This input stream manipulator skips the specified string. */

A vertex of a contig graph, which is a pair of a contig index and * an orientation. */

A k-mer. */

This input stream manipulator discards characters until reaching * the delimeter. */

A pair of k-mer. */

A pair of nucleotides. */

* Records results of processing a sequencing read. * Each instance represents a row in the read log file generated * by the `--read-log` option of `

The length and coverage of a contig. */

No property. */

Skip the specified character if it's next in the input stream. */

Return the better of two distance estimates. * Return the estimate whose error is least, or when the errors are * equal, return the larger distance

Disallow parallel edges. */

A vertex of the overlap graph. */

Iterate through edges. */

A sequence of vertices. */

A contig index. */

A FASTA record. */

A SAM alignment of a query and its mate. */

Functor to add the number of k-mer in two contigs. */

A container of BranchRecord. */

Vertex index property map of a ContigNode. */

Count k-mer. */

The string representation of an edge name. */

A small struct for holding overlap information: just a sequence and offset from the focal read */

The string representation of a vertex name. */

Iterate through the out-edges. */

Iterate through the vertices of this graph. */

Allow parallel edges. */

The coordinates of a gap, its flanking scaftigs, and the sequence that * fills it. */

A contig sequence. */

A counting output iterator. */

DAWG visitor. */

A record of an indexed FASTA file. */

A FASTQ record. */

The coordinates of a gap and its flanking scaftigs. */

Return whether this edge is invalid. * An edge is invalid when the overlap is larger than the length of * either of its incident sequences. */

Return true if the edge e is a path overlap. */

Return true if the edge is a small overlap. */

Return the value of the bit at the specified index. */

A new vertex and two edges that will be added to the graph. */

Stores the output string and the read index number for an * alignment. */

An overlap of two sequences. */

An alignment of two overlapping contigs. */

Return whether the specified edges has sufficient support. */

Return whether the specified edge has sufficient support. */

A tuple of a target ID and position. */

* Represents a vertex in the de Bruijn graph. */

* Iterate over hash values for k-mers in a * given DNA sequence. * * This implementation uses a rolling hash * function to efficiently calculate

A SAM alignment of a single query. */

* Time the duration between the construction and destruction of this * timer object and log that duration. */

A color map that always returns white. */

Return whether the specified edge is inconsistent. */

overlap alignment between two sequences t and h */

Functor used for sorting contigs based on degree, then size, * and then ID. */