Convert the specified bitmask to an ambiguity code. */

* builds the upgma guide tree in the given diag_col */

* Calculate number of bases to trim from left end of sequence. */

* calculates the overlap weight for the given diag */

* Transform a sequence in its canonical orientation. */

Return whether any k-mer in the query is aligned more than once. */

Remove all the edges and vertices from this graph. */

Remove all out edges from this vertex. */

Compare two k-mer. */

* Memory copy with bit-level resolution. * * @param src source data to copy (byte array) * @param dest destination of copied data (byte array) * @

Copy a file */

Return the number of occurrences of the specified symbol. */

* creates the collection of all diags * * The pointer returned (and the ones included in the struct) * has to be deallocted explicitely from m

* create random squence of the given length using the characters * of the given score matrix * * The pointer returned (and the ones included in the

* creates temporary probability distribution */

Get the end bit position for the window. */

Return true if both paths are equal, ignoring ambiguous nodes. */

Return the expected value */

* prints the given alignment in fasta format * to the given file. */

Find a constraint by ID. */

Find suffix overlaps. */

* finds all relevant diags by the DIALIGN METHOD * * The pointer returned (and the ones included in the struct) * has to be deallocted explici

Set the mate mapping fields. */

* Return an alignment flipped as necessary to produce an alignment * pair whose expected orientation is forward-reverse. If the * expected orientat

* frees temporary probability distribution */

* Get the full size (in bits) of the bloom filter that * this window is a part of. */

Return the score of a gap, either newly opened or extended. */

Get the base (ACGT) at a given position */

Return a hash value that does not change with reverse complementation. */

Return the distance from vertex u to v. */

* Get the seed hash value for the current k-mer. The seed hash * value is used to calculate multiple pseudo-independant * hash functions. */

Return the index of the specified name. */

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

Return the terminal nucleotide as a character. */

Return the name of the specified index. */

Get number of distinct edges visited */

Return the number of contigs by which the two paths overlap. */

Return a path, complemented if necessary. */

Return the sequence of vertex u. */

* guided aligner method * NOTE: all diags are freeded within this routine */

Find a path for the specified distance estimates. * @param out [out] the solution path */

Initialize dialign. */

Populate a branch group with the inital branches from a sequence

* Return true if k-mer is in its lexicographically smallest orientation */

Return whether this branch is extendable. */

* Return true if the Bloom filter contains all of the * "good" kmers in the given sequence. */

Return true if this vertex has been removed. */

Load this collection from disk. */

Load a Bloom filter from a file */

Return the minimum value. */

Return the frequency of the most-common base*/