Returns the next value from the appropriate pipe, deletes * closed pipes and returns */

Find the value of s that maximizes the scaffold N50. */

Return the number of outgoing edges. */

Sort and output the specified paths. */

* Write a single block of a 'variableStep' WIG file. * * @param chr chromosome name * @param start start coordinate of block * @param length lengt

Parse the specified command line. */

* Translate path extension result code to a string. */

* Translate a path in the de Bruijn graph to an equivalent * DNA sequence. */

* Append a contig to the output FASTA stream. */

Print statistics of the specified histogram. h not passed by * reference because we want to make a copy **/

* prints a diagional */

* prints a score matrix */

Process an a branch group extension. */

Remove tips. * For an edge (u,v), remove the vertex v if deg+(u) > 1 * and deg-(v) = 1 and deg+(v) = 0. */

* Generate a Quadratic Residue (QR) seed. The background theory * for QR seeds is described in: * * Egidi, Lavinia, and Giovanni Manzini. "Multi

* Generate a spaced seed pattern (bitmask) for two equal-length * Quadratic Residue (QR) seeds separated by a gap. The first * QR seed is in the

Read a graph from the specified file. */

Read a graph from the specified file. */

Read a graph from the specified file. */

* reads the probability distribution for diagonal lengths from the file * indicated by filename parameter. * * The pointer returned (and the ones i

* reads sequence collection (seq_col) from the file * indicated by filename parameter. * * The pointer returned (and the ones included in the struc

* reads score matrix from the file * indicated by filename parameter. * * The pointer returned (and the ones included in the struct) * has to be

Print an intermediate progress message during assembly */

Remove the specified sequence if it exists. */

Remove the edge (u,v) from this graph. */

Remove the edge (u,v) from this graph. */

Return the status of an MPI request. * Wraps MPI_Request_get_status. */

Reverse complement this k-mer pair. */

Return the reverse complement of this dinucleotide. */

Build scaffold paths, memoized. */

Return the score of the alignment of a and b. * @param [out] consensus the consensus of a and b * @return the score */

Return the sequence of the specified contig node. The sequence * may be ambiguous or reverse complemented. */

Mark this seed as a duplicate. */

Set the last base of each k-mer. */

Shift both k-mer. */

Shift the sequence left and append a new base to the end. * @return the base shifted out */

Return the size of the string. */

Return the number of elements. */

Get the start bit position for the window. */

Return the first symbol of the specified suffix. */

Execute the specified shell command and exit if it fails. */

Calculate the tier overlap between two reads

Return a vector representing this histogram. */

Check if all the queues are empty

Prune tips shorter than maxBranchCull. */

Initialize the uncompress module. */

Extend a suffix array coordinate by one character to the left. */

Check the stop conditions for the bubble growth

Return the nth vertex. */

Returns an iterator-range to the vertices. */

Write a bubble to the specified file. */

the backtrack step in smith_waterman