static int testEval() {
// verify eval results are symmetrical (White/Black, right/left)
const int CASES = 25;
static const string fens[CASES] = {
"8/4K3/8/1NR5/8/4k1r1/8/8 w - -",
"8/4K3/8/1N6/6p1/4k2p/8/8 w - -",
"8/4K3/8/1r6/6B1/4k2N/8/8 w - -",
"3b4/1n3n2/1pk3Np/p7/P4P1p/1P6/5BK1/3R4 b - -",
"8/3r1ppk/8/P6P/3n4/2K5/R2B4/8 b - -",
"1rb1r1k1/2q2pb1/pp1p4/2n1pPPQ/Pn1BP3/1NN4R/1PP4P/R5K1 b - -",
"6k1/1b4p1/5p1p/pq3P2/1p1BP3/1P2QR1P/P1r3PK/8 w - -",
"8/5pk1/7p/3p1R2/p1p3P1/2P2K1P/1P1r4/8 w - -",
"6k1/p3pp2/6p1/7P/R7/b1q2P2/B1P1K2P/7R b - -",
"r7/1b4k1/pp1np1p1/3pq1NN/7P/4P3/PP4P1/1Q3RK1 b - -",
"4b3/2p4p/pp1bk3/2p3p1/2P5/PPB2PP1/7P/3K1N2 w - -",
"r1bqr1k1/ppp2ppp/3p4/4n3/2PN4/P1Q1P3/1PB2PPP/R4RK1 b - -",
"r4rk1/1ppqbppp/p2p1n2/8/1n1PP3/1Q3N2/PP1N1PPP/R1B1R1K1 b - -",
"r6k/1p4bp/1p1n1pp1/1B6/8/P4NP1/1P3P1P/2R3K1 w - -",
"r1b2r1k/pp3n1p/2p1p3/3Pnppq/3PP3/1P1N1PP1/P5BP/R1Q2RK1 w - -",
"2kr3r/1bpnqp2/1p2p3/p2p3p/P1PPBPp1/2P1P1P1/2QN2P1/1R2K2R w K -",
"8/1R6/3k4/2p5/2p1B3/5K2/8/8 w - -",
"1BR2rk1/pP1nbpp1/B2P2p1/8/8/8/1P4P1/3n2K1 b - -",
"r1b1k2r/1p1n1pp1/p6p/2p5/4Nb2/5NP1/PPP2P1P/1K1R1B1R b kq -",
"r1b2rk1/1p1n1pp1/p6p/2p5/4Nb2/3R1NP1/PPP2P1P/1K1R1B2 b - -",
"1kr5/1p1b2R1/p3p2Q/2bp3P/8/P1PB1P2/1P1K1P2/R6q b - -",
"rb3rk1/1p1RRpp1/p6p/r1p5/4Nb2/5NP1/PPP2P1P/1K3B2 b - -",
"5rk1/1pqn2pp/4pn2/p7/2P5/4PP2/1B2BP1P/3Q1RK1 w - -",
"3k1q2/p3p1p1/1p1nQ3/3P4/P2P4/B2P4/6KP/8 b - -",
"6k1/4R1P1/5P2/5K1p/7r/8/8/8 w - -"
};
int errs = 0;
for (int i = 0; i < CASES; i++) {
Board board;
if (!BoardIO::readFEN(board, fens[i].c_str())) {
cerr << "testEval case " << i << " error in FEN: " << fens[i] << endl;
++errs;
continue;
}
Scoring *s = new Scoring();
int eval1 = s->evalu8(board);
board.flip();
int eval2 = s->evalu8(board);
if (eval1 != eval2) {
++errs;
cerr << "testEval case " << i << " eval mismatch" << endl;
}
delete s;
}
return errs;
}
double Game::GameState::Score(int player)
{
int other = OtherPlayer(player);
if (playerState[player]->HasWon()) return 1;
if (playerState[other]->HasWon()) return 0;
Scoring *sc = &scoring[player];
sc->Reset();
sc->SetAligned(SCORE_ALIGN_PLAYER, playerState[player]->nbAlignementDone, boardDesc->align);
sc->SetAligned(SCORE_ALIGN_OTHER, playerState[other]->nbAlignementDone, boardDesc->align);
sc->SetRandom();
return (*sc)();
}
static int testEval() {
// verify eval results are symmetrical (White/Black, right/left)
const int CASES = 9;
static const string fens[CASES] = {
"8/4K3/8/1NR5/8/4k1r1/8/8 w - -",
"8/4K3/8/1N6/6p1/4k2p/8/8 w - -",
"8/4K3/8/1r6/6B1/4k2N/8/8 w - -",
"3b4/1n3n2/1pk3Np/p7/P4P1p/1P6/5BK1/3R4 b - -",
"8/3r1ppk/8/P6P/3n4/2K5/R2B4/8 b - -",
"1rb1r1k1/2q2pb1/pp1p4/2n1pPPQ/Pn1BP3/1NN4R/1PP4P/R5K1 b - -",
"6k1/1b4p1/5p1p/pq3P2/1p1BP3/1P2QR1P/P1r3PK/8 w - -",
"8/5pk1/7p/3p1R2/p1p3P1/2P2K1P/1P1r4/8 w - -",
"6k1/p3pp2/6p1/7P/R7/b1q2P2/B1P1K2P/7R b - -"
};
int errs = 0;
for (int i = 0; i < CASES; i++) {
Board board;
if (!BoardIO::readFEN(board, fens[i].c_str())) {
cerr << "testEval case " << i << " error in FEN: " << fens[i] << endl;
++errs;
continue;
}
Scoring *s = new Scoring();
int eval1 = s->evalu8(board);
board.flip();
int eval2 = s->evalu8(board);
if (eval1 != eval2) {
++errs;
cerr << "testEval case " << i << " eval mismatch" << endl;
}
board.flip2();
int eval3 = s->evalu8(board);
if (eval1 != eval3) {
++errs;
cerr << "testEval case " << i << " eval mismatch" << endl;
}
delete s;
}
return errs;
}
/**
* A way of feeding simply tests to the seed alignment infrastructure.
*/
int main(int argc, char **argv) {
EList<string> strs;
// GCTATATAGCGCGCTCGCATCATTTTGTGT
strs.push_back(string("CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA"
"NNNNNNNNNN"
"CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA"));
// GCTATATAGCGCGCTTGCATCATTTTGTGT
// ^
bool packed = false;
int color = 0;
pair<GFM*, GFM*> gfms = GFM::fromStrings<SString<char> >(
strs,
packed,
REF_READ_REVERSE,
Ebwt::default_bigEndian,
Ebwt::default_lineRate,
Ebwt::default_offRate,
Ebwt::default_ftabChars,
".aligner_seed2.cpp.tmp",
Ebwt::default_useBlockwise,
Ebwt::default_bmax,
Ebwt::default_bmaxMultSqrt,
Ebwt::default_bmaxDivN,
Ebwt::default_dcv,
Ebwt::default_seed,
false, // verbose
false, // autoMem
false); // sanity
gfms.first->loadIntoMemory (-1, true, true, true, true, false);
gfms.second->loadIntoMemory(1, true, true, true, true, false);
int testnum = 0;
// Query is longer than ftab and matches exactly twice
for(int rc = 0; rc < 2; rc++) {
for(int i = 0; i < 2; i++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
BTDnaString seq ("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
if(rc) {
seq.reverseComp();
qual.reverse();
}
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
(i == 0) ? 0 : (seq.length() - 1), // 5' offset into read of root
(i == 0) ? true : false, // left-to-right?
rc == 0, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(2, dr.sink().nelt());
}
}
// Query has length euqal to ftab and matches exactly twice
for(int i = 0; i < 2; i++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length equal to ftab" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
BTDnaString seq ("GCTATATAGC", true);
BTString qual("ABCDEFGHIa");
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
(i == 0) ? 0 : (seq.length() - 1), // 5' offset into read of root
(i == 0) ? true : false, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(2, dr.sink().nelt());
}
// Query has length less than ftab length and matches exactly twice
for(int i = 0; i < 2; i++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length less than ftab" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
BTDnaString seq ("GCTATATAG", true);
BTString qual("ABCDEFGHI");
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
(i == 0) ? 0 : (seq.length() - 1), // 5' offset into read of root
(i == 0) ? true : false, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(2, dr.sink().nelt());
}
// Search root is in the middle of the read, requiring a bounce
for(int i = 0; i < 2; i++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Search root in middle of read" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
// 012345678901234567890123456789
BTDnaString seq ("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
TIndexOffU top, bot;
top = bot = 0;
bool ret = gfms.first->contains("GCGCTCGCATCATTTTGTGT", &top, &bot);
cerr << ret << ", " << top << ", " << bot << endl;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
(i == 0) ? 10 : (seq.length() - 1 - 10), // 5' offset into read of root
(i == 0) ? true : false, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(2, dr.sink().nelt());
}
delete gfms.first;
delete gfms.second;
strs.clear();
strs.push_back(string("CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA"
"NNNNNNNNNN"
"CATGTCAGCTATATAGCG"));
gfms = GFM::fromStrings<SString<char> >(
strs,
packed,
REF_READ_REVERSE,
GFM::default_bigEndian,
GFM::default_lineRate,
GFM::default_offRate,
GFM::default_ftabChars,
".aligner_seed2.cpp.tmp",
GFM::default_useBlockwise,
GFM::default_bmax,
GfM::default_bmaxMultSqrt,
GFM::default_bmaxDivN,
GFM::default_dcv,
GFM::default_seed,
false, // verbose
false, // autoMem
false); // sanity
gfms.first->loadIntoMemory (-1, true, true, true, true, false);
gfms.second->loadIntoMemory(1, true, true, true, true, false);
// Query is longer than ftab and matches exactly once. One search root for
// forward read.
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
BTDnaString seq ("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
for(size_t j = 0; j < seq.length(); j++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab and matches exactly once" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
assert_eq(1, dr.sink().nelt());
}
}
}
// Query is longer than ftab and its reverse complement matches exactly
// once. Search roots on forward and reverse-comp reads.
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
BTDnaString seq ("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
for(size_t j = 0; j < seq.length(); j++) {
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab and reverse complement matches exactly once" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
// Set up the read
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
false, // forward?
1.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
assert_eq(1, dr.sink().nelt());
}
}
}
// Query is longer than ftab and matches exactly once with one mismatch
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// ||||||||||||||||||||||||||||||
BTDnaString orig("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
// 012345678901234567890123456789
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
for(size_t k = 0; k < orig.length(); k++) {
BTDnaString seq = orig;
seq.set(seq[k] ^ 3, k);
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
size_t kk = k;
//if(rc) {
// kk = seq.length() - k - 1;
//}
if(beg <= kk && end > kk) {
continue;
}
if((j > kk) ? (j - kk <= 2) : (kk - j <= 2)) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab and matches exactly once with 1mm" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(0, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
}
// Query is longer than ftab and matches exactly once with one N mismatch
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// ||||||||||||||||||||||||||||||
BTDnaString orig("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
// 012345678901234567890123456789
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
for(size_t k = 0; k < orig.length(); k++) {
BTDnaString seq = orig;
seq.set(4, k);
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= k && end > k) {
continue;
}
if((j > k) ? (j - k <= 2) : (k - j <= 2)) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab and matches exactly once with 1mm" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(0, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.n(40), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
}
// Throw a bunch of queries with a bunch of Ns in and try to force an assert
{
RandomSource rnd(79);
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// ||||||||||||||||||||||||||||||
BTDnaString orig("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
// 012345678901234567890123456789
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
if(i == 1) {
orig.reverseComp();
qual.reverse();
}
for(size_t trials = 0; trials < 100; trials++) {
BTDnaString seq = orig;
size_t ns = 10;
for(size_t k = 0; k < ns; k++) {
size_t pos = rnd.nextU32() % seq.length();
seq.set(4, pos);
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query with a bunch of Ns" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(GFM::default_ftabChars, 1.0);
conf.expol = DESC_EX_NONE;
// Set up the search roots
for(size_t k = 0; k < ns; k++) {
size_t j = rnd.nextU32() % seq.length();
bool ltr = (rnd.nextU2() == 0) ? true : false;
bool fw = (rnd.nextU2() == 0) ? true : false;
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
ltr, // left-to-right?
fw, // forward?
0.0f); // root priority
}
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
}
}
}
// Query is longer than ftab and matches exactly once with one mismatch
{
RandomSource rnd(77);
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// ||||||||||||||||||||||||||||||
BTDnaString orig("GCTATATAGCGCGCTCGCATCATTTTGTGT", true);
// 012345678901234567890123456789
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIabc");
// revcomp: ACACAAAATGATGCGAGCGCGCTATATAGC
// revqual: cbaIHGFEDCBAihgfedcbaIHGFEDCBA
bool fwi = (i == 0);
if(!fwi) {
orig.reverseComp();
}
for(size_t k = 0; k < orig.length(); k++) {
BTDnaString seq = orig;
seq.set(seq[k] ^ 3, k);
cerr << "Test " << (++testnum) << endl;
cerr << " Query with length greater than ftab and matches exactly once with 1mm. Many search roots." << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(0, 1.0);
conf.expol = DESC_EX_NONE;
// Set up several random search roots
bool onegood = false;
for(size_t y = 0; y < 10; y++) {
size_t j = rnd.nextU32() % seq.length();
bool ltr = (rnd.nextU2() == 0) ? true : false;
bool fw = (rnd.nextU2() == 0) ? true : false;
dr.addRoot(
conf, // DescentConfig
(TReadOff)j, // 5' offset into read of root
ltr, // left-to-right?
fw, // forward?
(float)((float)y * 1.0f)); // root priority
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if(!ltr) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
bool good = true;
if(fw != fwi) {
good = false;
}
if(beg <= k && end > k) {
good = false;
}
if((j > k) ? (j - k <= 2) : (k - j <= 2)) {
good = false;
}
if(good) {
onegood = true;
}
}
if(!onegood) {
continue;
}
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
// Query is longer than ftab and matches exactly once with one read gap
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
for(int k = 0; k < 2; k++) {
// Set up the read
// GCTATATAGCGCGCCTGCATCATTTTGTGT
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// |||||||||||||||///////////////
BTDnaString seq ("GCTATATAGCGCGCTGCATCATTTTGTGT", true);
// 01234567890123456789012345678
// 87654321098765432109876543210
BTString qual("ABCDEFGHIabcdefghiABCDEFGHIab");
if(k == 1) {
seq.reverseComp();
qual.reverse();
}
assert_eq(seq.length(), qual.length());
// js iterate over offsets from 5' end for the search root
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
if(k == 1) {
beg = seq.length() - beg - 1;
}
size_t end = beg + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
assert_geq(end, beg);
if(beg <= 15 && end >= 15) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a read gap of length 1" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
Read q("test", seq.toZBuf(), qual.toZBuf());
assert(q.repOk());
dr.initRead(q, -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(0, 0.5);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
k == 0, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.readGapOpen() + 0 * sc.readGapExtend(), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}}
}
// Query is longer than ftab and matches exactly once with one read gap of
// length 3
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
for(int k = 0; k < 2; k++) {
// Set up the read
// GCTATATAGCGCGCGCTCATCATTTTGTGT
// Ref: CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAACCA
// |||||||||||||| |||||||||||||
BTDnaString seq ("GCTATATAGCGCGC" "CATCATTTTGTGT", true);
// 01234567890123 4567890123456
// 65432109876543 2109876543210
BTString qual("ABCDEFGHIabcde" "fghiABCDEFGHI");
if(k == 1) {
seq.reverseComp();
qual.reverse();
}
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
if(k == 1) {
beg = seq.length() - beg - 1;
}
size_t end = beg + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 14 && end >= 14) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a read gap of length 3" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(0, 0.2);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
k == 0, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
// Need to adjust the mismatch penalty up to avoid alignments
// with lots of mismatches.
sc.setMmPen(COST_MODEL_CONSTANT, 6, 6);
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.readGapOpen() + 2 * sc.readGapExtend(), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}}
}
// Query is longer than ftab and matches exactly once with one reference gap
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGC" "TCGCATCATTTTGTGTGTAAACCA
// |||||||||||||| ||||||||||||||||
BTDnaString seq ("GCTATATAGCGCGCA""TCGCATCATTTTGTGT", true);
// 012345678901234 5678901234567890
BTString qual("ABCDEFGHIabcdef""ghiABCDEFGHIabcd");
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 14 && end >= 14) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a reference gap of length 1" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(1, 0.5);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
// Need to adjust the mismatch penalty up to avoid alignments
// with lots of mismatches.
sc.setMmPen(COST_MODEL_CONSTANT, 6, 6);
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.refGapOpen() + 0 * sc.refGapExtend(), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
// Query is longer than ftab and matches exactly once with one reference gap
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCTATATAGCGCGC" "TCGCATCATTTTGTGTGTAAACCA
// |||||||||||||| ||||||||||||||||
BTDnaString seq ("GCTATATAGCGCGCATG""TCGCATCATTTTGTGT", true);
// 01234567890123456 7890123456789012
BTString qual("ABCDEFGHIabcdefgh""iABCDEFGHIabcdef");
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 14 && end >= 14) {
continue;
}
if(beg <= 15 && end >= 15) {
continue;
}
if(beg <= 16 && end >= 16) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a reference gap of length 1" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -30, 30);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(1, 0.25);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
// Need to adjust the mismatch penalty up to avoid alignments
// with lots of mismatches.
sc.setMmPen(COST_MODEL_CONSTANT, 6, 6);
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.refGapOpen() + 2 * sc.refGapExtend(), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
// Query is longer than ftab and matches exactly once with one read gap,
// one ref gap, and one mismatch
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCT ATATAGCGCGCT CGCATCATTTTGTGTGTAAACCA
// |||||||||| |||||||||||| |||||| |||||||||||||
BTDnaString seq ("CATGTCAGCT""GATATAGCGCGCT" "GCATCAATTTGTGTGTAAAC", true);
// 0123456789 0123456789012 34567890123456789012
BTString qual("ABCDEFGHIa""bcdefghiACDEF" "GHIabcdefghijkABCDEF");
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 10 && end >= 10) {
continue;
}
if(beg <= 22 && end >= 22) {
continue;
}
if(beg <= 30 && end >= 30) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a read gap of length 1" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -50, 50);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(1, 0.5);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(1, dr.sink().nrange());
assert_eq(sc.readGapOpen() + sc.refGapOpen() + sc.mm((int)'d' - 33), dr.sink()[0].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(1, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
delete gfms.first;
delete gfms.second;
// Ref CATGTCAGCT-ATATAGCGCGCTCGCATCATTTTGTGTGTAAAC
// |||||||||| |||||||||||| |||||| |||||||||||||
// Rd CATGTCAGCTGATATAGCGCGCT-GCATCAATTTGTGTGTAAAC
strs.clear();
strs.push_back(string("CATGTCAGCTATATAGCGCGCTCGCATCATTTTGTGTGTAAAC"
"NNNNNNNNNN"
"CATGTCAGCTGATATAGCGCGCTCGCATCATTTTGTGTGTAAAC" // same but without first ref gap
"N"
"CATGTCAGCTATATAGCGCGCTGCATCATTTTGTGTGTAAAC" // same but without first read gap
"N"
"CATGTCAGCTATATAGCGCGCTCGCATCAATTTGTGTGTAAAC" // same but without first mismatch
"N"
"CATGTCAGCTGATATAGCGCGCTGCATCAATTTGTGTGTAAAC" // Exact match for read
));
gfms = GFM::fromStrings<SString<char> >(
strs,
packed,
REF_READ_REVERSE,
GFM::default_bigEndian,
GFM::default_lineRate,
GFM::default_offRate,
GFM::default_ftabChars,
".aligner_seed2.cpp.tmp",
GFM::default_useBlockwise,
GFM::default_bmax,
GFM::default_bmaxMultSqrt,
GFM::default_bmaxDivN,
GFM::default_dcv,
GFM::default_seed,
false, // verbose
false, // autoMem
false); // sanity
gfms.first->loadIntoMemory (color, -1, true, true, true, true, false);
gfms.second->loadIntoMemory(color, 1, true, true, true, true, false);
// Query is longer than ftab and matches exactly once with one read gap,
// one ref gap, and one mismatch
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCT ATATAGCGCGCT CGCATCATTTTGTGTGTAAACCA
// |||||||||| |||||||||||| |||||| |||||||||||||
BTDnaString seq ("CATGTCAGCT""GATATAGCGCGCT" "GCATCAATTTGTGTGTAAAC", true);
// 0123456789 0123456789012 34567890123456789012
BTString qual("ABCDEFGHIa""bcdefghiACDEF" "GHIabcdefghijkABCDEF");
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 10 && end >= 10) {
continue;
}
if(beg <= 22 && end >= 22) {
continue;
}
if(beg <= 30 && end >= 30) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches once with a read gap of length 1" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -50, 50);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(1, 0.5);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(5, dr.sink().nrange());
assert_eq(0, dr.sink()[0].pen);
assert_eq(min(sc.readGapOpen(), sc.refGapOpen()) + sc.mm((int)'d' - 33), dr.sink()[1].pen);
assert_eq(max(sc.readGapOpen(), sc.refGapOpen()) + sc.mm((int)'d' - 33), dr.sink()[2].pen);
assert_eq(sc.readGapOpen() + sc.refGapOpen(), dr.sink()[3].pen);
assert_eq(sc.readGapOpen() + sc.refGapOpen() + sc.mm((int)'d' - 33), dr.sink()[4].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(5, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
// Query is longer than ftab and matches exactly once with one read gap,
// one ref gap, one mismatch, and one N
{
size_t last_topf = std::numeric_limits<size_t>::max();
size_t last_botf = std::numeric_limits<size_t>::max();
for(int i = 0; i < 2; i++) {
// Set up the read
// Ref: CATGTCAGCT ATATAGCGCGCT CGCATCATTTTGTGTGTAAACCA
// |||||||||| |||||||||||| |||||| |||||| ||||||
BTDnaString seq ("CATGTCAGCT""GATATAGCGCGCT" "GCATCAATTTGTGNGTAAAC", true);
// 0123456789 0123456789012 34567890123456789012
BTString qual("ABCDEFGHIa""bcdefghiACDEF" "GHIabcdefghijkABCDEF");
for(size_t j = 0; j < seq.length(); j++) {
// Assume left-to-right
size_t beg = j;
size_t end = j + GFM::default_ftabChars;
// Mismatch penalty is 3, so we have to skip starting
// points that are within 2 from the mismatch
if((i > 0 && j > 0) || j == seq.length()-1) {
// Right-to-left
if(beg < GFM::default_ftabChars) {
beg = 0;
} else {
beg -= GFM::default_ftabChars;
}
end -= GFM::default_ftabChars;
}
if(beg <= 10 && end >= 10) {
continue;
}
if(beg <= 22 && end >= 22) {
continue;
}
if(beg <= 30 && end >= 30) {
continue;
}
if(beg <= 36 && end >= 36) {
continue;
}
cerr << "Test " << (++testnum) << endl;
cerr << " Query matches with various patterns of gaps, mismatches and Ns" << endl;
DescentMetrics mets;
PerReadMetrics prm;
DescentDriver dr;
dr.initRead(Read("test", seq.toZBuf(), qual.toZBuf()), -50, 50);
// Set up the DescentConfig
DescentConfig conf;
// Changed
conf.cons.init(1, 0.5);
conf.expol = DESC_EX_NONE;
// Set up the search roots
dr.addRoot(
conf, // DescentConfig
j, // 5' offset into read of root
i == 0, // left-to-right?
true, // forward?
0.0f); // root priority
// Do the search
Scoring sc = Scoring::base1();
sc.setNPen(COST_MODEL_CONSTANT, 1);
dr.go(sc, *gfms.first, *gfms.second, mets, prm);
// Confirm that an exact-matching alignment was found
assert_eq(5, dr.sink().nrange());
assert_eq(sc.n(40), dr.sink()[0].pen);
assert_eq(sc.n(40) + min(sc.readGapOpen(), sc.refGapOpen()) + sc.mm((int)'d' - 33), dr.sink()[1].pen);
assert_eq(sc.n(40) + max(sc.readGapOpen(), sc.refGapOpen()) + sc.mm((int)'d' - 33), dr.sink()[2].pen);
assert_eq(sc.n(40) + sc.readGapOpen() + sc.refGapOpen(), dr.sink()[3].pen);
assert_eq(sc.n(40) + sc.readGapOpen() + sc.refGapOpen() + sc.mm((int)'d' - 33), dr.sink()[4].pen);
assert(last_topf == std::numeric_limits<size_t>::max() || last_topf == dr.sink()[0].topf);
assert(last_botf == std::numeric_limits<size_t>::max() || last_botf == dr.sink()[0].botf);
cerr << dr.sink()[0].topf << ", " << dr.sink()[0].botf << endl;
assert_eq(5, dr.sink().nelt());
last_topf = dr.sink()[0].topf;
last_botf = dr.sink()[0].botf;
}
}
}
delete gfms.first;
delete gfms.second;
cerr << "DONE" << endl;
}
static int testDrawEval() {
// verify detection of KBP and other draw situations
const int DRAW_CASES = 11;
static const string draw_fens[DRAW_CASES] = {
"k7/8/P7/B7/1K6/8/8/8 w - - 0 1", // KBP draw
"8/8/8/1k6/b7/p7/8/K7 b - - 0 1", // KBP draw
"8/8/8/8/7b/4k2p/8/6K1 b - - 0 1", // KBP draw
"8/7k/4B3/8/6KP/8/8/8 b - - 0 3", // KBP draw
"8/8/2KN3k/8/3N4/8/8/8 w - - 0 1", // KNN draw
"8/8/2KN3k/8/3N4/8/8/8 w - - 0 1", // KNN draw
"8/8/8/3n4/8/2kn3K/8/8 b - - 0 1", // KNN draw
"8/8/2K4k/8/3N4/8/8/8 w - - 0 1", // KN draw
"8/8/8/3n4/8/2k4K/8/8 b - - 0 1", // KN draw
"8/8/8/8/8/2k4K/8/8 b - - 0 1", // KK draw
"8/8/8/2B1b3/8/2k4K/8/8 b - - 0 1" // KB vs KB draw (same color)
// technically these are draws but not recognized yet:
//"8/8/8/1k6/b7/p7/8/2K5 b - - 0 1", // KBP draw
// 8/5k2/8/5B2/8/6KP/8/8 w - - 0 1 // KBP draw
};
const int NON_DRAW_CASES = 3;
static const string nondraw_fens[NON_DRAW_CASES] = {
"8/7k/8/6B1/6KP/8/8/8 w - - 0 3", // KBP right-color pawn
"8/3k3B/8/8/5K2/7P/8/8 b - - 0 1", // KBP opp king too far
"6K1/8/6b1/6k1/8/6B1/8/8 w - - 0 1" // opp color bishops
};
int errs = 0;
#if defined(NALIMOV_TBS) || defined(GAVIOTA_TBS)
int tmp = options.search.use_tablebases;
options.search.use_tablebases = 0;
#endif
for (int i = 0; i < DRAW_CASES; i++) {
Board board;
if (!BoardIO::readFEN(board, draw_fens[i].c_str())) {
cerr << "testDrawEval draw case " << i << " error in FEN: " << draw_fens[i] << endl;
++errs;
continue;
}
Scoring *s = new Scoring();
if (!s->isDraw(board)) {
cerr << "testDrawEval: error in draw case " << i << " fen=" << draw_fens[i] << endl;
++errs;
}
delete s;
}
for (int i = 0; i < NON_DRAW_CASES; i++) {
Board board;
if (!BoardIO::readFEN(board, nondraw_fens[i].c_str())) {
cerr << "testDrawEval non-draw case " << i << " error in FEN: " << nondraw_fens[i] << endl;
++errs;
continue;
}
Scoring *s = new Scoring();
if (s->isDraw(board)) {
cerr << "testDrawEval: error in non-draw case " << i << " fen=" << nondraw_fens[i] << endl;
++errs;
}
delete s;
}
#if defined(NALIMOV_TBS) || defined(GAVIOTA_TBS)
options.search.use_tablebases = tmp;
#endif
return errs;
}
static float computeScore(
bool const inverted,
AutoTextArray<sse4> const & ATA,
pattern_type const & pattern,
Scoring const & scoring,
unsigned int const pos,
unsigned int const patl
)
{
if ( inverted )
{
double rawscore = 1.0f;
char const * mapped = inverted ? pattern.transposed : pattern.mapped;
unsigned int j = patl;
unsigned int wordpos = pos/32;
u_int64_t const firstword = ATA.getTextWord( wordpos );
u_int64_t const mask = 0x3ull;
unsigned int const firstrest = 32-(pos % 32);
unsigned int firstloopstop = std::min(firstrest,patl);
unsigned int shift = 2*(firstrest-1);
unsigned int i = 0;
unsigned int rest = patl;
for ( ; i < firstloopstop; ++i, shift-=2 )
{
unsigned int const refbase = ((firstword>>shift)&mask);
unsigned int const patbase = mapped[i];
unsigned int const quality = pattern.getQuality(--j);
double const localrawscore = scoring.getRawLogScoreTable(refbase,patbase,quality);
rawscore += localrawscore;
// assert ( ((firstword>>shift)&mask) == ATA[pos+i] );
}
rest -= firstloopstop;
while ( rest >= 32 )
{
shift = 62;
unsigned int const loopstop = i+32;
u_int64_t const word = ATA.getTextWord(++wordpos);
for ( ; i < loopstop; ++i, shift -= 2 )
{
unsigned int const refbase = ((word>>shift)&mask);
unsigned int const patbase = mapped[i];
unsigned int const quality = pattern.getQuality(--j);
double const localrawscore = scoring.getRawLogScoreTable(refbase,patbase,quality);
rawscore += localrawscore;
// assert ( ((word>>shift)&mask) == ATA[pos+i] );
}
rest -= 32;
}
if ( rest )
{
shift = 62;
unsigned int const loopstop = i+rest;
u_int64_t const word = ATA.getTextWord(++wordpos);
for ( ; i < loopstop; ++i, shift -= 2 )
{
unsigned int const refbase = ((word>>shift)&mask);
unsigned int const patbase = mapped[i];
unsigned int const quality = pattern.getQuality(--j);
double const localrawscore = scoring.getRawLogScoreTable(refbase,patbase,quality);
rawscore += localrawscore;
// assert ( ((word>>shift)&mask) == ATA[pos+i] );
}
}
return rawscore;
}
else
{
