NewAlphabet creates a new alphabet from a list of symbols.

NewMultiMap creates a new empty multimap.

****************************************************************************** Concurrent higher-level functions ***********************************

Reverse returns the reverse of sequence. It performs a basic string reversal by working on the bytes. This function expects byte characters in the ra

SetEfficiency gets the estimated fidelity rate of a given set of GoldenGate overhangs.

SetLimit limits the number of active goroutines in this group to at most n. A negative value indicates no limit. Any subsequent call to the Go method

Symbols returns the list of symbols in the alphabet.

Translate will return an amino acid sequence which the given DNA will yield

hairpin calculates the free energy of a hairpin. Args: start: The index of start of hairpin end: The index of end of hairpin foldContext: The

headerWriteHelper helps write SAM headers in an ordered way.

stemEnergy iterates over the structures present in a stem, computes its energy contribution and sets the relevant energy field of the structures.

Bulge calculates the free energy associated with a bulge. Args: start: The start index of the bulge rightOfStart: The index to the right of star

Complement returns the complement of sequence. In [DNA] each nucleotide (A, T, C or G) is has a deterministic pair. A is paired with T and C is paired

ComplementRNA returns the complement of sequence. In [RNA] each nucleotide (A, U, C or G) is has a deterministic pair. A is paired with U and C is pai

Copy returns a deep copy of the translation table. This is to prevent an unintended update of data used in another process, since the tables are gener

EncodeFlag encodes the version, circularity, double-strandedness, and type into a single byte flag. Used for seqhash v2

FindKmerOverlaps finds kmerOverlaps from ligation reactions. It can be used with FindKmers to find ligation events in sequence data. Here is the prob

GcContentFixer is a generator to increase or decrease the overall GcContent of a CDS. GcContent is defined as the percentage of guanine and cytosine b

****************************************************************************** Specific cloning functions begin here. ******************************

Hash2Fragment creates a version 2 fragment seqhash. Fragment seqhashes are a special kind of seqhash that are used to identify fragments, usually rele

NewParser returns a Parser that uses r as the source from which to parse fastq formatted sequences.

NewParser creates a parser from an io.Reader for sam data. For larger alignments, you will want to increase the maxLineSize.

Next parsers the next read from a parser. Returns an `io.EOF` upon EOF.

ProteinSequence returns a random protein sequence string of a given length and seed. All returned sequences start M (Methionine) and end with * (stop

Read returns an enzymeMap from a Rebase data dump

getCodonFrequency takes a DNA sequence and returns a hashmap of its codons and their frequencies.

method to init loop parameters

jacobsonStockmayer entropy extrapolation formula is used for bulges, hairpins, etc that fall outside the maxLenPreCalulated upper limit for pre-calcul

***************************************************************************** End Section: Parsing Into Matrices *************************************

readMulti reads a multi Gbk from path and parses it into a slice of Genbank structs.

****************************************************************************** Aug 10, 2024 Interoperation with CFile ******************************

AddFeature adds a feature to a Genbank struct. NOTE: This method assumes feature is not referenced in another location as this only creates a shallow

BuildFeatureString is a helper function to build gbk feature strings for Build()

BuildLocationString is a recursive function that takes a location object and creates a gbk location string for Build()

****************************************************************************** Dec, 17, 2020 Compromise + Add codon table stuff begins here == Comp

CreateBarcodesWithBannedSequences creates a list of barcodes given a desired barcode length, the maxSubSequence shared in each barcode, Sequences may

Decode returns the symbol at a given index in the alphabet.

DecodeFlag decodes the single byte flag into its constituent parts. Outputs: version, circularity, doubleStranded, dnaRnaProtein. Used for seqhash v2

DeepCopy deep copies a read. Used for when you want to modify optionals then pipe elsewhere.

ForEachKey iterates over the multimap, once for each key with all values passed as a slice. do is a callback that takes the key, values slice for that

FragmentWithOverhangs fragments a sequence with only a certain overhang set. This is useful if you are constraining the set of possible overhangs when

Header returns the header

MapSlice efficiently applies a transformation to each element of a slice to create a new slice

MinimumFreeEnergy returns the free energy of an already folded RNA. For @param sequence A RNA sequence @param dotBracketStructure Se

NewParser returns a Parser that uses r as the source from which to parse genbank formatted sequences.

Next takes in a reader representing a multi gbk/gb/genbank file and outputs the next record

Parse parses the Rebase database into a map of enzymes

****************************************************************************** Nov, 20, 2020 Codon table JSON stuff begins here. In 2007, a Japanese

ParseWithHeader returns all records/reads/lines, plus the header, from the parser. It can only be called once on a given parser because it will read a

Put adds a key-value pair to the multimap.

ReadCodonJSON reads a codonTable JSON file.

RemoveRepeat is a generator to make a problematicSequenceFunc for repeats.

ReverseComplement returns the reversed complement of sequence. It is the equivalent of calling revComplement := Reverse(Complement(sequence)) This

SimulateSimple simulates a PCR reaction. It takes in a list of sequences and a list of primers, with support for complex multiplex reactions, produces

StandardizeDNA returns the alphabetically lesser strand of a double stranded DNA molecule.

Uint32Decode128 32 bits integer using XMM register, AVX

Uint32Decode256 32 bits integer using YMM register, AVX2

Uint32Decode512 32 bits integer using ZMM register, AVX512

Validate validates that the header has all required information, as described in the SAMv1 specification document. Not implemented yet.