* auxiliary method that fills random data into the sequence (see next func.) */

The size of the original gap. */

Return the distance from vertex u to v. */

Return the size of the bit array. */

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

Return the largest length of all contig in m. */

Return the earlies position of all contigs in m. */

Return the number of k-mer that have been eroded. */

return the current status of the branch

* heapify */

Initialize global variables for k-mer size and spaced seed pattern */

* PROTEIN DEFAULT VALUES! * ****************************/

Return whether this set has two or more elements. */

Return whether this path is a cycle. */

Return whether the characters a and b match. * @param c [out] the consensus character */

Return true if this branch is longer than maxLength. */

Return a map of contig IDs to their distance along this path. * Repeat contigs, which would have more than one position, are not * represented in th

Mark every contig in path as seen. */

Return the maximum value. */

Return the minimum probability. */

Return the N50. */

Negate each element of this histogram. */

Return the number of edges. */

Open the bubble file. */

Output a new contig. */

Print the load of the hash table. */

Record the trimmed contigs. */

Remove outliers from the histogram. A sample is an outlier * if it is outside the range [Q1 - k*(Q3-Q1), Q3 + k*(Q3-Q1)] * where k = 20. */

Remove paths subsumed by the specified path. * @param seed [out] the ID of the subsuming path * @param overlaps [out] paths that are found to overla

Reset all spaced seed params to their default values */

Build scaffold paths. * @param output write the results * @return the scaffold N50 */

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

Indicate that this is a colour-space collection. */

Set the coverage-related parameters e and c from the given k-mer * coverage histogram. */

sparse_hash_set requires that set_deleted_key() * is called before calling erase(). This key cannot * be an existing kmer in m_data. This function s

Set the next contig name returned by createContigName. */

set the no extension flag

* DNA DEFAULT VALUES! * ****************************/

Shift the k-mer and set the value of the new incoming base. */

Shrink the hash table. */

* prints the given alignment in a simple way. */

Return the size of the bit array. */

Return the number of reads at this position. */

Return the sum. */

Returns the target vertex of this edge. */

Returns the target vertex of this edge. */

Trim off the bottom fraction/2 and top fraction/2 data points. * At least (1 - fraction) of the data will remain. */

Open a pipe to uncompress the specified file. * Not thread safe. * @return a file descriptor */

Clear the specified flag for all vertices. */

Requires len >= 240.

* changes the startpos's and length of the diag such that * it becomes consistent with the given alignment. If the diag * has more than one part tha

Add an edge if the two paths overlap. * @param pivot the pivot at which to seed the alignment * @return whether an overlap was found */

Add edge (u,v) to this graph. */

Adds edge (u,v) to this graph. */

Add a vertex to this graph. */

Align the sequences of the specified paths. * @return the consensus sequence */

Align two sequences using the Needlman-Wunsch algorithm. */

Return whether one ambiguity code is a subset of the other. */

Return the string of Ns. */

Return the largest weight in the arg min of partial sum of * weights. */

Print an intermediate progress message during assembly */