Function checkAlignment

test/runTests.cpp:592–641

* Checks if alignment is correct. */

 * Checks if alignment is correct.
 */
bool checkAlignment(const char* query, int queryLength,
                    const char* target,
                    int score, int pos, EdlibAlignMode mode,
                    unsigned char* alignment, int alignmentLength) {
    int alignScore = 0;
    int qIdx = queryLength - 1;
    int tIdx = pos;
    for (int i = alignmentLength - 1; i >= 0; i--) {
        if (alignment[i] == EDLIB_EDOP_MATCH) { // match
            if (query[qIdx] != target[tIdx]) {
                printf("Should be match but is a mismatch! (tIdx, qIdx, i): (%d, %d, %d)\n", tIdx, qIdx, i);
                return false;
            }
            qIdx--;
            tIdx--;
        } else if (alignment[i] == EDLIB_EDOP_MISMATCH) { // mismatch
            if (query[qIdx] == target[tIdx]) {
                printf("Should be mismatch but is a match! (tIdx, qIdx, i): (%d, %d, %d)\n", tIdx, qIdx, i);
                return false;
            }
            alignScore += 1;
            qIdx--;
            tIdx--;
        } else if (alignment[i] == EDLIB_EDOP_INSERT) {
            alignScore += 1;
            qIdx--;
        } else if (alignment[i] == EDLIB_EDOP_DELETE) {
            if (!(mode == EDLIB_MODE_HW && qIdx == -1))
                alignScore += 1;
            tIdx--;
        }
        if (tIdx < -1 || qIdx < -1) {
            printf("Alignment went outside of matrix! (tIdx, qIdx, i): (%d, %d, %d)\n", tIdx, qIdx, i);
            return false;
        }
    }
    if (qIdx != -1) {
        printf("Alignment did not reach end!\n");
        return false;
    }
    if (alignScore != score) {
        printf("Wrong score in alignment! %d should be %d\n", alignScore, score);
        return false;
    }
    if (alignmentLength > 0 && alignment[0] == EDLIB_EDOP_INSERT && tIdx >= 0) {
        printf("Alignment starts with insertion in target, while it could start with mismatch!\n");
        return false;
    }
    return true;
}

/**
 * @param alignment