* Does ceiling division x / y. * Note: x and y must be non-negative and x + y must not overflow. */

Returns true if all tests passed, false otherwise.

* Build Peq table for given query and alphabet. * Peq is table of dimensions alphabetLength+1 x maxNumBlocks. * Bit i of Peq[s * maxNumBlocks + b] i

* @param [in] block * @return Values of cells in block, starting with bottom cell in block. */

* Corresponds to Advance_Block function from Myers. * Calculates one word(block), which is part of a column. * Highest bit of word (one most to the

* Returns new sequence that is reverse of given sequence. * Free returned array with delete[]. */

* Uses Myers' bit-vector algorithm to find edit distance for global(NW) alignment method. * @param [in] Peq Query profile. * @param [in] W Size of

* Checks if alignment is correct. */

* @param alignment * @param alignmentLength * @param endLocation * @return Return start location of alignment in target, if there is none return -1

* Finds one possible alignment that gives optimal score (bestScore). * It will split problem into smaller problems using Hirschberg's algorithm and w

* @param [in] block * @param [in] k * @return True if all cells in block have value larger than k, otherwise false. */

* Uses Myers' bit-vector algorithm to find edit distance for one of semi-global alignment methods. * @param [in] Peq Query profile. * @param [in] W

Reads sequences from fasta file. * @param [in] path Path to fasta file containing sequences. * @param [out] seqs Sequences will be stored here, each

* @param a Element from transformed sequence. * @param b Element from transformed sequence. * @return True if a and b are defined as equal

* Finds one possible alignment that gives optimal score (bestScore). * Uses Hirschberg's algorithm to split problem into two sub-problems, solve them

* Finds one possible alignment that gives optimal score by moving back through the dynamic programming matrix, * that is stored in alignData. Consume

* Writes values of cells in block into given array, starting with first/top cell. * @param [in] block * @param [out] dest Array into which cell val

* Writes values of cells in block into given array, starting with last/bottom cell. * @param [in] block * @param [out] dest Array into which cell v

* Takes char query and char target, recognizes alphabet and transforms them into unsigned char sequences * where elements in sequences are not any mo

For debugging

Check if edlib works for whole range of char values.