edlib 0.0.3 → 0.0.5

data/ext/edlib/edlib.cpp

@@ -0,0 +1,1482 @@
+#include "edlib.h"
+
+#include <stdint.h>
+#include <cstdlib>
+#include <algorithm>
+#include <vector>
+#include <cstring>
+#include <string>
+
+using namespace std;
+
+typedef uint64_t Word;
+static const int WORD_SIZE = sizeof(Word) * 8; // Size of Word in bits
+static const Word WORD_1 = static_cast<Word>(1);
+static const Word HIGH_BIT_MASK = WORD_1 << (WORD_SIZE - 1);  // 100..00
+static const int MAX_UCHAR = 255;
+
+// Data needed to find alignment.
+struct AlignmentData {
+    Word* Ps;
+    Word* Ms;
+    int* scores;
+    int* firstBlocks;
+    int* lastBlocks;
+
+    AlignmentData(int maxNumBlocks, int targetLength) {
+        // We build a complete table and mark first and last block for each column
+        // (because algorithm is banded so only part of each columns is used).
+        // TODO: do not build a whole table, but just enough blocks for each column.
+         Ps     = new Word[maxNumBlocks * targetLength];
+         Ms     = new Word[maxNumBlocks * targetLength];
+         scores = new  int[maxNumBlocks * targetLength];
+         firstBlocks = new int[targetLength];
+         lastBlocks  = new int[targetLength];
+    }
+
+    ~AlignmentData() {
+        delete[] Ps;
+        delete[] Ms;
+        delete[] scores;
+        delete[] firstBlocks;
+        delete[] lastBlocks;
+    }
+};
+
+struct Block {
+    Word P;  // Pvin
+    Word M;  // Mvin
+    int score; // score of last cell in block;
+
+    Block() {}
+    Block(Word p, Word m, int s) :P(p), M(m), score(s) {}
+};
+
+
+/**
+ * Defines equality relation on alphabet characters.
+ * By default each character is always equal only to itself, but you can also provide additional equalities.
+ */
+class EqualityDefinition {
+private:
+    bool matrix[MAX_UCHAR + 1][MAX_UCHAR + 1];
+public:
+    EqualityDefinition(const string& alphabet,
+                       const EdlibEqualityPair* additionalEqualities = NULL,
+                       const int additionalEqualitiesLength = 0) {
+        for (int i = 0; i < static_cast<int>(alphabet.size()); i++) {
+            for (int j = 0; j < static_cast<int>(alphabet.size()); j++) {
+                matrix[i][j] = (i == j);
+            }
+        }
+        if (additionalEqualities != NULL) {
+            for (int i = 0; i < additionalEqualitiesLength; i++) {
+                size_t firstTransformed = alphabet.find(additionalEqualities[i].first);
+                size_t secondTransformed = alphabet.find(additionalEqualities[i].second);
+                if (firstTransformed != string::npos && secondTransformed != string::npos) {
+                    matrix[firstTransformed][secondTransformed] = matrix[secondTransformed][firstTransformed] = true;
+                }
+            }
+        }
+    }
+
+    /**
+     * @param a  Element from transformed sequence.
+     * @param b  Element from transformed sequence.
+     * @return True if a and b are defined as equal, false otherwise.
+     */
+    bool areEqual(unsigned char a, unsigned char b) const {
+        return matrix[a][b];
+    }
+};
+
+static int myersCalcEditDistanceSemiGlobal(const Word* Peq, int W, int maxNumBlocks,
+                                           int queryLength,
+                                           const unsigned char* target, int targetLength,
+                                           int k, EdlibAlignMode mode,
+                                           int* bestScore_, int** positions_, int* numPositions_);
+
+static int myersCalcEditDistanceNW(const Word* Peq, int W, int maxNumBlocks,
+                                   int queryLength,
+                                   const unsigned char* target, int targetLength,
+                                   int k, int* bestScore_,
+                                   int* position_, bool findAlignment,
+                                   AlignmentData** alignData, int targetStopPosition);
+
+
+static int obtainAlignment(
+        const unsigned char* query, const unsigned char* rQuery, int queryLength,
+        const unsigned char* target, const unsigned char* rTarget, int targetLength,
+        const EqualityDefinition& equalityDefinition, int alphabetLength, int bestScore,
+        unsigned char** alignment, int* alignmentLength);
+
+static int obtainAlignmentHirschberg(
+        const unsigned char* query, const unsigned char* rQuery, int queryLength,
+        const unsigned char* target, const unsigned char* rTarget, int targetLength,
+        const EqualityDefinition& equalityDefinition, int alphabetLength, int bestScore,
+        unsigned char** alignment, int* alignmentLength);
+
+static int obtainAlignmentTraceback(int queryLength, int targetLength,
+                                    int bestScore, const AlignmentData* alignData,
+                                    unsigned char** alignment, int* alignmentLength);
+
+static string transformSequences(const char* queryOriginal, int queryLength,
+                                 const char* targetOriginal, int targetLength,
+                                 unsigned char** queryTransformed,
+                                 unsigned char** targetTransformed);
+
+static inline int ceilDiv(int x, int y);
+
+static inline unsigned char* createReverseCopy(const unsigned char* seq, int length);
+
+static inline Word* buildPeq(const int alphabetLength,
+                             const unsigned char* query,
+                             const int queryLength,
+                             const EqualityDefinition& equalityDefinition);
+
+
+/**
+ * Main edlib method.
+ */
+extern "C" EdlibAlignResult edlibAlign(const char* const queryOriginal, const int queryLength,
+                                       const char* const targetOriginal, const int targetLength,
+                                       const EdlibAlignConfig config) {
+    EdlibAlignResult result;
+    result.status = EDLIB_STATUS_OK;
+    result.editDistance = -1;
+    result.endLocations = result.startLocations = NULL;
+    result.numLocations = 0;
+    result.alignment = NULL;
+    result.alignmentLength = 0;
+    result.alphabetLength = 0;
+
+    /*------------ TRANSFORM SEQUENCES AND RECOGNIZE ALPHABET -----------*/
+    unsigned char* query, * target;
+    string alphabet = transformSequences(queryOriginal, queryLength, targetOriginal, targetLength,
+                                         &query, &target);
+    result.alphabetLength = static_cast<int>(alphabet.size());
+    /*-------------------------------------------------------*/
+
+    // Handle special situation when at least one of the sequences has length 0.
+    if (queryLength == 0 || targetLength == 0) {
+        if (config.mode == EDLIB_MODE_NW) {
+            result.editDistance = std::max(queryLength, targetLength);
+            result.endLocations = static_cast<int *>(malloc(sizeof(int) * 1));
+            result.endLocations[0] = targetLength - 1;
+            result.numLocations = 1;
+        } else if (config.mode == EDLIB_MODE_SHW || config.mode == EDLIB_MODE_HW) {
+            result.editDistance = queryLength;
+            result.endLocations = static_cast<int *>(malloc(sizeof(int) * 1));
+            result.endLocations[0] = -1;
+            result.numLocations = 1;
+        } else {
+            result.status = EDLIB_STATUS_ERROR;
+        }
+
+        free(query);
+        free(target);
+        return result;
+    }
+
+    /*--------------------- INITIALIZATION ------------------*/
+    int maxNumBlocks = ceilDiv(queryLength, WORD_SIZE); // bmax in Myers
+    int W = maxNumBlocks * WORD_SIZE - queryLength; // number of redundant cells in last level blocks
+    EqualityDefinition equalityDefinition(alphabet, config.additionalEqualities, config.additionalEqualitiesLength);
+    Word* Peq = buildPeq(static_cast<int>(alphabet.size()), query, queryLength, equalityDefinition);
+    /*-------------------------------------------------------*/
+
+    /*------------------ MAIN CALCULATION -------------------*/
+    // TODO: Store alignment data only after k is determined? That could make things faster.
+    int positionNW; // Used only when mode is NW.
+    AlignmentData* alignData = NULL;
+    bool dynamicK = false;
+    int k = config.k;
+    if (k < 0) { // If valid k is not given, auto-adjust k until solution is found.
+        dynamicK = true;
+        k = WORD_SIZE; // Gives better results than smaller k.
+    }
+
+    do {
+        if (config.mode == EDLIB_MODE_HW || config.mode == EDLIB_MODE_SHW) {
+            myersCalcEditDistanceSemiGlobal(Peq, W, maxNumBlocks,
+                                            queryLength, target, targetLength,
+                                            k, config.mode, &(result.editDistance),
+                                            &(result.endLocations), &(result.numLocations));
+        } else {  // mode == EDLIB_MODE_NW
+            myersCalcEditDistanceNW(Peq, W, maxNumBlocks,
+                                    queryLength, target, targetLength,
+                                    k, &(result.editDistance), &positionNW,
+                                    false, &alignData, -1);
+        }
+        k *= 2;
+    } while(dynamicK && result.editDistance == -1);
+
+    if (result.editDistance >= 0) {  // If there is solution.
+        // If NW mode, set end location explicitly.
+        if (config.mode == EDLIB_MODE_NW) {
+            result.endLocations = static_cast<int *>(malloc(sizeof(int) * 1));
+            result.endLocations[0] = targetLength - 1;
+            result.numLocations = 1;
+        }
+
+        // Find starting locations.
+        if (config.task == EDLIB_TASK_LOC || config.task == EDLIB_TASK_PATH) {
+            result.startLocations = static_cast<int *>(malloc(result.numLocations * sizeof(int)));
+            if (config.mode == EDLIB_MODE_HW) {  // If HW, I need to calculate start locations.
+                const unsigned char* rTarget = createReverseCopy(target, targetLength);
+                const unsigned char* rQuery  = createReverseCopy(query, queryLength);
+                // Peq for reversed query.
+                Word* rPeq = buildPeq(static_cast<int>(alphabet.size()), rQuery, queryLength, equalityDefinition);
+                for (int i = 0; i < result.numLocations; i++) {
+                    int endLocation = result.endLocations[i];
+                    if (endLocation == -1) {
+                        // NOTE: Sometimes one of optimal solutions is that query starts before target, like this:
+                        //                       AAGG <- target
+                        //                   CCTT     <- query
+                        //   It will never be only optimal solution and it does not happen often, however it is
+                        //   possible and in that case end location will be -1. What should we do with that?
+                        //   Should we just skip reporting such end location, although it is a solution?
+                        //   If we do report it, what is the start location? -4? -1? Nothing?
+                        // TODO: Figure this out. This has to do in general with how we think about start
+                        //   and end locations.
+                        //   Also, we have alignment later relying on this locations to limit the space of it's
+                        //   search -> how can it do it right if these locations are negative or incorrect?
+                        result.startLocations[i] = 0;  // I put 0 for now, but it does not make much sense.
+                    } else {
+                        int bestScoreSHW, numPositionsSHW;
+                        int* positionsSHW;
+                        myersCalcEditDistanceSemiGlobal(
+                                rPeq, W, maxNumBlocks,
+                                queryLength, rTarget + targetLength - endLocation - 1, endLocation + 1,
+                                result.editDistance, EDLIB_MODE_SHW,
+                                &bestScoreSHW, &positionsSHW, &numPositionsSHW);
+                        // Taking last location as start ensures that alignment will not start with insertions
+                        // if it can start with mismatches instead.
+                        result.startLocations[i] = endLocation - positionsSHW[numPositionsSHW - 1];
+                        free(positionsSHW);
+                    }
+                }
+                delete[] rTarget;
+                delete[] rQuery;
+                delete[] rPeq;
+            } else {  // If mode is SHW or NW
+                for (int i = 0; i < result.numLocations; i++) {
+                    result.startLocations[i] = 0;
+                }
+            }
+        }
+
+        // Find alignment -> all comes down to finding alignment for NW.
+        // Currently we return alignment only for first pair of locations.
+        if (config.task == EDLIB_TASK_PATH) {
+            int alnStartLocation = result.startLocations[0];
+            int alnEndLocation = result.endLocations[0];
+            const unsigned char* alnTarget = target + alnStartLocation;
+            const int alnTargetLength = alnEndLocation - alnStartLocation + 1;
+            const unsigned char* rAlnTarget = createReverseCopy(alnTarget, alnTargetLength);
+            const unsigned char* rQuery  = createReverseCopy(query, queryLength);
+            obtainAlignment(query, rQuery, queryLength,
+                            alnTarget, rAlnTarget, alnTargetLength,
+                            equalityDefinition, static_cast<int>(alphabet.size()), result.editDistance,
+                            &(result.alignment), &(result.alignmentLength));
+            delete[] rAlnTarget;
+            delete[] rQuery;
+        }
+    }
+    /*-------------------------------------------------------*/
+
+    //--- Free memory ---//
+    delete[] Peq;
+    free(query);
+    free(target);
+    if (alignData) delete alignData;
+    //-------------------//
+
+    return result;
+}
+
+extern "C" char* edlibAlignmentToCigar(const unsigned char* const alignment, const int alignmentLength,
+                                       const EdlibCigarFormat cigarFormat) {
+    if (cigarFormat != EDLIB_CIGAR_EXTENDED && cigarFormat != EDLIB_CIGAR_STANDARD) {
+        return 0;
+    }
+
+    // Maps move code from alignment to char in cigar.
+    //                        0    1    2    3
+    char moveCodeToChar[] = {'=', 'I', 'D', 'X'};
+    if (cigarFormat == EDLIB_CIGAR_STANDARD) {
+        moveCodeToChar[0] = moveCodeToChar[3] = 'M';
+    }
+
+    vector<char>* cigar = new vector<char>();
+    char lastMove = 0;  // Char of last move. 0 if there was no previous move.
+    int numOfSameMoves = 0;
+    for (int i = 0; i <= alignmentLength; i++) {
+        // if new sequence of same moves started
+        if (i == alignmentLength || (moveCodeToChar[alignment[i]] != lastMove && lastMove != 0)) {
+            // Write number of moves to cigar string.
+            int numDigits = 0;
+            for (; numOfSameMoves; numOfSameMoves /= 10) {
+                cigar->push_back('0' + numOfSameMoves % 10);
+                numDigits++;
+            }
+            reverse(cigar->end() - numDigits, cigar->end());
+            // Write code of move to cigar string.
+            cigar->push_back(lastMove);
+            // If not at the end, start new sequence of moves.
+            if (i < alignmentLength) {
+                // Check if alignment has valid values.
+                if (alignment[i] > 3) {
+                    delete cigar;
+                    return 0;
+                }
+                numOfSameMoves = 0;
+            }
+        }
+        if (i < alignmentLength) {
+            lastMove = moveCodeToChar[alignment[i]];
+            numOfSameMoves++;
+        }
+    }
+    cigar->push_back(0);  // Null character termination.
+    char* cigar_ = static_cast<char *>(malloc(cigar->size() * sizeof(char)));
+    memcpy(cigar_, &(*cigar)[0], cigar->size() * sizeof(char));
+    delete cigar;
+
+    return cigar_;
+}
+
+/**
+ * Build Peq table for given query and alphabet.
+ * Peq is table of dimensions alphabetLength+1 x maxNumBlocks.
+ * Bit i of Peq[s * maxNumBlocks + b] is 1 if i-th symbol from block b of query equals symbol s, otherwise it is 0.
+ * NOTICE: free returned array with delete[]!
+ */
+static inline Word* buildPeq(const int alphabetLength,
+                             const unsigned char* const query,
+                             const int queryLength,
+                             const EqualityDefinition& equalityDefinition) {
+    int maxNumBlocks = ceilDiv(queryLength, WORD_SIZE);
+    // table of dimensions alphabetLength+1 x maxNumBlocks. Last symbol is wildcard.
+    Word* Peq = new Word[(alphabetLength + 1) * maxNumBlocks];
+
+    // Build Peq (1 is match, 0 is mismatch). NOTE: last column is wildcard(symbol that matches anything) with just 1s
+    for (int symbol = 0; symbol <= alphabetLength; symbol++) {
+        for (int b = 0; b < maxNumBlocks; b++) {
+            if (symbol < alphabetLength) {
+                Peq[symbol * maxNumBlocks + b] = 0;
+                for (int r = (b+1) * WORD_SIZE - 1; r >= b * WORD_SIZE; r--) {
+                    Peq[symbol * maxNumBlocks + b] <<= 1;
+                    // NOTE: We pretend like query is padded at the end with W wildcard symbols
+                    if (r >= queryLength || equalityDefinition.areEqual(query[r], symbol))
+                        Peq[symbol * maxNumBlocks + b] += 1;
+                }
+            } else { // Last symbol is wildcard, so it is all 1s
+                Peq[symbol * maxNumBlocks + b] = static_cast<Word>(-1);
+            }
+        }
+    }
+
+    return Peq;
+}
+
+
+/**
+ * Returns new sequence that is reverse of given sequence.
+ * Free returned array with delete[].
+ */
+static inline unsigned char* createReverseCopy(const unsigned char* const seq, const int length) {
+    unsigned char* rSeq = new unsigned char[length];
+    for (int i = 0; i < length; i++) {
+        rSeq[i] = seq[length - i - 1];
+    }
+    return rSeq;
+}
+
+/**
+ * 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 left) is most bottom cell of block from column.
+ * Pv[i] and Mv[i] define vin of cell[i]: vin = cell[i] - cell[i-1].
+ * @param [in] Pv  Bitset, Pv[i] == 1 if vin is +1, otherwise Pv[i] == 0.
+ * @param [in] Mv  Bitset, Mv[i] == 1 if vin is -1, otherwise Mv[i] == 0.
+ * @param [in] Eq  Bitset, Eq[i] == 1 if match, 0 if mismatch.
+ * @param [in] hin  Will be +1, 0 or -1.
+ * @param [out] PvOut  Bitset, PvOut[i] == 1 if vout is +1, otherwise PvOut[i] == 0.
+ * @param [out] MvOut  Bitset, MvOut[i] == 1 if vout is -1, otherwise MvOut[i] == 0.
+ * @param [out] hout  Will be +1, 0 or -1.
+ */
+static inline int calculateBlock(Word Pv, Word Mv, Word Eq, const int hin,
+                                 Word &PvOut, Word &MvOut) {
+    // hin can be 1, -1 or 0.
+    // 1  -> 00...01
+    // 0  -> 00...00
+    // -1 -> 11...11 (2-complement)
+
+    Word hinIsNeg = static_cast<Word>(hin >> 2) & WORD_1; // 00...001 if hin is -1, 00...000 if 0 or 1
+
+    Word Xv = Eq | Mv;
+    // This is instruction below written using 'if': if (hin < 0) Eq |= (Word)1;
+    Eq |= hinIsNeg;
+    Word Xh = (((Eq & Pv) + Pv) ^ Pv) | Eq;
+
+    Word Ph = Mv | ~(Xh | Pv);
+    Word Mh = Pv & Xh;
+
+    int hout = 0;
+    // This is instruction below written using 'if': if (Ph & HIGH_BIT_MASK) hout = 1;
+    hout = (Ph & HIGH_BIT_MASK) >> (WORD_SIZE - 1);
+    // This is instruction below written using 'if': if (Mh & HIGH_BIT_MASK) hout = -1;
+    hout -= (Mh & HIGH_BIT_MASK) >> (WORD_SIZE - 1);
+
+    Ph <<= 1;
+    Mh <<= 1;
+
+    // This is instruction below written using 'if': if (hin < 0) Mh |= (Word)1;
+    Mh |= hinIsNeg;
+    // This is instruction below written using 'if': if (hin > 0) Ph |= (Word)1;
+    Ph |= static_cast<Word>((hin + 1) >> 1);
+
+    PvOut = Mh | ~(Xv | Ph);
+    MvOut = Ph & Xv;
+
+    return hout;
+}
+
+/**
+ * Does ceiling division x / y.
+ * Note: x and y must be non-negative and x + y must not overflow.
+ */
+static inline int ceilDiv(const int x, const int y) {
+    return x % y ? x / y + 1 : x / y;
+}
+
+static inline int min(const int x, const int y) {
+    return x < y ? x : y;
+}
+
+static inline int max(const int x, const int y) {
+    return x > y ? x : y;
+}
+
+
+/**
+ * @param [in] block
+ * @return Values of cells in block, starting with bottom cell in block.
+ */
+static inline vector<int> getBlockCellValues(const Block block) {
+    vector<int> scores(WORD_SIZE);
+    int score = block.score;
+    Word mask = HIGH_BIT_MASK;
+    for (int i = 0; i < WORD_SIZE - 1; i++) {
+        scores[i] = score;
+        if (block.P & mask) score--;
+        if (block.M & mask) score++;
+        mask >>= 1;
+    }
+    scores[WORD_SIZE - 1] = score;
+    return scores;
+}
+
+/**
+ * Writes values of cells in block into given array, starting with first/top cell.
+ * @param [in] block
+ * @param [out] dest  Array into which cell values are written. Must have size of at least WORD_SIZE.
+ */
+static inline void readBlock(const Block block, int* const dest) {
+    int score = block.score;
+    Word mask = HIGH_BIT_MASK;
+    for (int i = 0; i < WORD_SIZE - 1; i++) {
+        dest[WORD_SIZE - 1 - i] = score;
+        if (block.P & mask) score--;
+        if (block.M & mask) score++;
+        mask >>= 1;
+    }
+    dest[0] = score;
+}
+
+/**
+ * Writes values of cells in block into given array, starting with last/bottom cell.
+ * @param [in] block
+ * @param [out] dest  Array into which cell values are written. Must have size of at least WORD_SIZE.
+ */
+static inline void readBlockReverse(const Block block, int* const dest) {
+    int score = block.score;
+    Word mask = HIGH_BIT_MASK;
+    for (int i = 0; i < WORD_SIZE - 1; i++) {
+        dest[i] = score;
+        if (block.P & mask) score--;
+        if (block.M & mask) score++;
+        mask >>= 1;
+    }
+    dest[WORD_SIZE - 1] = score;
+}
+
+/**
+ * @param [in] block
+ * @param [in] k
+ * @return True if all cells in block have value larger than k, otherwise false.
+ */
+static inline bool allBlockCellsLarger(const Block block, const int k) {
+    vector<int> scores = getBlockCellValues(block);
+    for (int i = 0; i < WORD_SIZE; i++) {
+        if (scores[i] <= k) return false;
+    }
+    return true;
+}
+
+
+/**
+ * Uses Myers' bit-vector algorithm to find edit distance for one of semi-global alignment methods.
+ * @param [in] Peq  Query profile.
+ * @param [in] W  Size of padding in last block.
+ *                TODO: Calculate this directly from query, instead of passing it.
+ * @param [in] maxNumBlocks  Number of blocks needed to cover the whole query.
+ *                           TODO: Calculate this directly from query, instead of passing it.
+ * @param [in] queryLength
+ * @param [in] target
+ * @param [in] targetLength
+ * @param [in] k
+ * @param [in] mode  EDLIB_MODE_HW or EDLIB_MODE_SHW
+ * @param [out] bestScore_  Edit distance.
+ * @param [out] positions_  Array of 0-indexed positions in target at which best score was found.
+                            Make sure to free this array with free().
+ * @param [out] numPositions_  Number of positions in the positions_ array.
+ * @return Status.
+ */
+static int myersCalcEditDistanceSemiGlobal(
+        const Word* const Peq, const int W, const int maxNumBlocks,
+        const int queryLength,
+        const unsigned char* const target, const int targetLength,
+        int k, const EdlibAlignMode mode,
+        int* const bestScore_, int** const positions_, int* const numPositions_) {
+    *positions_ = NULL;
+    *numPositions_ = 0;
+
+    // firstBlock is 0-based index of first block in Ukkonen band.
+    // lastBlock is 0-based index of last block in Ukkonen band.
+    int firstBlock = 0;
+    int lastBlock = min(ceilDiv(k + 1, WORD_SIZE), maxNumBlocks) - 1; // y in Myers
+    Block *bl; // Current block
+
+    Block* blocks = new Block[maxNumBlocks];
+
+    // For HW, solution will never be larger then queryLength.
+    if (mode == EDLIB_MODE_HW) {
+        k = min(queryLength, k);
+    }
+
+    // Each STRONG_REDUCE_NUM column is reduced in more expensive way.
+    // This gives speed up of about 2 times for small k.
+    const int STRONG_REDUCE_NUM = 2048;
+
+    // Initialize P, M and score
+    bl = blocks;
+    for (int b = 0; b <= lastBlock; b++) {
+        bl->score = (b + 1) * WORD_SIZE;
+        bl->P = static_cast<Word>(-1); // All 1s
+        bl->M = static_cast<Word>(0);
+        bl++;
+    }
+
+    int bestScore = -1;
+    vector<int> positions; // TODO: Maybe put this on heap?
+    const int startHout = mode == EDLIB_MODE_HW ? 0 : 1; // If 0 then gap before query is not penalized;
+    const unsigned char* targetChar = target;
+    for (int c = 0; c < targetLength; c++) { // for each column
+        const Word* Peq_c = Peq + (*targetChar) * maxNumBlocks;
+
+        //----------------------- Calculate column -------------------------//
+        int hout = startHout;
+        bl = blocks + firstBlock;
+        Peq_c += firstBlock;
+        for (int b = firstBlock; b <= lastBlock; b++) {
+            hout = calculateBlock(bl->P, bl->M, *Peq_c, hout, bl->P, bl->M);
+            bl->score += hout;
+            bl++; Peq_c++;
+        }
+        bl--; Peq_c--;
+        //------------------------------------------------------------------//
+
+        //---------- Adjust number of blocks according to Ukkonen ----------//
+        if ((lastBlock < maxNumBlocks - 1) && (bl->score - hout <= k) // bl is pointing to last block
+            && ((*(Peq_c + 1) & WORD_1) || hout < 0)) { // Peq_c is pointing to last block
+            // If score of left block is not too big, calculate one more block
+            lastBlock++; bl++; Peq_c++;
+            bl->P = static_cast<Word>(-1); // All 1s
+            bl->M = static_cast<Word>(0);
+            bl->score = (bl - 1)->score - hout + WORD_SIZE + calculateBlock(bl->P, bl->M, *Peq_c, hout, bl->P, bl->M);
+        } else {
+            while (lastBlock >= firstBlock && bl->score >= k + WORD_SIZE) {
+                lastBlock--; bl--; Peq_c--;
+            }
+        }
+
+        // Every some columns, do some expensive but also more efficient block reducing.
+        // This is important!
+        //
+        // Reduce the band by decreasing last block if possible.
+        if (c % STRONG_REDUCE_NUM == 0) {
+            while (lastBlock >= 0 && lastBlock >= firstBlock && allBlockCellsLarger(*bl, k)) {
+                lastBlock--; bl--; Peq_c--;
+            }
+        }
+        // For HW, even if all cells are > k, there still may be solution in next
+        // column because starting conditions at upper boundary are 0.
+        // That means that first block is always candidate for solution,
+        // and we can never end calculation before last column.
+        if (mode == EDLIB_MODE_HW && lastBlock == -1) {
+            lastBlock++; bl++; Peq_c++;
+        }
+
+        // Reduce band by increasing first block if possible. Not applicable to HW.
+        if (mode != EDLIB_MODE_HW) {
+            while (firstBlock <= lastBlock && blocks[firstBlock].score >= k + WORD_SIZE) {
+                firstBlock++;
+            }
+            if (c % STRONG_REDUCE_NUM == 0) { // Do strong reduction every some blocks
+                while (firstBlock <= lastBlock && allBlockCellsLarger(blocks[firstBlock], k)) {
+                    firstBlock++;
+                }
+            }
+        }
+
+        // If band stops to exist finish
+        if (lastBlock < firstBlock) {
+            *bestScore_ = bestScore;
+            if (bestScore != -1) {
+                *positions_ = static_cast<int *>(malloc(sizeof(int) * static_cast<int>(positions.size())));
+                *numPositions_ = static_cast<int>(positions.size());
+                copy(positions.begin(), positions.end(), *positions_);
+            }
+            delete[] blocks;
+            return EDLIB_STATUS_OK;
+        }
+        //------------------------------------------------------------------//
+
+        //------------------------- Update best score ----------------------//
+        if (lastBlock == maxNumBlocks - 1) {
+            int colScore = bl->score;
+            if (colScore <= k) { // Scores > k dont have correct values (so we cannot use them), but are certainly > k.
+                // NOTE: Score that I find in column c is actually score from column c-W
+                if (bestScore == -1 || colScore <= bestScore) {
+                    if (colScore != bestScore) {
+                        positions.clear();
+                        bestScore = colScore;
+                        // Change k so we will look only for equal or better
+                        // scores then the best found so far.
+                        k = bestScore;
+                    }
+                    positions.push_back(c - W);
+                }
+            }
+        }
+        //------------------------------------------------------------------//
+
+        targetChar++;
+    }
+
+
+    // Obtain results for last W columns from last column.
+    if (lastBlock == maxNumBlocks - 1) {
+        vector<int> blockScores = getBlockCellValues(*bl);
+        for (int i = 0; i < W; i++) {
+            int colScore = blockScores[i + 1];
+            if (colScore <= k && (bestScore == -1 || colScore <= bestScore)) {
+                if (colScore != bestScore) {
+                    positions.clear();
+                    k = bestScore = colScore;
+                }
+                positions.push_back(targetLength - W + i);
+            }
+        }
+    }
+
+    *bestScore_ = bestScore;
+    if (bestScore != -1) {
+        *positions_ = static_cast<int *>(malloc(sizeof(int) * static_cast<int>(positions.size())));
+        *numPositions_ = static_cast<int>(positions.size());
+        copy(positions.begin(), positions.end(), *positions_);
+    }
+
+    delete[] blocks;
+    return EDLIB_STATUS_OK;
+}
+
+
+/**
+ * Uses Myers' bit-vector algorithm to find edit distance for global(NW) alignment method.
+ * @param [in] Peq  Query profile.
+ * @param [in] W  Size of padding in last block.
+ *                TODO: Calculate this directly from query, instead of passing it.
+ * @param [in] maxNumBlocks  Number of blocks needed to cover the whole query.
+ *                           TODO: Calculate this directly from query, instead of passing it.
+ * @param [in] queryLength
+ * @param [in] target
+ * @param [in] targetLength
+ * @param [in] k
+ * @param [out] bestScore_  Edit distance.
+ * @param [out] position_  0-indexed position in target at which best score was found.
+ * @param [in] findAlignment  If true, whole matrix is remembered and alignment data is returned.
+ *                            Quadratic amount of memory is consumed.
+ * @param [out] alignData  Data needed for alignment traceback (for reconstruction of alignment).
+ *                         Set only if findAlignment is set to true, otherwise it is NULL.
+ *                         Make sure to free this array using delete[].
+ * @param [out] targetStopPosition  If set to -1, whole calculation is performed normally, as expected.
+ *         If set to p, calculation is performed up to position p in target (inclusive)
+ *         and column p is returned as the only column in alignData.
+ * @return Status.
+ */
+static int myersCalcEditDistanceNW(const Word* const Peq, const int W, const int maxNumBlocks,
+                                   const int queryLength,
+                                   const unsigned char* const target, const int targetLength,
+                                   int k, int* const bestScore_,
+                                   int* const position_, const bool findAlignment,
+                                   AlignmentData** const alignData, const int targetStopPosition) {
+    if (targetStopPosition > -1 && findAlignment) {
+        // They can not be both set at the same time!
+        return EDLIB_STATUS_ERROR;
+    }
+
+    // Each STRONG_REDUCE_NUM column is reduced in more expensive way.
+    const int STRONG_REDUCE_NUM = 2048; // TODO: Choose this number dinamically (based on query and target lengths?), so it does not affect speed of computation
+
+    if (k < abs(targetLength - queryLength)) {
+        *bestScore_ = *position_ = -1;
+        return EDLIB_STATUS_OK;
+    }
+
+    k = min(k, max(queryLength, targetLength));  // Upper bound for k
+
+    // firstBlock is 0-based index of first block in Ukkonen band.
+    // lastBlock is 0-based index of last block in Ukkonen band.
+    int firstBlock = 0;
+    // This is optimal now, by my formula.
+    int lastBlock = min(maxNumBlocks, ceilDiv(min(k, (k + queryLength - targetLength) / 2) + 1, WORD_SIZE)) - 1;
+    Block* bl; // Current block
+
+    Block* blocks = new Block[maxNumBlocks];
+
+    // Initialize P, M and score
+    bl = blocks;
+    for (int b = 0; b <= lastBlock; b++) {
+        bl->score = (b + 1) * WORD_SIZE;
+        bl->P = static_cast<Word>(-1); // All 1s
+        bl->M = static_cast<Word>(0);
+        bl++;
+    }
+
+    // If we want to find alignment, we have to store needed data.
+    if (findAlignment)
+        *alignData = new AlignmentData(maxNumBlocks, targetLength);
+    else if (targetStopPosition > -1)
+        *alignData = new AlignmentData(maxNumBlocks, 1);
+    else
+        *alignData = NULL;
+
+    const unsigned char* targetChar = target;
+    for (int c = 0; c < targetLength; c++) { // for each column
+        const Word* Peq_c = Peq + *targetChar * maxNumBlocks;
+
+        //----------------------- Calculate column -------------------------//
+        int hout = 1;
+        bl = blocks + firstBlock;
+        for (int b = firstBlock; b <= lastBlock; b++) {
+            hout = calculateBlock(bl->P, bl->M, Peq_c[b], hout, bl->P, bl->M);
+            bl->score += hout;
+            bl++;
+        }
+        bl--;
+        //------------------------------------------------------------------//
+        // bl now points to last block
+
+        // Update k. I do it only on end of column because it would slow calculation too much otherwise.
+        // NOTICE: I add W when in last block because it is actually result from W cells to the left and W cells up.
+        k = min(k, bl->score
+                + max(targetLength - c - 1, queryLength - ((1 + lastBlock) * WORD_SIZE - 1) - 1)
+                + (lastBlock == maxNumBlocks - 1 ? W : 0));
+
+        //---------- Adjust number of blocks according to Ukkonen ----------//
+        //--- Adjust last block ---//
+        // If block is not beneath band, calculate next block. Only next because others are certainly beneath band.
+        if (lastBlock + 1 < maxNumBlocks
+            && !(//score[lastBlock] >= k + WORD_SIZE ||  // NOTICE: this condition could be satisfied if above block also!
+                 ((lastBlock + 1) * WORD_SIZE - 1
+                  > k - bl->score + 2 * WORD_SIZE - 2 - targetLength + c + queryLength))) {
+            lastBlock++; bl++;
+            bl->P = static_cast<Word>(-1); // All 1s
+            bl->M = static_cast<Word>(0);
+            int newHout = calculateBlock(bl->P, bl->M, Peq_c[lastBlock], hout, bl->P, bl->M);
+            bl->score = (bl - 1)->score - hout + WORD_SIZE + newHout;
+            hout = newHout;
+        }
+
+        // While block is out of band, move one block up.
+        // NOTE: Condition used here is more loose than the one from the article, since I simplified the max() part of it.
+        // I could consider adding that max part, for optimal performance.
+        while (lastBlock >= firstBlock
+               && (bl->score >= k + WORD_SIZE
+                   || ((lastBlock + 1) * WORD_SIZE - 1 >
+                       // TODO: Does not work if do not put +1! Why???
+                       k - bl->score + 2 * WORD_SIZE - 2 - targetLength + c + queryLength + 1))) {
+            lastBlock--; bl--;
+        }
+        //-------------------------//
+
+        //--- Adjust first block ---//
+        // While outside of band, advance block
+        while (firstBlock <= lastBlock
+               && (blocks[firstBlock].score >= k + WORD_SIZE
+                   || ((firstBlock + 1) * WORD_SIZE - 1 <
+                       blocks[firstBlock].score - k - targetLength + queryLength + c))) {
+            firstBlock++;
+        }
+        //--------------------------/
+
+
+        // TODO: consider if this part is useful, it does not seem to help much
+        if (c % STRONG_REDUCE_NUM == 0) { // Every some columns do more expensive but more efficient reduction
+            while (lastBlock >= firstBlock) {
+                // If all cells outside of band, remove block
+                vector<int> scores = getBlockCellValues(*bl);
+                int numCells = lastBlock == maxNumBlocks - 1 ? WORD_SIZE - W : WORD_SIZE;
+                int r = lastBlock * WORD_SIZE + numCells - 1;
+                bool reduce = true;
+                for (int i = WORD_SIZE - numCells; i < WORD_SIZE; i++) {
+                    // TODO: Does not work if do not put +1! Why???
+                    if (scores[i] <= k && r <= k - scores[i] - targetLength + c + queryLength + 1) {
+                        reduce = false;
+                        break;
+                    }
+                    r--;
+                }
+                if (!reduce) break;
+                lastBlock--; bl--;
+            }
+
+            while (firstBlock <= lastBlock) {
+                // If all cells outside of band, remove block
+                vector<int> scores = getBlockCellValues(blocks[firstBlock]);
+                int numCells = firstBlock == maxNumBlocks - 1 ? WORD_SIZE - W : WORD_SIZE;
+                int r = firstBlock * WORD_SIZE + numCells - 1;
+                bool reduce = true;
+                for (int i = WORD_SIZE - numCells; i < WORD_SIZE; i++) {
+                    if (scores[i] <= k && r >= scores[i] - k - targetLength + c + queryLength) {
+                        reduce = false;
+                        break;
+                    }
+                    r--;
+                }
+                if (!reduce) break;
+                firstBlock++;
+            }
+        }
+
+
+        // If band stops to exist finish
+        if (lastBlock < firstBlock) {
+            *bestScore_ = *position_ = -1;
+            delete[] blocks;
+            return EDLIB_STATUS_OK;
+        }
+        //------------------------------------------------------------------//
+
+
+        //---- Save column so it can be used for reconstruction ----//
+        if (findAlignment && c < targetLength) {
+            bl = blocks + firstBlock;
+            for (int b = firstBlock; b <= lastBlock; b++) {
+                (*alignData)->Ps[maxNumBlocks * c + b] = bl->P;
+                (*alignData)->Ms[maxNumBlocks * c + b] = bl->M;
+                (*alignData)->scores[maxNumBlocks * c + b] = bl->score;
+                (*alignData)->firstBlocks[c] = firstBlock;
+                (*alignData)->lastBlocks[c] = lastBlock;
+                bl++;
+            }
+        }
+        //----------------------------------------------------------//
+        //---- If this is stop column, save it and finish ----//
+        if (c == targetStopPosition) {
+            for (int b = firstBlock; b <= lastBlock; b++) {
+                (*alignData)->Ps[b] = (blocks + b)->P;
+                (*alignData)->Ms[b] = (blocks + b)->M;
+                (*alignData)->scores[b] = (blocks + b)->score;
+                (*alignData)->firstBlocks[0] = firstBlock;
+                (*alignData)->lastBlocks[0] = lastBlock;
+            }
+            *bestScore_ = -1;
+            *position_ = targetStopPosition;
+            delete[] blocks;
+            return EDLIB_STATUS_OK;
+        }
+        //----------------------------------------------------//
+
+        targetChar++;
+    }
+
+    if (lastBlock == maxNumBlocks - 1) { // If last block of last column was calculated
+        // Obtain best score from block -> it is complicated because query is padded with W cells
+        int bestScore = getBlockCellValues(blocks[lastBlock])[W];
+        if (bestScore <= k) {
+            *bestScore_ = bestScore;
+            *position_ = targetLength - 1;
+            delete[] blocks;
+            return EDLIB_STATUS_OK;
+        }
+    }
+
+    *bestScore_ = *position_ = -1;
+    delete[] blocks;
+    return EDLIB_STATUS_OK;
+}
+
+
+/**
+ * Finds one possible alignment that gives optimal score by moving back through the dynamic programming matrix,
+ * that is stored in alignData. Consumes large amount of memory: O(queryLength * targetLength).
+ * @param [in] queryLength  Normal length, without W.
+ * @param [in] targetLength  Normal length, without W.
+ * @param [in] bestScore  Best score.
+ * @param [in] alignData  Data obtained during finding best score that is useful for finding alignment.
+ * @param [out] alignment  Alignment.
+ * @param [out] alignmentLength  Length of alignment.
+ * @return Status code.
+ */
+static int obtainAlignmentTraceback(const int queryLength, const int targetLength,
+                                    const int bestScore, const AlignmentData* const alignData,
+                                    unsigned char** const alignment, int* const alignmentLength) {
+    const int maxNumBlocks = ceilDiv(queryLength, WORD_SIZE);
+    const int W = maxNumBlocks * WORD_SIZE - queryLength;
+
+    *alignment = static_cast<unsigned char*>(malloc((queryLength + targetLength - 1) * sizeof(unsigned char)));
+    *alignmentLength = 0;
+    int c = targetLength - 1; // index of column
+    int b = maxNumBlocks - 1; // index of block in column
+    int currScore = bestScore; // Score of current cell
+    int lScore  = -1; // Score of left cell
+    int uScore  = -1; // Score of upper cell
+    int ulScore = -1; // Score of upper left cell
+    Word currP = alignData->Ps[c * maxNumBlocks + b]; // P of current block
+    Word currM = alignData->Ms[c * maxNumBlocks + b]; // M of current block
+    // True if block to left exists and is in band
+    bool thereIsLeftBlock = c > 0 && b >= alignData->firstBlocks[c-1] && b <= alignData->lastBlocks[c-1];
+    // We set initial values of lP and lM to 0 only to avoid compiler warnings, they should not affect the
+    // calculation as both lP and lM should be initialized at some moment later (but compiler can not
+    // detect it since this initialization is guaranteed by "business" logic).
+    Word lP = 0, lM = 0;
+    if (thereIsLeftBlock) {
+        lP = alignData->Ps[(c - 1) * maxNumBlocks + b]; // P of block to the left
+        lM = alignData->Ms[(c - 1) * maxNumBlocks + b]; // M of block to the left
+    }
+    currP <<= W;
+    currM <<= W;
+    int blockPos = WORD_SIZE - W - 1; // 0 based index of current cell in blockPos
+
+    // TODO(martin): refactor this whole piece of code. There are too many if-else statements,
+    // it is too easy for a bug to hide and to hard to effectively cover all the edge-cases.
+    // We need better separation of logic and responsibilities.
+    while (true) {
+        if (c == 0) {
+            thereIsLeftBlock = true;
+            lScore = b * WORD_SIZE + blockPos + 1;
+            ulScore = lScore - 1;
+        }
+
+        // TODO: improvement: calculate only those cells that are needed,
+        //       for example if I calculate upper cell and can move up,
+        //       there is no need to calculate left and upper left cell
+        //---------- Calculate scores ---------//
+        if (lScore == -1 && thereIsLeftBlock) {
+            lScore = alignData->scores[(c - 1) * maxNumBlocks + b]; // score of block to the left
+            for (int i = 0; i < WORD_SIZE - blockPos - 1; i++) {
+                if (lP & HIGH_BIT_MASK) lScore--;
+                if (lM & HIGH_BIT_MASK) lScore++;
+                lP <<= 1;
+                lM <<= 1;
+            }
+        }
+        if (ulScore == -1) {
+            if (lScore != -1) {
+                ulScore = lScore;
+                if (lP & HIGH_BIT_MASK) ulScore--;
+                if (lM & HIGH_BIT_MASK) ulScore++;
+            }
+            else if (c > 0 && b-1 >= alignData->firstBlocks[c-1] && b-1 <= alignData->lastBlocks[c-1]) {
+                // This is the case when upper left cell is last cell in block,
+                // and block to left is not in band so lScore is -1.
+                ulScore = alignData->scores[(c - 1) * maxNumBlocks + b - 1];
+            }
+        }
+        if (uScore == -1) {
+            uScore = currScore;
+            if (currP & HIGH_BIT_MASK) uScore--;
+            if (currM & HIGH_BIT_MASK) uScore++;
+            currP <<= 1;
+            currM <<= 1;
+        }
+        //-------------------------------------//
+
+        // TODO: should I check if there is upper block?
+
+        //-------------- Move --------------//
+        // Move up - insertion to target - deletion from query
+        if (uScore != -1 && uScore + 1 == currScore) {
+            currScore = uScore;
+            lScore = ulScore;
+            uScore = ulScore = -1;
+            if (blockPos == 0) { // If entering new (upper) block
+                if (b == 0) { // If there are no cells above (only boundary cells)
+                    (*alignment)[(*alignmentLength)++] = EDLIB_EDOP_INSERT; // Move up
+                    for (int i = 0; i < c + 1; i++) // Move left until end
+                        (*alignment)[(*alignmentLength)++] = EDLIB_EDOP_DELETE;
+                    break;
+                } else {
+                    blockPos = WORD_SIZE - 1;
+                    b--;
+                    currP = alignData->Ps[c * maxNumBlocks + b];
+                    currM = alignData->Ms[c * maxNumBlocks + b];
+                    if (c > 0 && b >= alignData->firstBlocks[c-1] && b <= alignData->lastBlocks[c-1]) {
+                        thereIsLeftBlock = true;
+                        lP = alignData->Ps[(c - 1) * maxNumBlocks + b]; // TODO: improve this, too many operations
+                        lM = alignData->Ms[(c - 1) * maxNumBlocks + b];
+                    } else {
+                        thereIsLeftBlock = false;
+                        // TODO(martin): There may not be left block, but there can be left boundary - do we
+                        // handle this correctly then? Are l and ul score set correctly? I should check that / refactor this.
+                    }
+                }
+            } else {
+                blockPos--;
+                lP <<= 1;
+                lM <<= 1;
+            }
+            // Mark move
+            (*alignment)[(*alignmentLength)++] = EDLIB_EDOP_INSERT;
+        }
+        // Move left - deletion from target - insertion to query
+        else if (lScore != -1 && lScore + 1 == currScore) {
+            currScore = lScore;
+            uScore = ulScore;
+            lScore = ulScore = -1;
+            c--;
+            if (c == -1) { // If there are no cells to the left (only boundary cells)
+                (*alignment)[(*alignmentLength)++] = EDLIB_EDOP_DELETE; // Move left
+                int numUp = b * WORD_SIZE + blockPos + 1;
+                for (int i = 0; i < numUp; i++) // Move up until end
+                    (*alignment)[(*alignmentLength)++] = EDLIB_EDOP_INSERT;
+                break;
+            }
+            currP = lP;
+            currM = lM;
+            if (c > 0 && b >= alignData->firstBlocks[c-1] && b <= alignData->lastBlocks[c-1]) {
+                thereIsLeftBlock = true;
+                lP = alignData->Ps[(c - 1) * maxNumBlocks + b];
+                lM = alignData->Ms[(c - 1) * maxNumBlocks + b];
+            } else {
+                if (c == 0) { // If there are no cells to the left (only boundary cells)
+                    thereIsLeftBlock = true;
+                    lScore = b * WORD_SIZE + blockPos + 1;
+                    ulScore = lScore - 1;
+                } else {
+                    thereIsLeftBlock = false;
+                }
+            }
+            // Mark move
+            (*alignment)[(*alignmentLength)++] = EDLIB_EDOP_DELETE;
+        }
+        // Move up left - (mis)match
+        else if (ulScore != -1) {
+            unsigned char moveCode = ulScore == currScore ? EDLIB_EDOP_MATCH : EDLIB_EDOP_MISMATCH;
+            currScore = ulScore;
+            uScore = lScore = ulScore = -1;
+            c--;
+            if (c == -1) { // If there are no cells to the left (only boundary cells)
+                (*alignment)[(*alignmentLength)++] = moveCode; // Move left
+                int numUp = b * WORD_SIZE + blockPos;
+                for (int i = 0; i < numUp; i++) // Move up until end
+                    (*alignment)[(*alignmentLength)++] = EDLIB_EDOP_INSERT;
+                break;
+            }
+            if (blockPos == 0) { // If entering upper left block
+                if (b == 0) { // If there are no more cells above (only boundary cells)
+                    (*alignment)[(*alignmentLength)++] = moveCode; // Move up left
+                    for (int i = 0; i < c + 1; i++) // Move left until end
+                        (*alignment)[(*alignmentLength)++] = EDLIB_EDOP_DELETE;
+                    break;
+                }
+                blockPos = WORD_SIZE - 1;
+                b--;
+                currP = alignData->Ps[c * maxNumBlocks + b];
+                currM = alignData->Ms[c * maxNumBlocks + b];
+            } else { // If entering left block
+                blockPos--;
+                currP = lP;
+                currM = lM;
+                currP <<= 1;
+                currM <<= 1;
+            }
+            // Set new left block
+            if (c > 0 && b >= alignData->firstBlocks[c-1] && b <= alignData->lastBlocks[c-1]) {
+                thereIsLeftBlock = true;
+                lP = alignData->Ps[(c - 1) * maxNumBlocks + b];
+                lM = alignData->Ms[(c - 1) * maxNumBlocks + b];
+            } else {
+                if (c == 0) { // If there are no cells to the left (only boundary cells)
+                    thereIsLeftBlock = true;
+                    lScore = b * WORD_SIZE + blockPos + 1;
+                    ulScore = lScore - 1;
+                } else {
+                    thereIsLeftBlock = false;
+                }
+            }
+            // Mark move
+            (*alignment)[(*alignmentLength)++] = moveCode;
+        } else {
+            // Reached end - finished!
+            break;
+        }
+        //----------------------------------//
+    }
+
+    *alignment = static_cast<unsigned char*>(realloc(*alignment, (*alignmentLength) * sizeof(unsigned char)));
+    reverse(*alignment, *alignment + (*alignmentLength));
+    return EDLIB_STATUS_OK;
+}
+
+
+/**
+ * Finds one possible alignment that gives optimal score (bestScore).
+ * It will split problem into smaller problems using Hirschberg's algorithm and when they are small enough,
+ * it will solve them using traceback algorithm.
+ * @param [in] query
+ * @param [in] rQuery  Reversed query.
+ * @param [in] queryLength
+ * @param [in] target
+ * @param [in] rTarget  Reversed target.
+ * @param [in] targetLength
+ * @param [in] equalityDefinition
+ * @param [in] alphabetLength
+ * @param [in] bestScore  Best(optimal) score.
+ * @param [out] alignment  Sequence of edit operations that make target equal to query.
+ * @param [out] alignmentLength  Length of alignment.
+ * @return Status code.
+ */
+static int obtainAlignment(
+        const unsigned char* const query, const unsigned char* const rQuery, const int queryLength,
+        const unsigned char* const target, const unsigned char* const rTarget, const int targetLength,
+        const EqualityDefinition& equalityDefinition, const int alphabetLength, const int bestScore,
+        unsigned char** const alignment, int* const alignmentLength) {
+
+    // Handle special case when one of sequences has length of 0.
+    if (queryLength == 0 || targetLength == 0) {
+        *alignmentLength = targetLength + queryLength;
+        *alignment = static_cast<unsigned char*>(malloc((*alignmentLength) * sizeof(unsigned char)));
+        for (int i = 0; i < *alignmentLength; i++) {
+            (*alignment)[i] = queryLength == 0 ? EDLIB_EDOP_DELETE : EDLIB_EDOP_INSERT;
+        }
+        return EDLIB_STATUS_OK;
+    }
+
+    const int maxNumBlocks = ceilDiv(queryLength, WORD_SIZE);
+    const int W = maxNumBlocks * WORD_SIZE - queryLength;
+    int statusCode;
+
+    // TODO: think about reducing number of memory allocations in alignment functions, probably
+    // by sharing some memory that is allocated only once. That refers to: Peq, columns in Hirschberg,
+    // and it could also be done for alignments - we could have one big array for alignment that would be
+    // sparsely populated by each of steps in recursion, and at the end we would just consolidate those results.
+
+    // If estimated memory consumption for traceback algorithm is smaller than 1MB use it,
+    // otherwise use Hirschberg's algorithm. By running few tests I choose boundary of 1MB as optimal.
+    long long alignmentDataSize = (2ll * sizeof(Word) + sizeof(int)) * maxNumBlocks * targetLength
+        + 2ll * sizeof(int) * targetLength;
+    if (alignmentDataSize < 1024 * 1024) {
+        int score_, endLocation_;  // Used only to call function.
+        AlignmentData* alignData = NULL;
+        Word* Peq = buildPeq(alphabetLength, query, queryLength, equalityDefinition);
+        myersCalcEditDistanceNW(Peq, W, maxNumBlocks,
+                                queryLength,
+                                target, targetLength,
+                                bestScore,
+                                &score_, &endLocation_, true, &alignData, -1);
+        //assert(score_ == bestScore);
+        //assert(endLocation_ == targetLength - 1);
+
+        statusCode = obtainAlignmentTraceback(queryLength, targetLength,
+                                              bestScore, alignData, alignment, alignmentLength);
+        delete alignData;
+        delete[] Peq;
+    } else {
+        statusCode = obtainAlignmentHirschberg(query, rQuery, queryLength,
+                                               target, rTarget, targetLength,
+                                               equalityDefinition, alphabetLength, bestScore,
+                                               alignment, alignmentLength);
+    }
+    return statusCode;
+}
+
+
+/**
+ * Finds one possible alignment that gives optimal score (bestScore).
+ * Uses Hirschberg's algorithm to split problem into two sub-problems, solve them and combine them together.
+ * @param [in] query
+ * @param [in] rQuery  Reversed query.
+ * @param [in] queryLength
+ * @param [in] target
+ * @param [in] rTarget  Reversed target.
+ * @param [in] targetLength
+ * @param [in] alphabetLength
+ * @param [in] bestScore  Best(optimal) score.
+ * @param [out] alignment  Sequence of edit operations that make target equal to query.
+ * @param [out] alignmentLength  Length of alignment.
+ * @return Status code.
+ */
+static int obtainAlignmentHirschberg(
+        const unsigned char* const query, const unsigned char* const rQuery, const int queryLength,
+        const unsigned char* const target, const unsigned char* const rTarget, const int targetLength,
+        const EqualityDefinition& equalityDefinition, const int alphabetLength, const int bestScore,
+        unsigned char** const alignment, int* const alignmentLength) {
+
+    const int maxNumBlocks = ceilDiv(queryLength, WORD_SIZE);
+    const int W = maxNumBlocks * WORD_SIZE - queryLength;
+
+    Word* Peq = buildPeq(alphabetLength, query, queryLength, equalityDefinition);
+    Word* rPeq = buildPeq(alphabetLength, rQuery, queryLength, equalityDefinition);
+
+    // Used only to call functions.
+    int score_, endLocation_;
+
+    // Divide dynamic matrix into two halfs, left and right.
+    const int leftHalfWidth = targetLength / 2;
+    const int rightHalfWidth = targetLength - leftHalfWidth;
+
+    // Calculate left half.
+    AlignmentData* alignDataLeftHalf = NULL;
+    int leftHalfCalcStatus = myersCalcEditDistanceNW(
+            Peq, W, maxNumBlocks, queryLength, target, targetLength, bestScore,
+            &score_, &endLocation_, false, &alignDataLeftHalf, leftHalfWidth - 1);
+
+    // Calculate right half.
+    AlignmentData* alignDataRightHalf = NULL;
+    int rightHalfCalcStatus = myersCalcEditDistanceNW(
+            rPeq, W, maxNumBlocks, queryLength, rTarget, targetLength, bestScore,
+            &score_, &endLocation_, false, &alignDataRightHalf, rightHalfWidth - 1);
+
+    delete[] Peq;
+    delete[] rPeq;
+
+    if (leftHalfCalcStatus == EDLIB_STATUS_ERROR || rightHalfCalcStatus == EDLIB_STATUS_ERROR) {
+        if (alignDataLeftHalf) delete alignDataLeftHalf;
+        if (alignDataRightHalf) delete alignDataRightHalf;
+        return EDLIB_STATUS_ERROR;
+    }
+
+    // Unwrap the left half.
+    int firstBlockIdxLeft = alignDataLeftHalf->firstBlocks[0];
+    int lastBlockIdxLeft = alignDataLeftHalf->lastBlocks[0];
+    // TODO: avoid this allocation by using some shared array?
+    // scoresLeft contains scores from left column, starting with scoresLeftStartIdx row (query index)
+    // and ending with scoresLeftEndIdx row (0-indexed).
+    int scoresLeftLength = (lastBlockIdxLeft - firstBlockIdxLeft + 1) * WORD_SIZE;
+    int* scoresLeft = new int[scoresLeftLength];
+    for (int blockIdx = firstBlockIdxLeft; blockIdx <= lastBlockIdxLeft; blockIdx++) {
+        Block block(alignDataLeftHalf->Ps[blockIdx], alignDataLeftHalf->Ms[blockIdx],
+                    alignDataLeftHalf->scores[blockIdx]);
+        readBlock(block, scoresLeft + (blockIdx - firstBlockIdxLeft) * WORD_SIZE);
+    }
+    int scoresLeftStartIdx = firstBlockIdxLeft * WORD_SIZE;
+    // If last block contains padding, shorten the length of scores for the length of padding.
+    if (lastBlockIdxLeft == maxNumBlocks - 1) {
+        scoresLeftLength -= W;
+    }
+
+    // Unwrap the right half (I also reverse it while unwraping).
+    int firstBlockIdxRight = alignDataRightHalf->firstBlocks[0];
+    int lastBlockIdxRight = alignDataRightHalf->lastBlocks[0];
+    int scoresRightLength = (lastBlockIdxRight - firstBlockIdxRight + 1) * WORD_SIZE;
+    int* scoresRight = new int[scoresRightLength];
+    int* scoresRightOriginalStart = scoresRight;
+    for (int blockIdx = firstBlockIdxRight; blockIdx <= lastBlockIdxRight; blockIdx++) {
+        Block block(alignDataRightHalf->Ps[blockIdx], alignDataRightHalf->Ms[blockIdx],
+                    alignDataRightHalf->scores[blockIdx]);
+        readBlockReverse(block, scoresRight + (lastBlockIdxRight - blockIdx) * WORD_SIZE);
+    }
+    int scoresRightStartIdx = queryLength - (lastBlockIdxRight + 1) * WORD_SIZE;
+    // If there is padding at the beginning of scoresRight (that can happen because of reversing that we do),
+    // move pointer forward to remove the padding (that is why we remember originalStart).
+    if (scoresRightStartIdx < 0) {
+        //assert(scoresRightStartIdx == -1 * W);
+        scoresRight += W;
+        scoresRightStartIdx += W;
+        scoresRightLength -= W;
+    }
+
+    delete alignDataLeftHalf;
+    delete alignDataRightHalf;
+
+    //--------------------- Find the best move ----------------//
+    // Find the query/row index of cell in left column which together with its lower right neighbour
+    // from right column gives the best score (when summed). We also have to consider boundary cells
+    // (those cells at -1 indexes).
+    //  x|
+    //  -+-
+    //   |x
+    int queryIdxLeftStart = max(scoresLeftStartIdx, scoresRightStartIdx - 1);
+    int queryIdxLeftEnd = min(scoresLeftStartIdx + scoresLeftLength - 1,
+                          scoresRightStartIdx + scoresRightLength - 2);
+    int leftScore = -1, rightScore = -1;
+    int queryIdxLeftAlignment = -1;  // Query/row index of cell in left column where alignment is passing through.
+    bool queryIdxLeftAlignmentFound = false;
+    for (int queryIdx = queryIdxLeftStart; queryIdx <= queryIdxLeftEnd; queryIdx++) {
+        leftScore = scoresLeft[queryIdx - scoresLeftStartIdx];
+        rightScore = scoresRight[queryIdx + 1 - scoresRightStartIdx];
+        if (leftScore + rightScore == bestScore) {
+            queryIdxLeftAlignment = queryIdx;
+            queryIdxLeftAlignmentFound = true;
+            break;
+        }
+    }
+    // Check boundary cells.
+    if (!queryIdxLeftAlignmentFound && scoresLeftStartIdx == 0 && scoresRightStartIdx == 0) {
+        leftScore = leftHalfWidth;
+        rightScore = scoresRight[0];
+        if (leftScore + rightScore == bestScore) {
+            queryIdxLeftAlignment = -1;
+            queryIdxLeftAlignmentFound = true;
+        }
+    }
+    if (!queryIdxLeftAlignmentFound && scoresLeftStartIdx + scoresLeftLength == queryLength
+        && scoresRightStartIdx + scoresRightLength == queryLength) {
+        leftScore = scoresLeft[scoresLeftLength - 1];
+        rightScore = rightHalfWidth;
+        if (leftScore + rightScore == bestScore) {
+            queryIdxLeftAlignment = queryLength - 1;
+            queryIdxLeftAlignmentFound = true;
+        }
+    }
+
+    delete[] scoresLeft;
+    delete[] scoresRightOriginalStart;
+
+    if (queryIdxLeftAlignmentFound == false) {
+        // If there was no move that is part of optimal alignment, then there is no such alignment
+        // or given bestScore is not correct!
+        return EDLIB_STATUS_ERROR;
+    }
+    //----------------------------------------------------------//
+
+    // Calculate alignments for upper half of left half (upper left - ul)
+    // and lower half of right half (lower right - lr).
+    const int ulHeight = queryIdxLeftAlignment + 1;
+    const int lrHeight = queryLength - ulHeight;
+    const int ulWidth = leftHalfWidth;
+    const int lrWidth = rightHalfWidth;
+    unsigned char* ulAlignment = NULL; int ulAlignmentLength;
+    int ulStatusCode = obtainAlignment(query, rQuery + lrHeight, ulHeight,
+                                       target, rTarget + lrWidth, ulWidth,
+                                       equalityDefinition, alphabetLength, leftScore,
+                                       &ulAlignment, &ulAlignmentLength);
+    unsigned char* lrAlignment = NULL; int lrAlignmentLength;
+    int lrStatusCode = obtainAlignment(query + ulHeight, rQuery, lrHeight,
+                                       target + ulWidth, rTarget, lrWidth,
+                                       equalityDefinition, alphabetLength, rightScore,
+                                       &lrAlignment, &lrAlignmentLength);
+    if (ulStatusCode == EDLIB_STATUS_ERROR || lrStatusCode == EDLIB_STATUS_ERROR) {
+        if (ulAlignment) free(ulAlignment);
+        if (lrAlignment) free(lrAlignment);
+        return EDLIB_STATUS_ERROR;
+    }
+
+    // Build alignment by concatenating upper left alignment with lower right alignment.
+    *alignmentLength = ulAlignmentLength + lrAlignmentLength;
+    *alignment = static_cast<unsigned char*>(malloc((*alignmentLength) * sizeof(unsigned char)));
+    memcpy(*alignment, ulAlignment, ulAlignmentLength);
+    memcpy(*alignment + ulAlignmentLength, lrAlignment, lrAlignmentLength);
+
+    free(ulAlignment);
+    free(lrAlignment);
+    return EDLIB_STATUS_OK;
+}
+
+
+/**
+ * Takes char query and char target, recognizes alphabet and transforms them into unsigned char sequences
+ * where elements in sequences are not any more letters of alphabet, but their index in alphabet.
+ * Most of internal edlib functions expect such transformed sequences.
+ * This function will allocate queryTransformed and targetTransformed, so make sure to free them when done.
+ * Example:
+ *   Original sequences: "ACT" and "CGT".
+ *   Alphabet would be recognized as "ACTG". Alphabet length = 4.
+ *   Transformed sequences: [0, 1, 2] and [1, 3, 2].
+ * @param [in] queryOriginal
+ * @param [in] queryLength
+ * @param [in] targetOriginal
+ * @param [in] targetLength
+ * @param [out] queryTransformed  It will contain values in range [0, alphabet length - 1].
+ * @param [out] targetTransformed  It will contain values in range [0, alphabet length - 1].
+ * @return  Alphabet as a string of unique characters, where index of each character is its value in transformed
+ *          sequences.
+ */
+static string transformSequences(const char* const queryOriginal, const int queryLength,
+                                 const char* const targetOriginal, const int targetLength,
+                                 unsigned char** const queryTransformed,
+                                 unsigned char** const targetTransformed) {
+    // Alphabet is constructed from letters that are present in sequences.
+    // Each letter is assigned an ordinal number, starting from 0 up to alphabetLength - 1,
+    // and new query and target are created in which letters are replaced with their ordinal numbers.
+    // This query and target are used in all the calculations later.
+    *queryTransformed = static_cast<unsigned char *>(malloc(sizeof(unsigned char) * queryLength));
+    *targetTransformed = static_cast<unsigned char *>(malloc(sizeof(unsigned char) * targetLength));
+
+    string alphabet = "";
+
+    // Alphabet information, it is constructed on fly while transforming sequences.
+    // letterIdx[c] is index of letter c in alphabet.
+    unsigned char letterIdx[MAX_UCHAR + 1];
+    bool inAlphabet[MAX_UCHAR + 1]; // inAlphabet[c] is true if c is in alphabet
+    for (int i = 0; i < MAX_UCHAR + 1; i++) inAlphabet[i] = false;
+
+    for (int i = 0; i < queryLength; i++) {
+        unsigned char c = static_cast<unsigned char>(queryOriginal[i]);
+        if (!inAlphabet[c]) {
+            inAlphabet[c] = true;
+            letterIdx[c] = static_cast<unsigned char>(alphabet.size());
+            alphabet += queryOriginal[i];
+        }
+        (*queryTransformed)[i] = letterIdx[c];
+    }
+    for (int i = 0; i < targetLength; i++) {
+        unsigned char c = static_cast<unsigned char>(targetOriginal[i]);
+        if (!inAlphabet[c]) {
+            inAlphabet[c] = true;
+            letterIdx[c] = static_cast<unsigned char>(alphabet.size());
+            alphabet += targetOriginal[i];
+        }
+        (*targetTransformed)[i] = letterIdx[c];
+    }
+
+    return alphabet;
+}
+
+
+extern "C" EdlibAlignConfig edlibNewAlignConfig(int k, EdlibAlignMode mode, EdlibAlignTask task,
+                                                const EdlibEqualityPair* additionalEqualities,
+                                                int additionalEqualitiesLength) {
+    EdlibAlignConfig config;
+    config.k = k;
+    config.mode = mode;
+    config.task = task;
+    config.additionalEqualities = additionalEqualities;
+    config.additionalEqualitiesLength = additionalEqualitiesLength;
+    return config;
+}
+
+extern "C" EdlibAlignConfig edlibDefaultAlignConfig(void) {
+    return edlibNewAlignConfig(-1, EDLIB_MODE_NW, EDLIB_TASK_DISTANCE, NULL, 0);
+}
+
+extern "C" void edlibFreeAlignResult(EdlibAlignResult result) {
+    if (result.endLocations) free(result.endLocations);
+    if (result.startLocations) free(result.startLocations);
+    if (result.alignment) free(result.alignment);
+}