utils

Documentation

Index

• func CountDinuc(seq []byte, wk []int) int
• type Config
  • func ReadConfig(filename string) *Config
• type ReadInSeq
  • func NewReadInSeq(seqfile, dpath string) *ReadInSeq
  • func (ris *ReadInSeq) Next() bool

Functions

func CountDinuc

func CountDinuc(seq []byte, wk []int) int

Types

type Config

type Config struct {

	// The name of the fastq file containing the reads.
	ReadFileName string

	// The name of the fasta or plain text file containing the
	// target sequences (genes).
	GeneFileName string

	// The name of the file containing the target sequence (gene)
	// identifiers.
	GeneIdFileName string

	// The file path where the results are written.
	ResultsFileName string

	// The left end point of each window with a read.
	Windows []int

	// The width of each window.
	WindowWidth int

	// The size of the Bloom filter in bits.
	BloomSize uint64

	// The number of hash functions to use in the Bloom filter.
	NumHash int

	// The minimum allowed proportion of matching bases.
	PMatch float64

	// The exact-match subsequence must have this many distinct
	// dinucleotide subsequences.
	MinDinuc int

	// Use this location to place temporary files.  If blank or
	// missing, a temporary directory is generated of the form
	// tmp/######## in the local directory.
	TempDir string

	// The directory where log files are written.  By default the
	// logs are placed into muscato_logs/###### in the local
	// directory, where the number matches the default prefix of
	// the temporary directory.
	LogDir string

	// Skip all reads shorter than this length.
	MinReadLength int

	// Truncate all reads at this length.
	MaxReadLength int

	// The confirmatory matching step returns at most this many
	// matches for each k-mer seqeunces.  Since a k-mer sequence
	// may match many reads and many genes, setting MaxMatches to
	// a low value may lead to some reads not being mapped, or not
	// multi-mapping as well as possible.
	MaxMatches int

	// The maximum number of confirmation processes that are run
	// simultaneously.
	MaxConfirmProcs int

	// Number of additional mismatches beyond the best possible
	// number of mismatches that are allowed when retaining the
	// target sequence matches to each read.
	MMTol int

	// Either "first" (default) or "best".  If first, returns the
	// first MaxMatches matches for each window.  If best, returns
	// the MaxMatches matches for each window with the fewest
	// mismatched values.
	MatchMode string

	// The number of parallel processes to use for sorting.
	SortPar int

	// The temporary directory for GNU sort.  If not specified,
	// use TempDir/sort.
	SortTemp string

	// The -S parameter for Gnu sort.
	SortMem string

	// If true, temporary files are not removed upon program
	// completion.  If false, which is the default, the temporary
	// files are removed.
	NoCleanTemp bool

	// If true, generate CPU profile data.
	CPUProfile bool
}

func ReadConfig

func ReadConfig(filename string) *Config

type ReadInSeq

type ReadInSeq struct {
	Name string
	Seq  string
	// contains filtered or unexported fields
}

ReadInSeq reads the sequencing reads, returns names and sequences

func NewReadInSeq

func NewReadInSeq(seqfile, dpath string) *ReadInSeq

func (*ReadInSeq) Next

func (ris *ReadInSeq) Next() bool