BuildIndex builds index from a list of input files.

CheckIndexBuildingOptions checks some important options.

ClearSubstrPairs removes nested/embedded and same anchors.

Note: set should not have duplicates.

Execute adds all child commands to the root command sets flags appropriately.

NewChainer creates a new chainer.

NewChainer creates a new chainer.

NewIndexSearcher creates a new searcher.

NewSeqComparator creates a new SeqComparator with given options.

ParseByteSize parses byte size from string.

RC computes the reverse complement sequence.

RecycleChaining2Result reycles the chaining paths.

RecycleChainingResult reycles the chaining results.

RecycleSeqComparatorResult recycles a SeqComparatorResult.

RecycleSubstrPairs recycles a list of SubstrPairs.

TrimSubStrPairs trims anchors for query/subjects with tandem repeats in either end.

BITS_BATCH_IDX is the number of bits to store the genome batch index.

BITS_FLAGS is the number of bits to store two bits.

BITS_GENOME_IDX is the number of bits to store the genome index.

BITS_IDX is the number of bits to strore batch index and genome index.

BITS_IDX_FLAGS is the sum of BITS_IDX and BITS_FLAGS.

BITS_NONE_IDX is the number of bits to store data except for batch index and genome index.

BITS_NONE_POS is the number of bits except for position.

BITS_POSITION is the number of bits to store the k-mer position/coordinate.

BITS_SUFFIX_IDX is the flag to indicate if the k-mer is reversed.

BITS_STRAND is the flag to indicate if the k-mer is from the reverse complement strand.

DirGenomes is the directory of genomes datas.

DirSeeds is the directory of k-mer-value data files.

ExtSeeds is file extention of k-mer-value data files.

ExtTmpDir is the path extension for temporary files.

FileGenomeChunks store lists of batch+genome index of genome chunks.

FileGenomeIndex maps genome id to genome batch id and index in the batch.

FileGenomes is the name of each genome file.

FileInfo is the summary file.

FileMasks is the file for storing lexichash mask.

FileSeedPositions is the name of seed position file.

MASK_GENOME_IDX is the mask of genome index.

MASK_NONE_IDX is the mask of non-index data.

MASK_REVERSE is the mask of reversed flag.

MAX_GENOME_SIZE is the maximum genome size, 268435456.

NO_VALID_SEQS means there are no valid sequences in a genome file.

TOO_LARGE_GENOME means the genome is too big to index.

TOO_MANY_SEQS means there are too many sequences, as we require: $total_bases + ($num_contigs - 1) * $interval_size <= 268,435,456.

os.Getpagesize().

COMMIT is the last commit.

DefaultChaining2Options is the defalt vaule of Chaining2Option.

DefaultChainingOptions is the defalt vaule of ChainingOption.

DefaultSeqComparatorOptions contains the default options for SeqComparatorOptions.

MainVersion is use for checking compatibility.

MinorVersion is less important.

RootCmd represents the base command when called without any subcommands.

Strands could be used to output strand for a reverse complement flag.

VERSION is the version.

Chain2Result represents a result of a chain.

Chainer is an object for chaining the lexichash substrings between query and reference sequences.

Chainer2 is an object for chaining the anchors in two similar sequences.

Chaining2Options contains all options in chaining.

ChainingOptions contains all options in chaining.

Index creates a LexicMap index from a path and supports searching with query sequences.

IndexBuildingOptions contains all options for building an LexicMap index.

IndexInfo contains summary of the index.

IndexSearchingOptions contains all options for searching.

Options contains the global flags.

Query is an object for each query sequence, it also contains the query result.

SearchResult stores a search result in a genome for the given query sequence.

SeqComparator is for fast and accurate similarity estimation of two sequences, which are in the same strand (important).

SeqComparatorOptions contains options for comparing two sequences.

SeqComparatorResult contains the details of a seq comparison result.

SimilarityDetail is the similarity detail of one reference sequence.

SubstrPair represents a pair of found substrings/seeds, it's also called an anchor.