Versions in this module Expand all Collapse all v1 v1.0.1 May 1, 2024 Changes in this version + func AlnPosToRefPosCounterSeq(record []dna.Base, AlnPos int, refStart int, alnStart int) int + func ScanN(aln []Fasta, queryName string) [][]int v1.0.0 Aug 25, 2023 Changes in this version + var ErrSeekEndOutsideChr = errors.New("requested bases past end of chr, output truncated") + var ErrSeekStartOutsideChr = errors.New(...) + func AllAreEqual(alpha []Fasta, beta []Fasta) bool + func AllAreEqualIgnoreOrder(alpha []Fasta, beta []Fasta) bool + func AllToUpper(records []Fasta) + func AlnPosToRefPos(record Fasta, AlnPos int) int + func AlnPosToRefPosCounter(record Fasta, AlnPos int, refStart int, alnStart int) int + func AssemblyStats(infile string, countLowerAsGaps bool) (int, int, int, int, int) + func BinFasta(genome []Fasta, binNum int) map[int][]Fasta + func BinGenomeNoBreaks(genome []Fasta, binNum int, minSize int) map[int][]Fasta + func CalculateN50(contigList []int, halfGenome int) int + func GoReadToChan(filename string) <-chan Fasta + func IsEqual(alpha Fasta, beta Fasta) bool + func IsFasta(filename string) bool + func MakeContigList(records []Fasta, countLowerAsGaps bool) []int + func NumSegregatingSites(aln []Fasta) int + func PairwiseMutationDistanceInRange(seq1 Fasta, seq2 Fasta, alnStart int, alnEnd int) int + func PairwiseMutationDistanceReferenceWindow(seq1 Fasta, seq2 Fasta, alnStart int, windowSize int) (int, bool, int) + func ReadToChan(file *fileio.EasyReader, data chan<- Fasta, wg *sync.WaitGroup) + func ReadToString(filename string) map[string]string + func RefPosToAlnPos(record Fasta, RefPos int) int + func RefPosToAlnPosCounter(record Fasta, RefPos int, refStart int, alnStart int) int + func ReverseComplement(record Fasta) + func ReverseComplementAll(records []Fasta) + func SeekByIndex(sr *Seeker, chr, start, end int) ([]dna.Base, error) + func SeekByName(sr *Seeker, chr string, start, end int) ([]dna.Base, error) + func SortByName(seqs []Fasta) + func SortBySeq(seqs []Fasta) + func ToChromInfo(records []Fasta) []chromInfo.ChromInfo + func ToMap(ref []Fasta) map[string][]dna.Base + func ToUpper(fa Fasta) + func Write(filename string, records []Fasta) + func WriteAssemblyStats(assemblyName string, outfile string, N50 int, halfGenome int, genomeLength int, ...) + func WriteFasta(file io.Writer, rec Fasta, lineLength int) + func WriteToFileHandle(file io.Writer, records []Fasta, lineLength int) + type Fasta struct + Name string + Seq []dna.Base + func Copy(f Fasta) Fasta + func CopyAll(f []Fasta) []Fasta + func CopySubset(records []Fasta, start int, end int) []Fasta + func CreateAllGaps(name string, numGaps int) Fasta + func CreateAllNs(name string, numN int) Fasta + func DistColumn(records []Fasta) []Fasta + func Extract(f Fasta, start int, end int, name string) Fasta + func ExtractMulti(records []Fasta, start int, end int) []Fasta + func NextFasta(file *fileio.EasyReader) (Fasta, bool) + func NextFastaForced(file *fileio.EasyReader) (Fasta, bool) + func Read(filename string) []Fasta + func ReadForced(filename string) []Fasta + func Remove(slice []Fasta, i int) []Fasta + func RemoveGaps(records []Fasta) []Fasta + func RemoveMissingMult(records []Fasta) []Fasta + func SegregatingSites(aln []Fasta) []Fasta + func TrimName(fa Fasta) Fasta + type FastaMap map[string][]dna.Base + type Index struct + func CreateIndex(filename string) Index + func (idx Index) String() string + type Seeker struct + func NewSeeker(fasta, index string) *Seeker + func (rs *Seeker) Close() error
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