option = 2; pub const hts_fmt_option_CRAM_OPT_SEQS_PER_SLICE: hts_fmt_option = 3; pub const hts_fmt_option_CRAM_OPT_SLICES_PER_CONTAINER: hts_fmt_option = 4; pub const hts_fmt_option_CRAM_OPT_RANGE: hts_fmt_option = 5; pub const hts_fmt_option_CRAM_OPT_VERSION: hts_fmt_option = 6; pub const hts_fmt_option_CRAM_OPT_EMBED_REF: hts_fmt_option = 7; pub const hts_fmt_option_CRAM_OPT_IGNORE_MD5: hts_fmt_option = 8; pub const hts_fmt_option_CRAM_OPT_REFERENCE: hts_fmt_option = 9; pub const hts_fmt_option_CRAM_OPT_MULTI_SEQ_PER_SLICE: hts_fmt_option = 10; pub const hts_fmt_option_CRAM_OPT_NO_REF: hts_fmt_option = 11; pub const hts_fmt_option_CRAM_OPT_USE_BZIP2: hts_fmt_option = 12; pub const hts_fmt_option_CRAM_OPT_SHARED_REF: hts_fmt_option = 13; pub const hts_fmt_option_CRAM_OPT_NTHREADS: hts_fmt_option = 14; pub const hts_fmt_option_CRAM_OPT_THREAD_POOL: hts_fmt_option = 15; pub const hts_fmt_option_CRAM_OPT_USE_LZMA: hts_fmt_option = 16; pub const hts_fmt_option_CRAM_OPT_USE_RANS: hts_fmt_option = 17; pub const hts_fmt_option_CRAM_OPT_REQUIRED_FIELDS: hts_fmt_option = 18; pub const hts_fmt_option_CRAM_OPT_LOSSY_NAMES: hts_fmt_option = 19; pub const hts_fmt_option_CRAM_OPT_BASES_PER_SLICE: hts_fmt_option = 20; pub const hts_fmt_option_CRAM_OPT_STORE_MD: hts_fmt_option = 21; pub const hts_fmt_option_CRAM_OPT_STORE_NM: hts_fmt_option = 22; pub const hts_fmt_option_HTS_OPT_COMPRESSION_LEVEL: hts_fmt_option = 100; pub const hts_fmt_option_HTS_OPT_NTHREADS: hts_fmt_option = 101; pub const hts_fmt_option_HTS_OPT_THREAD_POOL: hts_fmt_option = 102; pub const hts_fmt_option_HTS_OPT_CACHE_SIZE: hts_fmt_option = 103; pub const hts_fmt_option_HTS_OPT_BLOCK_SIZE: hts_fmt_option = 104; pub type hts_fmt_option = ::std::os::raw::c_uint; #[repr(C)] #[derive(Copy, Clone)] pub struct hts_opt { pub arg: *mut ::std::os::raw::c_char, pub opt: hts_fmt_option, pub val: hts_opt__bindgen_ty_1, pub next: *mut hts_opt, } #[repr(C)] #[derive(Copy, Clone)] pub union hts_opt__bindgen_ty_1 { pub i: ::std::os::raw::c_int, pub s: *mut ::std::os::raw::c_char, _bindgen_union_align: u64, } extern "C" { pub fn hts_opt_add( opts: *mut *mut hts_opt, c_arg: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_opt_apply(fp: *mut htsFile, opts: *mut hts_opt) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_opt_free(opts: *mut hts_opt); } extern "C" { pub fn hts_parse_format( opt: *mut htsFormat, str_: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_parse_opt_list( opt: *mut htsFormat, str_: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub static seq_nt16_table: [::std::os::raw::c_uchar; 256usize]; } extern "C" { pub static mut seq_nt16_str: [::std::os::raw::c_char; 0usize]; } extern "C" { pub static mut seq_nt16_int: [::std::os::raw::c_int; 0usize]; } extern "C" { pub fn hts_version() -> *const ::std::os::raw::c_char; } extern "C" { pub fn hts_detect_format(fp: *mut hFILE, fmt: *mut htsFormat) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_format_description(format: *const htsFormat) -> *mut ::std::os::raw::c_char; } extern "C" { pub fn hts_open( fn_: *const ::std::os::raw::c_char, mode: *const ::std::os::raw::c_char, ) -> *mut htsFile; } extern "C" { pub fn hts_open_format( fn_: *const ::std::os::raw::c_char, mode: *const ::std::os::raw::c_char, fmt: *const htsFormat, ) -> *mut htsFile; } extern "C" { pub fn hts_hopen( fp: *mut hFILE, fn_: *const ::std::os::raw::c_char, mode: *const ::std::os::raw::c_char, ) -> *mut htsFile; } extern "C" { pub fn hts_close(fp: *mut htsFile) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_get_format(fp: *mut htsFile) -> *const htsFormat; } extern "C" { pub fn hts_format_file_extension(format: *const htsFormat) -> *const ::std::os::raw::c_char; } extern "C" { pub fn hts_set_opt(fp: *mut htsFile, opt: hts_fmt_option, ...) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_getline( fp: *mut htsFile, delimiter: ::std::os::raw::c_int, str_: *mut kstring_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_readlines( fn_: *const ::std::os::raw::c_char, _n: *mut ::std::os::raw::c_int, ) -> *mut *mut ::std::os::raw::c_char; } extern "C" { pub fn hts_readlist( fn_: *const ::std::os::raw::c_char, is_file: ::std::os::raw::c_int, _n: *mut ::std::os::raw::c_int, ) -> *mut *mut ::std::os::raw::c_char; } extern "C" { pub fn hts_set_threads(fp: *mut htsFile, n: ::std::os::raw::c_int) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_set_thread_pool(fp: *mut htsFile, p: *mut htsThreadPool) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_set_cache_size(fp: *mut htsFile, n: ::std::os::raw::c_int); } extern "C" { pub fn hts_set_fai_filename( fp: *mut htsFile, fn_aux: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_check_EOF(fp: *mut htsFile) -> ::std::os::raw::c_int; } pub type hts_pos_t = i64; #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct hts_pair_pos_t { pub beg: hts_pos_t, pub end: hts_pos_t, } pub type hts_pair32_t = hts_pair_pos_t; #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct hts_pair64_t { pub u: u64, pub v: u64, } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct hts_pair64_max_t { pub u: u64, pub v: u64, pub max: u64, } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct hts_reglist_t { pub reg: *const ::std::os::raw::c_char, pub intervals: *mut hts_pair_pos_t, pub tid: ::std::os::raw::c_int, pub count: u32, pub min_beg: hts_pos_t, pub max_end: hts_pos_t, } pub type hts_readrec_func = ::std::option::Option< unsafe extern "C" fn( fp: *mut BGZF, data: *mut ::std::os::raw::c_void, r: *mut ::std::os::raw::c_void, tid: *mut ::std::os::raw::c_int, beg: *mut hts_pos_t, end: *mut hts_pos_t, ) -> ::std::os::raw::c_int, >; pub type hts_seek_func = ::std::option::Option< unsafe extern "C" fn( fp: *mut ::std::os::raw::c_void, offset: i64, where_: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int, >; pub type hts_tell_func = ::std::option::Option i64>; #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct hts_itr_t { pub _bitfield_1: __BindgenBitfieldUnit<[u8; 4usize], u32>, pub tid: ::std::os::raw::c_int, pub n_off: ::std::os::raw::c_int, pub i: ::std::os::raw::c_int, pub n_reg: ::std::os::raw::c_int, pub beg: hts_pos_t, pub end: hts_pos_t, pub reg_list: *mut hts_reglist_t, pub curr_tid: ::std::os::raw::c_int, pub curr_reg: ::std::os::raw::c_int, pub curr_intv: ::std::os::raw::c_int, pub curr_beg: hts_pos_t, pub curr_end: hts_pos_t, pub curr_off: u64, pub nocoor_off: u64, pub off: *mut hts_pair64_max_t, pub readrec: hts_readrec_func, pub seek: hts_seek_func, pub tell: hts_tell_func, pub bins: hts_itr_t__bindgen_ty_1, } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct hts_itr_t__bindgen_ty_1 { pub n: ::std::os::raw::c_int, pub m: ::std::os::raw::c_int, pub a: *mut ::std::os::raw::c_int, } impl hts_itr_t { #[inline] pub fn read_rest(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(0usize, 1u8) as u32) } } #[inline] pub fn set_read_rest(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(0usize, 1u8, val as u64) } } #[inline] pub fn finished(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(1usize, 1u8) as u32) } } #[inline] pub fn set_finished(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(1usize, 1u8, val as u64) } } #[inline] pub fn is_cram(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(2usize, 1u8) as u32) } } #[inline] pub fn set_is_cram(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(2usize, 1u8, val as u64) } } #[inline] pub fn nocoor(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(3usize, 1u8) as u32) } } #[inline] pub fn set_nocoor(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(3usize, 1u8, val as u64) } } #[inline] pub fn multi(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(4usize, 1u8) as u32) } } #[inline] pub fn set_multi(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(4usize, 1u8, val as u64) } } #[inline] pub fn dummy(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(5usize, 27u8) as u32) } } #[inline] pub fn set_dummy(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(5usize, 27u8, val as u64) } } #[inline] pub fn new_bitfield_1( read_rest: u32, finished: u32, is_cram: u32, nocoor: u32, multi: u32, dummy: u32, ) -> __BindgenBitfieldUnit<[u8; 4usize], u32> { let mut __bindgen_bitfield_unit: __BindgenBitfieldUnit<[u8; 4usize], u32> = Default::default(); __bindgen_bitfield_unit.set(0usize, 1u8, { let read_rest: u32 = unsafe { ::std::mem::transmute(read_rest) }; read_rest as u64 }); __bindgen_bitfield_unit.set(1usize, 1u8, { let finished: u32 = unsafe { ::std::mem::transmute(finished) }; finished as u64 }); __bindgen_bitfield_unit.set(2usize, 1u8, { let is_cram: u32 = unsafe { ::std::mem::transmute(is_cram) }; is_cram as u64 }); __bindgen_bitfield_unit.set(3usize, 1u8, { let nocoor: u32 = unsafe { ::std::mem::transmute(nocoor) }; nocoor as u64 }); __bindgen_bitfield_unit.set(4usize, 1u8, { let multi: u32 = unsafe { ::std::mem::transmute(multi) }; multi as u64 }); __bindgen_bitfield_unit.set(5usize, 27u8, { let dummy: u32 = unsafe { ::std::mem::transmute(dummy) }; dummy as u64 }); __bindgen_bitfield_unit } } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct aux_key_t { pub key: ::std::os::raw::c_int, pub min_off: u64, pub max_off: u64, } pub type hts_itr_multi_t = hts_itr_t; extern "C" { pub fn hts_idx_init( n: ::std::os::raw::c_int, fmt: ::std::os::raw::c_int, offset0: u64, min_shift: ::std::os::raw::c_int, n_lvls: ::std::os::raw::c_int, ) -> *mut hts_idx_t; } extern "C" { pub fn hts_idx_destroy(idx: *mut hts_idx_t); } extern "C" { pub fn hts_idx_push( idx: *mut hts_idx_t, tid: ::std::os::raw::c_int, beg: hts_pos_t, end: hts_pos_t, offset: u64, is_mapped: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_idx_finish(idx: *mut hts_idx_t, final_offset: u64) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_idx_fmt(idx: *mut hts_idx_t) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_idx_tbi_name( idx: *mut hts_idx_t, tid: ::std::os::raw::c_int, name: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_idx_save( idx: *const hts_idx_t, fn_: *const ::std::os::raw::c_char, fmt: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_idx_save_as( idx: *const hts_idx_t, fn_: *const ::std::os::raw::c_char, fnidx: *const ::std::os::raw::c_char, fmt: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_idx_load( fn_: *const ::std::os::raw::c_char, fmt: ::std::os::raw::c_int, ) -> *mut hts_idx_t; } extern "C" { pub fn hts_idx_load2( fn_: *const ::std::os::raw::c_char, fnidx: *const ::std::os::raw::c_char, ) -> *mut hts_idx_t; } extern "C" { pub fn hts_idx_load3( fn_: *const ::std::os::raw::c_char, fnidx: *const ::std::os::raw::c_char, fmt: ::std::os::raw::c_int, flags: ::std::os::raw::c_int, ) -> *mut hts_idx_t; } extern "C" { pub fn hts_idx_get_meta(idx: *mut hts_idx_t, l_meta: *mut u32) -> *mut u8; } extern "C" { pub fn hts_idx_set_meta( idx: *mut hts_idx_t, l_meta: u32, meta: *mut u8, is_copy: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_idx_get_stat( idx: *const hts_idx_t, tid: ::std::os::raw::c_int, mapped: *mut u64, unmapped: *mut u64, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_idx_get_n_no_coor(idx: *const hts_idx_t) -> u64; } extern "C" { pub fn hts_parse_decimal( str_: *const ::std::os::raw::c_char, strend: *mut *mut ::std::os::raw::c_char, flags: ::std::os::raw::c_int, ) -> ::std::os::raw::c_longlong; } pub type hts_name2id_f = ::std::option::Option< unsafe extern "C" fn( arg1: *mut ::std::os::raw::c_void, arg2: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int, >; pub type hts_id2name_f = ::std::option::Option< unsafe extern "C" fn( arg1: *mut ::std::os::raw::c_void, arg2: ::std::os::raw::c_int, ) -> *const ::std::os::raw::c_char, >; extern "C" { pub fn hts_parse_reg64( str_: *const ::std::os::raw::c_char, beg: *mut hts_pos_t, end: *mut hts_pos_t, ) -> *const ::std::os::raw::c_char; } extern "C" { pub fn hts_parse_reg( str_: *const ::std::os::raw::c_char, beg: *mut ::std::os::raw::c_int, end: *mut ::std::os::raw::c_int, ) -> *const ::std::os::raw::c_char; } extern "C" { pub fn hts_parse_region( s: *const ::std::os::raw::c_char, tid: *mut ::std::os::raw::c_int, beg: *mut hts_pos_t, end: *mut hts_pos_t, getid: hts_name2id_f, hdr: *mut ::std::os::raw::c_void, flags: ::std::os::raw::c_int, ) -> *const ::std::os::raw::c_char; } extern "C" { pub fn hts_itr_query( idx: *const hts_idx_t, tid: ::std::os::raw::c_int, beg: hts_pos_t, end: hts_pos_t, readrec: hts_readrec_func, ) -> *mut hts_itr_t; } extern "C" { pub fn hts_itr_destroy(iter: *mut hts_itr_t); } pub type hts_itr_query_func = ::std::option::Option< unsafe extern "C" fn( idx: *const hts_idx_t, tid: ::std::os::raw::c_int, beg: hts_pos_t, end: hts_pos_t, readrec: hts_readrec_func, ) -> *mut hts_itr_t, >; extern "C" { pub fn hts_itr_querys( idx: *const hts_idx_t, reg: *const ::std::os::raw::c_char, getid: hts_name2id_f, hdr: *mut ::std::os::raw::c_void, itr_query: hts_itr_query_func, readrec: hts_readrec_func, ) -> *mut hts_itr_t; } extern "C" { pub fn hts_itr_next( fp: *mut BGZF, iter: *mut hts_itr_t, r: *mut ::std::os::raw::c_void, data: *mut ::std::os::raw::c_void, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_idx_seqnames( idx: *const hts_idx_t, n: *mut ::std::os::raw::c_int, getid: hts_id2name_f, hdr: *mut ::std::os::raw::c_void, ) -> *mut *const ::std::os::raw::c_char; } pub type hts_itr_multi_query_func = ::std::option::Option< unsafe extern "C" fn(idx: *const hts_idx_t, itr: *mut hts_itr_t) -> ::std::os::raw::c_int, >; extern "C" { pub fn hts_itr_multi_bam(idx: *const hts_idx_t, iter: *mut hts_itr_t) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_itr_multi_cram(idx: *const hts_idx_t, iter: *mut hts_itr_t) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_itr_regions( idx: *const hts_idx_t, reglist: *mut hts_reglist_t, count: ::std::os::raw::c_int, getid: hts_name2id_f, hdr: *mut ::std::os::raw::c_void, itr_specific: hts_itr_multi_query_func, readrec: hts_readrec_func, seek: hts_seek_func, tell: hts_tell_func, ) -> *mut hts_itr_t; } extern "C" { pub fn hts_itr_multi_next( fd: *mut htsFile, iter: *mut hts_itr_t, r: *mut ::std::os::raw::c_void, ) -> ::std::os::raw::c_int; } extern "C" { pub fn hts_reglist_create( argv: *mut *mut ::std::os::raw::c_char, argc: ::std::os::raw::c_int, r_count: *mut ::std::os::raw::c_int, hdr: *mut ::std::os::raw::c_void, getid: hts_name2id_f, ) -> *mut hts_reglist_t; } extern "C" { pub fn hts_reglist_free(reglist: *mut hts_reglist_t, count: ::std::os::raw::c_int); } extern "C" { pub fn hts_file_type(fname: *const ::std::os::raw::c_char) -> ::std::os::raw::c_int; } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct errmod_t { _unused: [u8; 0], } extern "C" { pub fn errmod_init(depcorr: f64) -> *mut errmod_t; } extern "C" { pub fn errmod_destroy(em: *mut errmod_t); } extern "C" { pub fn errmod_cal( em: *const errmod_t, n: ::std::os::raw::c_int, m: ::std::os::raw::c_int, bases: *mut u16, q: *mut f32, ) -> ::std::os::raw::c_int; } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct probaln_par_t { pub d: f32, pub e: f32, pub bw: ::std::os::raw::c_int, } extern "C" { pub fn probaln_glocal( ref_: *const u8, l_ref: ::std::os::raw::c_int, query: *const u8, l_query: ::std::os::raw::c_int, iqual: *const u8, c: *const probaln_par_t, state: *mut ::std::os::raw::c_int, q: *mut u8, ) -> ::std::os::raw::c_int; } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct hts_md5_context { _unused: [u8; 0], } extern "C" { pub fn hts_md5_init() -> *mut hts_md5_context; } extern "C" { pub fn hts_md5_update( ctx: *mut hts_md5_context, data: *const ::std::os::raw::c_void, size: ::std::os::raw::c_ulong, ); } extern "C" { pub fn hts_md5_final(digest: *mut ::std::os::raw::c_uchar, ctx: *mut hts_md5_context); } extern "C" { pub fn hts_md5_reset(ctx: *mut hts_md5_context); } extern "C" { pub fn hts_md5_hex(hex: *mut ::std::os::raw::c_char, digest: *const ::std::os::raw::c_uchar); } extern "C" { pub fn hts_md5_destroy(ctx: *mut hts_md5_context); } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct sam_hrecs_t { _unused: [u8; 0], } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct sam_hdr_t { pub n_targets: i32, pub ignore_sam_err: i32, pub l_text: size_t, pub target_len: *mut u32, pub cigar_tab: *const i8, pub target_name: *mut *mut ::std::os::raw::c_char, pub text: *mut ::std::os::raw::c_char, pub sdict: *mut ::std::os::raw::c_void, pub hrecs: *mut sam_hrecs_t, pub ref_count: u32, } pub type bam_hdr_t = sam_hdr_t; extern "C" { pub static bam_cigar_table: [i8; 256usize]; } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct bam1_core_t { pub pos: hts_pos_t, pub tid: i32, pub bin: u16, pub qual: u8, pub l_extranul: u8, pub flag: u16, pub l_qname: u16, pub n_cigar: u32, pub l_qseq: i32, pub mtid: i32, pub mpos: hts_pos_t, pub isize_: hts_pos_t, } #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct bam1_t { pub core: bam1_core_t, pub id: u64, pub data: *mut u8, pub l_data: ::std::os::raw::c_int, pub m_data: u32, pub _bitfield_1: __BindgenBitfieldUnit<[u8; 4usize], u8>, pub __bindgen_padding_0: u32, } impl bam1_t { #[inline] pub fn mempolicy(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(0usize, 2u8) as u32) } } #[inline] pub fn set_mempolicy(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(0usize, 2u8, val as u64) } } #[inline] pub fn new_bitfield_1(mempolicy: u32) -> __BindgenBitfieldUnit<[u8; 4usize], u8> { let mut __bindgen_bitfield_unit: __BindgenBitfieldUnit<[u8; 4usize], u8> = Default::default(); __bindgen_bitfield_unit.set(0usize, 2u8, { let mempolicy: u32 = unsafe { ::std::mem::transmute(mempolicy) }; mempolicy as u64 }); __bindgen_bitfield_unit } } extern "C" { pub fn sam_hdr_init() -> *mut sam_hdr_t; } extern "C" { pub fn bam_hdr_read(fp: *mut BGZF) -> *mut sam_hdr_t; } extern "C" { pub fn bam_hdr_write(fp: *mut BGZF, h: *const sam_hdr_t) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_destroy(h: *mut sam_hdr_t); } extern "C" { pub fn sam_hdr_dup(h0: *const sam_hdr_t) -> *mut sam_hdr_t; } pub type samFile = htsFile; extern "C" { pub fn sam_hdr_parse(l_text: size_t, text: *const ::std::os::raw::c_char) -> *mut sam_hdr_t; } extern "C" { pub fn sam_hdr_read(fp: *mut samFile) -> *mut sam_hdr_t; } extern "C" { pub fn sam_hdr_write(fp: *mut samFile, h: *const sam_hdr_t) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_length(h: *mut sam_hdr_t) -> size_t; } extern "C" { pub fn sam_hdr_str(h: *mut sam_hdr_t) -> *const ::std::os::raw::c_char; } extern "C" { pub fn sam_hdr_nref(h: *const sam_hdr_t) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_add_lines( h: *mut sam_hdr_t, lines: *const ::std::os::raw::c_char, len: size_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_add_line( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, ... ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_find_line_id( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, ID_key: *const ::std::os::raw::c_char, ID_val: *const ::std::os::raw::c_char, ks: *mut kstring_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_find_line_pos( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, pos: ::std::os::raw::c_int, ks: *mut kstring_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_remove_line_id( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, ID_key: *const ::std::os::raw::c_char, ID_value: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_remove_line_pos( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, position: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_update_line( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, ID_key: *const ::std::os::raw::c_char, ID_value: *const ::std::os::raw::c_char, ... ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_remove_except( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, ID_key: *const ::std::os::raw::c_char, ID_value: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_remove_lines( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, id: *const ::std::os::raw::c_char, rh: *mut ::std::os::raw::c_void, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_count_lines( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_line_index( bh: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, key: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_line_name( bh: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, pos: ::std::os::raw::c_int, ) -> *const ::std::os::raw::c_char; } extern "C" { pub fn sam_hdr_find_tag_id( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, ID_key: *const ::std::os::raw::c_char, ID_value: *const ::std::os::raw::c_char, key: *const ::std::os::raw::c_char, ks: *mut kstring_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_find_tag_pos( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, pos: ::std::os::raw::c_int, key: *const ::std::os::raw::c_char, ks: *mut kstring_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_remove_tag_id( h: *mut sam_hdr_t, type_: *const ::std::os::raw::c_char, ID_key: *const ::std::os::raw::c_char, ID_value: *const ::std::os::raw::c_char, key: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_name2tid( h: *mut sam_hdr_t, ref_: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_hdr_tid2name( h: *const sam_hdr_t, tid: ::std::os::raw::c_int, ) -> *const ::std::os::raw::c_char; } extern "C" { pub fn sam_hdr_tid2len(h: *const sam_hdr_t, tid: ::std::os::raw::c_int) -> hts_pos_t; } extern "C" { pub fn sam_hdr_pg_id( h: *mut sam_hdr_t, name: *const ::std::os::raw::c_char, ) -> *const ::std::os::raw::c_char; } extern "C" { pub fn sam_hdr_add_pg( h: *mut sam_hdr_t, name: *const ::std::os::raw::c_char, ... ) -> ::std::os::raw::c_int; } extern "C" { pub fn stringify_argv( argc: ::std::os::raw::c_int, argv: *mut *mut ::std::os::raw::c_char, ) -> *mut ::std::os::raw::c_char; } extern "C" { pub fn sam_hdr_incr_ref(h: *mut sam_hdr_t); } extern "C" { pub fn bam_init1() -> *mut bam1_t; } extern "C" { pub fn bam_destroy1(b: *mut bam1_t); } extern "C" { pub fn bam_read1(fp: *mut BGZF, b: *mut bam1_t) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_write1(fp: *mut BGZF, b: *const bam1_t) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_copy1(bdst: *mut bam1_t, bsrc: *const bam1_t) -> *mut bam1_t; } extern "C" { pub fn bam_dup1(bsrc: *const bam1_t) -> *mut bam1_t; } extern "C" { pub fn bam_cigar2qlen(n_cigar: ::std::os::raw::c_int, cigar: *const u32) -> hts_pos_t; } extern "C" { pub fn bam_cigar2rlen(n_cigar: ::std::os::raw::c_int, cigar: *const u32) -> hts_pos_t; } extern "C" { pub fn bam_endpos(b: *const bam1_t) -> hts_pos_t; } extern "C" { pub fn bam_str2flag(str_: *const ::std::os::raw::c_char) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_flag2str(flag: ::std::os::raw::c_int) -> *mut ::std::os::raw::c_char; } extern "C" { pub fn bam_set_qname( b: *mut bam1_t, qname: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_idx_init( fp: *mut htsFile, h: *mut sam_hdr_t, min_shift: ::std::os::raw::c_int, fnidx: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_idx_save(fp: *mut htsFile) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_index_load(fp: *mut htsFile, fn_: *const ::std::os::raw::c_char) -> *mut hts_idx_t; } extern "C" { pub fn sam_index_load2( fp: *mut htsFile, fn_: *const ::std::os::raw::c_char, fnidx: *const ::std::os::raw::c_char, ) -> *mut hts_idx_t; } extern "C" { pub fn sam_index_load3( fp: *mut htsFile, fn_: *const ::std::os::raw::c_char, fnidx: *const ::std::os::raw::c_char, flags: ::std::os::raw::c_int, ) -> *mut hts_idx_t; } extern "C" { pub fn sam_index_build( fn_: *const ::std::os::raw::c_char, min_shift: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_index_build2( fn_: *const ::std::os::raw::c_char, fnidx: *const ::std::os::raw::c_char, min_shift: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_index_build3( fn_: *const ::std::os::raw::c_char, fnidx: *const ::std::os::raw::c_char, min_shift: ::std::os::raw::c_int, nthreads: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_itr_queryi( idx: *const hts_idx_t, tid: ::std::os::raw::c_int, beg: hts_pos_t, end: hts_pos_t, ) -> *mut hts_itr_t; } extern "C" { pub fn sam_itr_querys( idx: *const hts_idx_t, hdr: *mut sam_hdr_t, region: *const ::std::os::raw::c_char, ) -> *mut hts_itr_t; } extern "C" { pub fn sam_itr_regions( idx: *const hts_idx_t, hdr: *mut sam_hdr_t, reglist: *mut hts_reglist_t, regcount: ::std::os::raw::c_uint, ) -> *mut hts_itr_t; } extern "C" { pub fn sam_itr_regarray( idx: *const hts_idx_t, hdr: *mut sam_hdr_t, regarray: *mut *mut ::std::os::raw::c_char, regcount: ::std::os::raw::c_uint, ) -> *mut hts_itr_t; } extern "C" { pub fn sam_parse_region( h: *mut sam_hdr_t, s: *const ::std::os::raw::c_char, tid: *mut ::std::os::raw::c_int, beg: *mut hts_pos_t, end: *mut hts_pos_t, flags: ::std::os::raw::c_int, ) -> *const ::std::os::raw::c_char; } extern "C" { pub fn sam_open_mode( mode: *mut ::std::os::raw::c_char, fn_: *const ::std::os::raw::c_char, format: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_open_mode_opts( fn_: *const ::std::os::raw::c_char, mode: *const ::std::os::raw::c_char, format: *const ::std::os::raw::c_char, ) -> *mut ::std::os::raw::c_char; } extern "C" { pub fn sam_hdr_change_HD( h: *mut sam_hdr_t, key: *const ::std::os::raw::c_char, val: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_parse1( s: *mut kstring_t, h: *mut sam_hdr_t, b: *mut bam1_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_format1( h: *const sam_hdr_t, b: *const bam1_t, str_: *mut kstring_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_read1(fp: *mut samFile, h: *mut sam_hdr_t, b: *mut bam1_t) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_write1( fp: *mut samFile, h: *const sam_hdr_t, b: *const bam1_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_aux_get(b: *const bam1_t, tag: *const ::std::os::raw::c_char) -> *mut u8; } extern "C" { pub fn bam_aux2i(s: *const u8) -> i64; } extern "C" { pub fn bam_aux2f(s: *const u8) -> f64; } extern "C" { pub fn bam_aux2A(s: *const u8) -> ::std::os::raw::c_char; } extern "C" { pub fn bam_aux2Z(s: *const u8) -> *mut ::std::os::raw::c_char; } extern "C" { pub fn bam_auxB_len(s: *const u8) -> u32; } extern "C" { pub fn bam_auxB2i(s: *const u8, idx: u32) -> i64; } extern "C" { pub fn bam_auxB2f(s: *const u8, idx: u32) -> f64; } extern "C" { pub fn bam_aux_append( b: *mut bam1_t, tag: *const ::std::os::raw::c_char, type_: ::std::os::raw::c_char, len: ::std::os::raw::c_int, data: *const u8, ) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_aux_del(b: *mut bam1_t, s: *mut u8) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_aux_update_str( b: *mut bam1_t, tag: *const ::std::os::raw::c_char, len: ::std::os::raw::c_int, data: *const ::std::os::raw::c_char, ) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_aux_update_int( b: *mut bam1_t, tag: *const ::std::os::raw::c_char, val: i64, ) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_aux_update_float( b: *mut bam1_t, tag: *const ::std::os::raw::c_char, val: f32, ) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_aux_update_array( b: *mut bam1_t, tag: *const ::std::os::raw::c_char, type_: u8, items: u32, data: *mut ::std::os::raw::c_void, ) -> ::std::os::raw::c_int; } #[repr(C)] #[derive(Copy, Clone)] pub union bam_pileup_cd { pub p: *mut ::std::os::raw::c_void, pub i: i64, pub f: f64, _bindgen_union_align: u64, } #[repr(C)] #[derive(Copy, Clone)] pub struct bam_pileup1_t { pub b: *mut bam1_t, pub qpos: i32, pub indel: ::std::os::raw::c_int, pub level: ::std::os::raw::c_int, pub _bitfield_1: __BindgenBitfieldUnit<[u8; 4usize], u32>, pub cd: bam_pileup_cd, pub cigar_ind: ::std::os::raw::c_int, } impl bam_pileup1_t { #[inline] pub fn is_del(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(0usize, 1u8) as u32) } } #[inline] pub fn set_is_del(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(0usize, 1u8, val as u64) } } #[inline] pub fn is_head(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(1usize, 1u8) as u32) } } #[inline] pub fn set_is_head(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(1usize, 1u8, val as u64) } } #[inline] pub fn is_tail(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(2usize, 1u8) as u32) } } #[inline] pub fn set_is_tail(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(2usize, 1u8, val as u64) } } #[inline] pub fn is_refskip(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(3usize, 1u8) as u32) } } #[inline] pub fn set_is_refskip(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(3usize, 1u8, val as u64) } } #[inline] pub fn aux(&self) -> u32 { unsafe { ::std::mem::transmute(self._bitfield_1.get(5usize, 27u8) as u32) } } #[inline] pub fn set_aux(&mut self, val: u32) { unsafe { let val: u32 = ::std::mem::transmute(val); self._bitfield_1.set(5usize, 27u8, val as u64) } } #[inline] pub fn new_bitfield_1( is_del: u32, is_head: u32, is_tail: u32, is_refskip: u32, aux: u32, ) -> __BindgenBitfieldUnit<[u8; 4usize], u32> { let mut __bindgen_bitfield_unit: __BindgenBitfieldUnit<[u8; 4usize], u32> = Default::default(); __bindgen_bitfield_unit.set(0usize, 1u8, { let is_del: u32 = unsafe { ::std::mem::transmute(is_del) }; is_del as u64 }); __bindgen_bitfield_unit.set(1usize, 1u8, { let is_head: u32 = unsafe { ::std::mem::transmute(is_head) }; is_head as u64 }); __bindgen_bitfield_unit.set(2usize, 1u8, { let is_tail: u32 = unsafe { ::std::mem::transmute(is_tail) }; is_tail as u64 }); __bindgen_bitfield_unit.set(3usize, 1u8, { let is_refskip: u32 = unsafe { ::std::mem::transmute(is_refskip) }; is_refskip as u64 }); __bindgen_bitfield_unit.set(5usize, 27u8, { let aux: u32 = unsafe { ::std::mem::transmute(aux) }; aux as u64 }); __bindgen_bitfield_unit } } pub type bam_plp_auto_f = ::std::option::Option< unsafe extern "C" fn( data: *mut ::std::os::raw::c_void, b: *mut bam1_t, ) -> ::std::os::raw::c_int, >; #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct __bam_plp_t { _unused: [u8; 0], } pub type bam_plp_t = *mut __bam_plp_t; #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct __bam_mplp_t { _unused: [u8; 0], } pub type bam_mplp_t = *mut __bam_mplp_t; extern "C" { pub fn bam_plp_init(func: bam_plp_auto_f, data: *mut ::std::os::raw::c_void) -> bam_plp_t; } extern "C" { pub fn bam_plp_destroy(iter: bam_plp_t); } extern "C" { pub fn bam_plp_push(iter: bam_plp_t, b: *const bam1_t) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_plp_next( iter: bam_plp_t, _tid: *mut ::std::os::raw::c_int, _pos: *mut ::std::os::raw::c_int, _n_plp: *mut ::std::os::raw::c_int, ) -> *const bam_pileup1_t; } extern "C" { pub fn bam_plp_auto( iter: bam_plp_t, _tid: *mut ::std::os::raw::c_int, _pos: *mut ::std::os::raw::c_int, _n_plp: *mut ::std::os::raw::c_int, ) -> *const bam_pileup1_t; } extern "C" { pub fn bam_plp64_next( iter: bam_plp_t, _tid: *mut ::std::os::raw::c_int, _pos: *mut hts_pos_t, _n_plp: *mut ::std::os::raw::c_int, ) -> *const bam_pileup1_t; } extern "C" { pub fn bam_plp64_auto( iter: bam_plp_t, _tid: *mut ::std::os::raw::c_int, _pos: *mut hts_pos_t, _n_plp: *mut ::std::os::raw::c_int, ) -> *const bam_pileup1_t; } extern "C" { pub fn bam_plp_set_maxcnt(iter: bam_plp_t, maxcnt: ::std::os::raw::c_int); } extern "C" { pub fn bam_plp_reset(iter: bam_plp_t); } extern "C" { pub fn bam_plp_constructor( plp: bam_plp_t, func: ::std::option::Option< unsafe extern "C" fn( data: *mut ::std::os::raw::c_void, b: *const bam1_t, cd: *mut bam_pileup_cd, ) -> ::std::os::raw::c_int, >, ); } extern "C" { pub fn bam_plp_destructor( plp: bam_plp_t, func: ::std::option::Option< unsafe extern "C" fn( data: *mut ::std::os::raw::c_void, b: *const bam1_t, cd: *mut bam_pileup_cd, ) -> ::std::os::raw::c_int, >, ); } extern "C" { pub fn bam_plp_insertion( p: *const bam_pileup1_t, ins: *mut kstring_t, del_len: *mut ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_mplp_init( n: ::std::os::raw::c_int, func: bam_plp_auto_f, data: *mut *mut ::std::os::raw::c_void, ) -> bam_mplp_t; } extern "C" { pub fn bam_mplp_init_overlaps(iter: bam_mplp_t) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_mplp_destroy(iter: bam_mplp_t); } extern "C" { pub fn bam_mplp_set_maxcnt(iter: bam_mplp_t, maxcnt: ::std::os::raw::c_int); } extern "C" { pub fn bam_mplp_auto( iter: bam_mplp_t, _tid: *mut ::std::os::raw::c_int, _pos: *mut ::std::os::raw::c_int, n_plp: *mut ::std::os::raw::c_int, plp: *mut *const bam_pileup1_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_mplp64_auto( iter: bam_mplp_t, _tid: *mut ::std::os::raw::c_int, _pos: *mut hts_pos_t, n_plp: *mut ::std::os::raw::c_int, plp: *mut *const bam_pileup1_t, ) -> ::std::os::raw::c_int; } extern "C" { pub fn bam_mplp_reset(iter: bam_mplp_t); } extern "C" { pub fn bam_mplp_constructor( iter: bam_mplp_t, func: ::std::option::Option< unsafe extern "C" fn( data: *mut ::std::os::raw::c_void, b: *const bam1_t, cd: *mut bam_pileup_cd, ) -> ::std::os::raw::c_int, >, ); } extern "C" { pub fn bam_mplp_destructor( iter: bam_mplp_t, func: ::std::option::Option< unsafe extern "C" fn( data: *mut ::std::os::raw::c_void, b: *const bam1_t, cd: *mut bam_pileup_cd, ) -> ::std::os::raw::c_int, >, ); } extern "C" { pub fn sam_cap_mapq( b: *mut bam1_t, ref_: *const ::std::os::raw::c_char, ref_len: hts_pos_t, thres: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } extern "C" { pub fn sam_prob_realn( b: *mut bam1_t, ref_: *const ::std::os::raw::c_char, ref_len: hts_pos_t, flag: ::std::os::raw::c_int, ) -> ::std::os::raw::c_int; } pub type __builtin_va_list = [__va_list_tag; 1usize]; #[repr(C)] #[derive(Debug, Copy, Clone)] pub struct __va_list_tag { pub gp_offset: ::std::os::raw::c_uint, pub fp_offset: ::std::os::raw::c_uint, pub overflow_arg_area: *mut ::std::os::raw::c_void, pub reg_save_area: *mut ::std::os::raw::c_void, }