Add an edge to this vertex. */

Add a vertex to this graph. */

This is the Smith-Waterman algorithm (a variation of * Needleman-Wunsch algorithm), finds one optimal local alignment * Modified to find overlap of

Return the allowed error for the given estimate. */

Return the first nucleotide. */

Return a unicode bar plot. * @param n number of buckets */

Return the number of bytes needed. */

Return the length of the specified path in k-mer. */

Calculate the ContigProperties of a path. */

Remove all edges to and from vertex v. */

Return the size of the FASTA file. */

Find every path that overlaps with the specified path. */

* Finds all diags of each pair of sequences in in_seq_col by using * the function above * * The pointer returned (and the ones included in the s

Return an alignment of the reverse complement of the query to * the same target. */

Open a pipe to uncompress the specified file. * @return a FILE pointer */

get a base code by the byte number and sub index

Return number of distinct nodes visited */

Return the in degree of vertex v. */

Return whether this vertex is a path or a contig. */

Return true if the specified sequence is marked. */

* Process the extension for this branch for the trimming algorithm * CurrSeq is the current sequence being inspected (the next member to * be added

Set the vertex_removed property. */

Return the count of symbol c in s[0, i). */

* calculates the score of the given diag by using the given score matrix. the * resulting score is stored within the diag * omitScore = -1: score

Remove tandem repeats from the set of paths. * @return the removed paths */

Remove the edge to v from this vertex. */

Remove vertex v from this graph. It is assumed that there * are no edges to or from vertex v. It is best to call * clear_vertex before remove_vert

* Initialize hash state from sequence. * @param kmer k-mer used to initialize hash state */

Return the reverse complement of this dinucleotide. */

Return the sequence of the specified contig. */

Set a base by byte number/ sub index beware, this does not check for out of bounds access

* Set the value for a commandline option, using "nolimit" * to represent NO_LIMIT. */

Return the size of this string. */

Return the number of elements in this dictionary. */

Return the size of the bit array. */

* Return the position of the first base of the query on the * target extrapolated from the start of the alignment. */

Remove samples less than the specified threshold. */

Return the specified weighted percentile. */

Add the specified k-mer to this collection. */

Add a branch to this group and extend the new branch with * the given k-mer. */

Add the path overlap edges to the specified graph. */

Returns an iterator-range to the adjacent vertices of * vertex u. */

Align the specified sequences. */

Remove all k-mers with multiplicity lower than the given threshold */

Return the specified element of the suffix array. */

* builds a pathname from a dir-name and a filename. * * The pointer returned (and the ones included in the struct) * has to be deallocted explicit

* Calculate quality string for a pseudo-read. A base will * have a score of CORRECTED_BASE_QUAL if it was corrected * by konnector or added by konn

Calculate the total multiplicity of this branch. */

Return true if checkpoint files exist and are readable */

Return the complementary adjacency. * If the assembly is in colour space, this is a no-op. */

Return the k-mer coverage histogram. */

Iterate through the edges of this graph. */

Extend this branch. */

Extend the specified path as long as is unambiguously possible and * add the result to the specified container. */