Delete a file if it exists */

Return the size (in discrete elements) of the bit array. */

Returns an iterator-range to the vertices. */

Return the bitwise-or of the specified ambiguity codes. */

If the last character of s is c, remove it and return true. */

Free all allocated memory and reset parameters to defaults */

Iterate through the edges of this graph. */

return the direction of growth

Return the specified number formatted as a percent. */

Remove the last k-mer. */

return position of current k-mer */

* Compute hash values for next k-mer to the left and * update internal state. * @param prevKmer k-mer we are rolling into * @param kmer current

Convert the specified ambiguity code to a bitmask. */

Return the complement of the specified nucleotide. */

* Convert each ambiguity code to the lexicographically smallest * matching base. */

* free alignment * */

* frees a diagcol and all data included in it */

Return whether this kmer has any adjacent kmer. */

* Overlay one sequence on top of another to create a new sequence. * In the cases of differences, the bases in the overlaid sequence * take preceden

* * prepares the alignment: calculates the position number of each residue * */

Read a bloom filter from a stream. */

Return the reverse complement of the specified k-mer. */

Write out a dot graph for the specified collection. */

Find the optimal global alignment of the two sequences using the * Needleman-Wunsch algorithm and the improvement by Gotoh to use an * affine gap pe

The size of the alphabet. */

Return the adjacency of this sequence. * @param considerMarks when true, treat a marked vertex as having * no edges */

Return the last character of s and remove it. */

* creates initial empty alignment data structure * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely

Return true if edge (u,v) exists. */

Return true if this sequence has no elements. */

The start of the gap. */

Return the specified path. */

Return the data of the specified key. */

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

Return true if all required members are initialized */

Return whether this seed is a duplciate. */

Mark the specified sequence in both directions. */

Uppercase only bases that are present in original reads. * @return number of mis-matching bases. */

Return the out degree. */

Returns an iterator-range to the out edges of vertex u. */

Return true if no message has been received. */

Remove noise from the histogram. Noise is defined as a * sample x where h[x-1] == 0 && h[x+1] == 0. */

* Reverse complement the hash state, so that rolling right becomes * rolling left, and vice versa. This operation is needed * whenever we reverse

Sample the suffix array. */

Set the specified adjacency. */

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

Swap this graph with graph x. */

Returns the number of unchaste reads. */

Return the first nucleotide. */