util

Documentation

Index

• func ByteLengthUint32(n uint32) uint8
• func ByteLengthUint64(n uint64) uint8
• func CtrlByte2ByteLengthsUint32(ctrl byte) int
• func CtrlByte2ByteLengthsUint64(ctrl byte) int
• func Hash64(key uint64) uint64
• func IsLowComplexity(code uint64, k uint8) bool
• func IsLowComplexityDust(code uint64, k uint8) bool
• func KmerBaseAt(code uint64, k uint8, i uint8) uint8
• func KmerHasPrefix(code uint64, prefix uint64, k1, k2 uint8) bool
• func KmerHasSuffix(code uint64, suffix uint64, k1, k2 uint8) bool
• func KmerLongestPrefix(code1, code2 uint64, k1, k2 uint8) uint8
• func KmerPrefix(code uint64, k uint8, n uint8) uint64
• func KmerSuffix(code uint64, k uint8, i uint8) uint64
• func MustKmerHasPrefix(code uint64, prefix uint64, k1, k2 uint8) bool
• func MustKmerHasSuffix(code uint64, suffix uint64, k1, k2 uint8) bool
• func MustKmerLongestPrefix(code1, code2 uint64, k1, k2 uint8) uint8
• func MustSharingPrefixKmersMismatch(code1, code2 uint64, k, p uint8) (n uint8)
• func MustSharingPrefixKmersSuffixMatches(code1, code2 uint64, k, p uint8) (n uint8)
• func Ns(b uint64, k uint8) (code uint64)
• func PutUint32s(buf []byte, v1, v2, v3, v4 uint32) (ctrl byte, n int)
• func PutUint64s(buf []byte, v1, v2 uint64) (ctrl byte, n int)
• func ReverseInts(s []int)
• func SharingPrefixKmersMismatch(code1, code2 uint64, k, p uint8) (n uint8)
• func SharingPrefixKmersSuffixMatches(code1, code2 uint64, k, p uint8) (n uint8)
• func Uint32s(ctrl byte, buf []byte) (v1, v2, v3, v4 uint32, n int)
• func Uint64s(ctrl byte, buf []byte) (v1, v2 uint64, n int)
• func UniqUint64s(list *[]uint64)

Functions

func ByteLengthUint32

func ByteLengthUint32(n uint32) uint8

ByteLengthUint32 returns the minimum number of bytes to store a integer.

func ByteLengthUint64

func ByteLengthUint64(n uint64) uint8

ByteLengthUint64 returns the minimum number of bytes to store a integer.

func CtrlByte2ByteLengthsUint32

func CtrlByte2ByteLengthsUint32(ctrl byte) int

CtrlByte2ByteLengthsUint32 returns the byte length for a given control byte.

func CtrlByte2ByteLengthsUint64

func CtrlByte2ByteLengthsUint64(ctrl byte) int

CtrlByte2ByteLengthsUint64 returns the byte length for a given control byte.

func Hash64

func Hash64(key uint64) uint64

https://gist.github.com/badboy/6267743 . version with mask: https://gist.github.com/lh3/974ced188be2f90422cc .

func IsLowComplexity

func IsLowComplexity(code uint64, k uint8) bool

IsLowComplexity checks k-mer complexity according to the frequencies of 2-mer and 3-mer.

func IsLowComplexityDust

func IsLowComplexityDust(code uint64, k uint8) bool

IsLowComplexity checks k-mer complexity with DUST algorithm

func KmerBaseAt

func KmerBaseAt(code uint64, k uint8, i uint8) uint8

KmerBaseAt returns the base in pos i (0-based).

func KmerHasPrefix

func KmerHasPrefix(code uint64, prefix uint64, k1, k2 uint8) bool

KmerHasPrefix checks if a k-mer has a prefix.

func KmerHasSuffix

func KmerHasSuffix(code uint64, suffix uint64, k1, k2 uint8) bool

KmerHasSuffix checks if a k-mer has a suffix.

func KmerLongestPrefix

func KmerLongestPrefix(code1, code2 uint64, k1, k2 uint8) uint8

KmerLongestPrefix returns the length of the longest prefix.

func KmerPrefix

func KmerPrefix(code uint64, k uint8, n uint8) uint64

KmerPrefix returns the first n bases. n needs to be > 0. The length of the prefix is n.

func KmerSuffix

func KmerSuffix(code uint64, k uint8, i uint8) uint64

KmerSuffix returns the suffix starting from position i (0-based). The length of the suffix is k - commonPrefix.

func MustKmerHasPrefix

func MustKmerHasPrefix(code uint64, prefix uint64, k1, k2 uint8) bool

MustKmerHasPrefix checks if a k-mer has a prefix, by assuming k1>=k2.

func MustKmerHasSuffix

func MustKmerHasSuffix(code uint64, suffix uint64, k1, k2 uint8) bool

MustKmerHasSuffix checks if a k-mer has a suffix, by assuming k1>=k2.

func MustKmerLongestPrefix

func MustKmerLongestPrefix(code1, code2 uint64, k1, k2 uint8) uint8

MustKmerLongestPrefix returns the length of the longest prefix. We assume k1 >= k2.

func MustSharingPrefixKmersMismatch

func MustSharingPrefixKmersMismatch(code1, code2 uint64, k, p uint8) (n uint8)

MustSharingPrefixKmersMismatch counts the number of mismatch between two k-mers sharing with a p-bp prefix. This function assumes p<k.

func MustSharingPrefixKmersSuffixMatches

func MustSharingPrefixKmersSuffixMatches(code1, code2 uint64, k, p uint8) (n uint8)

MustSharingPrefixKmersSuffixMatches counts the number of matches in the suffix region of two k-mers sharing with a p-bp prefix.

func Ns

func Ns(b uint64, k uint8) (code uint64)

func PutUint32s

func PutUint32s(buf []byte, v1, v2, v3, v4 uint32) (ctrl byte, n int)

PutUint32s encodes four uint32s into 4-16 bytes, and returns control byte and encoded byte length.

func PutUint64s

func PutUint64s(buf []byte, v1, v2 uint64) (ctrl byte, n int)

PutUint64s encodes two uint64s into 2-16 bytes, and returns control byte and encoded byte length.

func ReverseInts

func ReverseInts(s []int)

ReverseInts reverses a list of ints

func SharingPrefixKmersMismatch

func SharingPrefixKmersMismatch(code1, code2 uint64, k, p uint8) (n uint8)

SharingPrefixKmersMismatch counts the number of mismatch between two k-mers sharing with a p-bp prefix.

func SharingPrefixKmersSuffixMatches

func SharingPrefixKmersSuffixMatches(code1, code2 uint64, k, p uint8) (n uint8)

SharingPrefixKmersMatches counts the number of matches in the suffix region of two k-mers sharing with a p-bp prefix.

func Uint32s

func Uint32s(ctrl byte, buf []byte) (v1, v2, v3, v4 uint32, n int)

Uint32s decodes encoded bytes.

func Uint64s

func Uint64s(ctrl byte, buf []byte) (v1, v2 uint64, n int)

Uint64s decodes encoded bytes.

func UniqUint64s

func UniqUint64s(list *[]uint64)

UniqUint64s removes duplicates in a uint64 list