void SDTestObject::test<3>()
// construction via scalar values
// tests both constructor and initialize forms
{
SDCleanupCheck check;
LLSD b1(true); ensureTypeAndValue("construct boolean", b1, true);
LLSD b2 = true; ensureTypeAndValue("initialize boolean", b2, true);
LLSD i1(42); ensureTypeAndValue("construct int", i1, 42);
LLSD i2 =42; ensureTypeAndValue("initialize int", i2, 42);
LLSD d1(1.2); ensureTypeAndValue("construct double", d1, 1.2);
LLSD d2 = 1.2; ensureTypeAndValue("initialize double", d2, 1.2);
LLUUID newUUID;
newUUID.generate();
LLSD u1(newUUID);
ensureTypeAndValue("construct UUID", u1, newUUID);
LLSD u2 = newUUID;
ensureTypeAndValue("initialize UUID", u2, newUUID);
LLSD ss1(std::string("abc"));
ensureTypeAndValue("construct std::string", ss1, "abc");
LLSD ss2 = std::string("abc");
ensureTypeAndValue("initialize std::string",ss2, "abc");
LLSD sl1(std::string("def"));
ensureTypeAndValue("construct std::string", sl1, "def");
LLSD sl2 = std::string("def");
ensureTypeAndValue("initialize std::string", sl2, "def");
LLSD sc1("ghi");
ensureTypeAndValue("construct const char*", sc1, "ghi");
LLSD sc2 = "ghi";
ensureTypeAndValue("initialize const char*",sc2, "ghi");
LLDate aDay("2001-10-22T10:11:12.00Z");
LLSD t1(aDay); ensureTypeAndValue("construct LLDate", t1, aDay);
LLSD t2 = aDay; ensureTypeAndValue("initialize LLDate", t2, aDay);
LLURI path("http://slurl.com/secondlife/Ambleside/57/104/26/");
LLSD p1(path); ensureTypeAndValue("construct LLURI", p1, path);
LLSD p2 = path; ensureTypeAndValue("initialize LLURI", p2, path);
const char source[] = "once in a blue moon";
std::vector<U8> data;
copy(&source[0], &source[sizeof(source)], back_inserter(data));
LLSD x1(data); ensureTypeAndValue("construct vector<U8>", x1, data);
LLSD x2 = data; ensureTypeAndValue("initialize vector<U8>", x2, data);
}
void main(void)
{
// create our SubClass.. setting the CCobj to "WoofWoof"
SubClass sc1("WoofWoof");
// intentionally invoke copy construction.
// Order of Events.. Copy Contained class, automatically calling the defined CC.
// Copy BaseClass, automatically calling the default CC.
// Copy SubClass, automatically calling the default CC.
SubClass sc2 = sc1;
SubClass *p_sc3;
p_sc3 = (SubClass *)sc2.Clone();
// make sure it worked...
sc1.PrintName();
sc2.PrintName();
p_sc3->PrintName();
}
int main() {
boost::signal<void (const std::string&)> sig;
some_slot_type sc1("sc1");
some_slot_type sc2("sc2");
boost::signals::connection c1=sig.connect(sc1);
boost::signals::connection c2=sig.connect(sc2);
// 比较
std::cout << "c1==c2: " << (c1==c2) << '\n';
std::cout << "c1<c2: " << (c1<c2) << '\n';
// 检查连接
if (c1.connected())
std::cout << "c1 is connected to a signal\n";
// 交换并断开
sig("Hello there");
c1.swap(c2);
sig("We've swapped the connections");
c1.disconnect();
sig("Disconnected c1, which referred to sc2 after the swap");
}
template<typename Scalar> void geometry(void)
{
/* this test covers the following files:
Cross.h Quaternion.h, Transform.cpp
*/
typedef Matrix<Scalar,2,2> Matrix2;
typedef Matrix<Scalar,3,3> Matrix3;
typedef Matrix<Scalar,4,4> Matrix4;
typedef Matrix<Scalar,2,1> Vector2;
typedef Matrix<Scalar,3,1> Vector3;
typedef Matrix<Scalar,4,1> Vector4;
typedef Quaternion<Scalar> Quaternionx;
typedef AngleAxis<Scalar> AngleAxisx;
typedef Transform<Scalar,2> Transform2;
typedef Transform<Scalar,3> Transform3;
typedef Scaling<Scalar,2> Scaling2;
typedef Scaling<Scalar,3> Scaling3;
typedef Translation<Scalar,2> Translation2;
typedef Translation<Scalar,3> Translation3;
Scalar largeEps = test_precision<Scalar>();
if (ei_is_same_type<Scalar,float>::ret)
largeEps = 1e-2f;
Vector3 v0 = Vector3::Random(),
v1 = Vector3::Random(),
v2 = Vector3::Random();
Vector2 u0 = Vector2::Random();
Matrix3 matrot1;
Scalar a = ei_random<Scalar>(-Scalar(M_PI), Scalar(M_PI));
// cross product
VERIFY_IS_MUCH_SMALLER_THAN(v1.cross(v2).eigen2_dot(v1), Scalar(1));
Matrix3 m;
m << v0.normalized(),
(v0.cross(v1)).normalized(),
(v0.cross(v1).cross(v0)).normalized();
VERIFY(m.isUnitary());
// Quaternion: Identity(), setIdentity();
Quaternionx q1, q2;
q2.setIdentity();
VERIFY_IS_APPROX(Quaternionx(Quaternionx::Identity()).coeffs(), q2.coeffs());
q1.coeffs().setRandom();
VERIFY_IS_APPROX(q1.coeffs(), (q1*q2).coeffs());
// unitOrthogonal
VERIFY_IS_MUCH_SMALLER_THAN(u0.unitOrthogonal().eigen2_dot(u0), Scalar(1));
VERIFY_IS_MUCH_SMALLER_THAN(v0.unitOrthogonal().eigen2_dot(v0), Scalar(1));
VERIFY_IS_APPROX(u0.unitOrthogonal().norm(), Scalar(1));
VERIFY_IS_APPROX(v0.unitOrthogonal().norm(), Scalar(1));
VERIFY_IS_APPROX(v0, AngleAxisx(a, v0.normalized()) * v0);
VERIFY_IS_APPROX(-v0, AngleAxisx(Scalar(M_PI), v0.unitOrthogonal()) * v0);
VERIFY_IS_APPROX(ei_cos(a)*v0.squaredNorm(), v0.eigen2_dot(AngleAxisx(a, v0.unitOrthogonal()) * v0));
m = AngleAxisx(a, v0.normalized()).toRotationMatrix().adjoint();
VERIFY_IS_APPROX(Matrix3::Identity(), m * AngleAxisx(a, v0.normalized()));
VERIFY_IS_APPROX(Matrix3::Identity(), AngleAxisx(a, v0.normalized()) * m);
q1 = AngleAxisx(a, v0.normalized());
q2 = AngleAxisx(a, v1.normalized());
// angular distance
Scalar refangle = ei_abs(AngleAxisx(q1.inverse()*q2).angle());
if (refangle>Scalar(M_PI))
refangle = Scalar(2)*Scalar(M_PI) - refangle;
if((q1.coeffs()-q2.coeffs()).norm() > 10*largeEps)
{
VERIFY(ei_isApprox(q1.angularDistance(q2), refangle, largeEps));
}
// rotation matrix conversion
VERIFY_IS_APPROX(q1 * v2, q1.toRotationMatrix() * v2);
VERIFY_IS_APPROX(q1 * q2 * v2,
q1.toRotationMatrix() * q2.toRotationMatrix() * v2);
VERIFY( (q2*q1).isApprox(q1*q2, largeEps) || !(q2 * q1 * v2).isApprox(
q1.toRotationMatrix() * q2.toRotationMatrix() * v2));
q2 = q1.toRotationMatrix();
VERIFY_IS_APPROX(q1*v1,q2*v1);
matrot1 = AngleAxisx(Scalar(0.1), Vector3::UnitX())
* AngleAxisx(Scalar(0.2), Vector3::UnitY())
* AngleAxisx(Scalar(0.3), Vector3::UnitZ());
VERIFY_IS_APPROX(matrot1 * v1,
AngleAxisx(Scalar(0.1), Vector3(1,0,0)).toRotationMatrix()
* (AngleAxisx(Scalar(0.2), Vector3(0,1,0)).toRotationMatrix()
* (AngleAxisx(Scalar(0.3), Vector3(0,0,1)).toRotationMatrix() * v1)));
// angle-axis conversion
AngleAxisx aa = q1;
VERIFY_IS_APPROX(q1 * v1, Quaternionx(aa) * v1);
VERIFY_IS_NOT_APPROX(q1 * v1, Quaternionx(AngleAxisx(aa.angle()*2,aa.axis())) * v1);
// from two vector creation
VERIFY_IS_APPROX(v2.normalized(),(q2.setFromTwoVectors(v1,v2)*v1).normalized());
VERIFY_IS_APPROX(v2.normalized(),(q2.setFromTwoVectors(v1,v2)*v1).normalized());
// inverse and conjugate
VERIFY_IS_APPROX(q1 * (q1.inverse() * v1), v1);
VERIFY_IS_APPROX(q1 * (q1.conjugate() * v1), v1);
// AngleAxis
VERIFY_IS_APPROX(AngleAxisx(a,v1.normalized()).toRotationMatrix(),
Quaternionx(AngleAxisx(a,v1.normalized())).toRotationMatrix());
AngleAxisx aa1;
m = q1.toRotationMatrix();
aa1 = m;
VERIFY_IS_APPROX(AngleAxisx(m).toRotationMatrix(),
Quaternionx(m).toRotationMatrix());
// Transform
// TODO complete the tests !
a = 0;
while (ei_abs(a)<Scalar(0.1))
a = ei_random<Scalar>(-Scalar(0.4)*Scalar(M_PI), Scalar(0.4)*Scalar(M_PI));
q1 = AngleAxisx(a, v0.normalized());
Transform3 t0, t1, t2;
// first test setIdentity() and Identity()
t0.setIdentity();
VERIFY_IS_APPROX(t0.matrix(), Transform3::MatrixType::Identity());
t0.matrix().setZero();
t0 = Transform3::Identity();
VERIFY_IS_APPROX(t0.matrix(), Transform3::MatrixType::Identity());
t0.linear() = q1.toRotationMatrix();
t1.setIdentity();
t1.linear() = q1.toRotationMatrix();
v0 << 50, 2, 1;//= ei_random_matrix<Vector3>().cwiseProduct(Vector3(10,2,0.5));
t0.scale(v0);
t1.prescale(v0);
VERIFY_IS_APPROX( (t0 * Vector3(1,0,0)).norm(), v0.x());
//VERIFY(!ei_isApprox((t1 * Vector3(1,0,0)).norm(), v0.x()));
t0.setIdentity();
t1.setIdentity();
v1 << 1, 2, 3;
t0.linear() = q1.toRotationMatrix();
t0.pretranslate(v0);
t0.scale(v1);
t1.linear() = q1.conjugate().toRotationMatrix();
t1.prescale(v1.cwise().inverse());
t1.translate(-v0);
VERIFY((t0.matrix() * t1.matrix()).isIdentity(test_precision<Scalar>()));
t1.fromPositionOrientationScale(v0, q1, v1);
VERIFY_IS_APPROX(t1.matrix(), t0.matrix());
VERIFY_IS_APPROX(t1*v1, t0*v1);
t0.setIdentity(); t0.scale(v0).rotate(q1.toRotationMatrix());
t1.setIdentity(); t1.scale(v0).rotate(q1);
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
t0.setIdentity(); t0.scale(v0).rotate(AngleAxisx(q1));
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
VERIFY_IS_APPROX(t0.scale(a).matrix(), t1.scale(Vector3::Constant(a)).matrix());
VERIFY_IS_APPROX(t0.prescale(a).matrix(), t1.prescale(Vector3::Constant(a)).matrix());
// More transform constructors, operator=, operator*=
Matrix3 mat3 = Matrix3::Random();
Matrix4 mat4;
mat4 << mat3 , Vector3::Zero() , Vector4::Zero().transpose();
Transform3 tmat3(mat3), tmat4(mat4);
tmat4.matrix()(3,3) = Scalar(1);
VERIFY_IS_APPROX(tmat3.matrix(), tmat4.matrix());
Scalar a3 = ei_random<Scalar>(-Scalar(M_PI), Scalar(M_PI));
Vector3 v3 = Vector3::Random().normalized();
AngleAxisx aa3(a3, v3);
Transform3 t3(aa3);
Transform3 t4;
t4 = aa3;
VERIFY_IS_APPROX(t3.matrix(), t4.matrix());
t4.rotate(AngleAxisx(-a3,v3));
VERIFY_IS_APPROX(t4.matrix(), Matrix4::Identity());
t4 *= aa3;
VERIFY_IS_APPROX(t3.matrix(), t4.matrix());
v3 = Vector3::Random();
Translation3 tv3(v3);
Transform3 t5(tv3);
t4 = tv3;
VERIFY_IS_APPROX(t5.matrix(), t4.matrix());
t4.translate(-v3);
VERIFY_IS_APPROX(t4.matrix(), Matrix4::Identity());
t4 *= tv3;
VERIFY_IS_APPROX(t5.matrix(), t4.matrix());
Scaling3 sv3(v3);
Transform3 t6(sv3);
t4 = sv3;
VERIFY_IS_APPROX(t6.matrix(), t4.matrix());
t4.scale(v3.cwise().inverse());
VERIFY_IS_APPROX(t4.matrix(), Matrix4::Identity());
t4 *= sv3;
VERIFY_IS_APPROX(t6.matrix(), t4.matrix());
// matrix * transform
VERIFY_IS_APPROX(Transform3(t3.matrix()*t4).matrix(), Transform3(t3*t4).matrix());
// chained Transform product
VERIFY_IS_APPROX(((t3*t4)*t5).matrix(), (t3*(t4*t5)).matrix());
// check that Transform product doesn't have aliasing problems
t5 = t4;
t5 = t5*t5;
VERIFY_IS_APPROX(t5, t4*t4);
// 2D transformation
Transform2 t20, t21;
Vector2 v20 = Vector2::Random();
Vector2 v21 = Vector2::Random();
for (int k=0; k<2; ++k)
if (ei_abs(v21[k])<Scalar(1e-3)) v21[k] = Scalar(1e-3);
t21.setIdentity();
t21.linear() = Rotation2D<Scalar>(a).toRotationMatrix();
VERIFY_IS_APPROX(t20.fromPositionOrientationScale(v20,a,v21).matrix(),
t21.pretranslate(v20).scale(v21).matrix());
t21.setIdentity();
t21.linear() = Rotation2D<Scalar>(-a).toRotationMatrix();
VERIFY( (t20.fromPositionOrientationScale(v20,a,v21)
* (t21.prescale(v21.cwise().inverse()).translate(-v20))).matrix().isIdentity(test_precision<Scalar>()) );
// Transform - new API
// 3D
t0.setIdentity();
t0.rotate(q1).scale(v0).translate(v0);
// mat * scaling and mat * translation
t1 = (Matrix3(q1) * Scaling3(v0)) * Translation3(v0);
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// mat * transformation and scaling * translation
t1 = Matrix3(q1) * (Scaling3(v0) * Translation3(v0));
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
t0.setIdentity();
t0.prerotate(q1).prescale(v0).pretranslate(v0);
// translation * scaling and transformation * mat
t1 = (Translation3(v0) * Scaling3(v0)) * Matrix3(q1);
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// scaling * mat and translation * mat
t1 = Translation3(v0) * (Scaling3(v0) * Matrix3(q1));
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
t0.setIdentity();
t0.scale(v0).translate(v0).rotate(q1);
// translation * mat and scaling * transformation
t1 = Scaling3(v0) * (Translation3(v0) * Matrix3(q1));
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// transformation * scaling
t0.scale(v0);
t1 = t1 * Scaling3(v0);
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// transformation * translation
t0.translate(v0);
t1 = t1 * Translation3(v0);
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// translation * transformation
t0.pretranslate(v0);
t1 = Translation3(v0) * t1;
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// transform * quaternion
t0.rotate(q1);
t1 = t1 * q1;
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// translation * quaternion
t0.translate(v1).rotate(q1);
t1 = t1 * (Translation3(v1) * q1);
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// scaling * quaternion
t0.scale(v1).rotate(q1);
t1 = t1 * (Scaling3(v1) * q1);
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// quaternion * transform
t0.prerotate(q1);
t1 = q1 * t1;
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// quaternion * translation
t0.rotate(q1).translate(v1);
t1 = t1 * (q1 * Translation3(v1));
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// quaternion * scaling
t0.rotate(q1).scale(v1);
t1 = t1 * (q1 * Scaling3(v1));
VERIFY_IS_APPROX(t0.matrix(), t1.matrix());
// translation * vector
t0.setIdentity();
t0.translate(v0);
VERIFY_IS_APPROX(t0 * v1, Translation3(v0) * v1);
// scaling * vector
t0.setIdentity();
t0.scale(v0);
VERIFY_IS_APPROX(t0 * v1, Scaling3(v0) * v1);
// test transform inversion
t0.setIdentity();
t0.translate(v0);
t0.linear().setRandom();
VERIFY_IS_APPROX(t0.inverse(Affine), t0.matrix().inverse());
t0.setIdentity();
t0.translate(v0).rotate(q1);
VERIFY_IS_APPROX(t0.inverse(Isometry), t0.matrix().inverse());
// test extract rotation and scaling
t0.setIdentity();
t0.translate(v0).rotate(q1).scale(v1);
VERIFY_IS_APPROX(t0.rotation() * v1, Matrix3(q1) * v1);
Matrix3 mat_rotation, mat_scaling;
t0.setIdentity();
t0.translate(v0).rotate(q1).scale(v1);
t0.computeRotationScaling(&mat_rotation, &mat_scaling);
VERIFY_IS_APPROX(t0.linear(), mat_rotation * mat_scaling);
VERIFY_IS_APPROX(mat_rotation*mat_rotation.adjoint(), Matrix3::Identity());
VERIFY_IS_APPROX(mat_rotation.determinant(), Scalar(1));
t0.computeScalingRotation(&mat_scaling, &mat_rotation);
VERIFY_IS_APPROX(t0.linear(), mat_scaling * mat_rotation);
VERIFY_IS_APPROX(mat_rotation*mat_rotation.adjoint(), Matrix3::Identity());
VERIFY_IS_APPROX(mat_rotation.determinant(), Scalar(1));
// test casting
Transform<float,3> t1f = t1.template cast<float>();
VERIFY_IS_APPROX(t1f.template cast<Scalar>(),t1);
Transform<double,3> t1d = t1.template cast<double>();
VERIFY_IS_APPROX(t1d.template cast<Scalar>(),t1);
Translation3 tr1(v0);
Translation<float,3> tr1f = tr1.template cast<float>();
VERIFY_IS_APPROX(tr1f.template cast<Scalar>(),tr1);
Translation<double,3> tr1d = tr1.template cast<double>();
VERIFY_IS_APPROX(tr1d.template cast<Scalar>(),tr1);
Scaling3 sc1(v0);
Scaling<float,3> sc1f = sc1.template cast<float>();
VERIFY_IS_APPROX(sc1f.template cast<Scalar>(),sc1);
Scaling<double,3> sc1d = sc1.template cast<double>();
VERIFY_IS_APPROX(sc1d.template cast<Scalar>(),sc1);
Quaternion<float> q1f = q1.template cast<float>();
VERIFY_IS_APPROX(q1f.template cast<Scalar>(),q1);
Quaternion<double> q1d = q1.template cast<double>();
VERIFY_IS_APPROX(q1d.template cast<Scalar>(),q1);
AngleAxis<float> aa1f = aa1.template cast<float>();
VERIFY_IS_APPROX(aa1f.template cast<Scalar>(),aa1);
AngleAxis<double> aa1d = aa1.template cast<double>();
VERIFY_IS_APPROX(aa1d.template cast<Scalar>(),aa1);
Rotation2D<Scalar> r2d1(ei_random<Scalar>());
Rotation2D<float> r2d1f = r2d1.template cast<float>();
VERIFY_IS_APPROX(r2d1f.template cast<Scalar>(),r2d1);
Rotation2D<double> r2d1d = r2d1.template cast<double>();
VERIFY_IS_APPROX(r2d1d.template cast<Scalar>(),r2d1);
m = q1;
// m.col(1) = Vector3(0,ei_random<Scalar>(),ei_random<Scalar>()).normalized();
// m.col(0) = Vector3(-1,0,0).normalized();
// m.col(2) = m.col(0).cross(m.col(1));
#define VERIFY_EULER(I,J,K, X,Y,Z) { \
Vector3 ea = m.eulerAngles(I,J,K); \
Matrix3 m1 = Matrix3(AngleAxisx(ea[0], Vector3::Unit##X()) * AngleAxisx(ea[1], Vector3::Unit##Y()) * AngleAxisx(ea[2], Vector3::Unit##Z())); \
VERIFY_IS_APPROX(m, m1); \
VERIFY_IS_APPROX(m, Matrix3(AngleAxisx(ea[0], Vector3::Unit##X()) * AngleAxisx(ea[1], Vector3::Unit##Y()) * AngleAxisx(ea[2], Vector3::Unit##Z()))); \
}
VERIFY_EULER(0,1,2, X,Y,Z);
VERIFY_EULER(0,1,0, X,Y,X);
VERIFY_EULER(0,2,1, X,Z,Y);
VERIFY_EULER(0,2,0, X,Z,X);
VERIFY_EULER(1,2,0, Y,Z,X);
VERIFY_EULER(1,2,1, Y,Z,Y);
VERIFY_EULER(1,0,2, Y,X,Z);
VERIFY_EULER(1,0,1, Y,X,Y);
VERIFY_EULER(2,0,1, Z,X,Y);
VERIFY_EULER(2,0,2, Z,X,Z);
VERIFY_EULER(2,1,0, Z,Y,X);
VERIFY_EULER(2,1,2, Z,Y,Z);
// colwise/rowwise cross product
mat3.setRandom();
Vector3 vec3 = Vector3::Random();
Matrix3 mcross;
int i = ei_random<int>(0,2);
mcross = mat3.colwise().cross(vec3);
VERIFY_IS_APPROX(mcross.col(i), mat3.col(i).cross(vec3));
mcross = mat3.rowwise().cross(vec3);
VERIFY_IS_APPROX(mcross.row(i), mat3.row(i).cross(vec3));
}
//
// Main
//
int overlapLongMain(int argc, char** argv)
{
parseOverlapLongOptions(argc, argv);
// Open output file
std::ostream* pASQGWriter = createWriter(opt::outFile);
// Build and write the ASQG header
ASQG::HeaderRecord headerRecord;
headerRecord.setOverlapTag(opt::minOverlap);
headerRecord.setErrorRateTag(opt::errorRate);
headerRecord.setInputFileTag(opt::readsFile);
headerRecord.setTransitiveTag(true);
headerRecord.write(*pASQGWriter);
// Determine which index files to use. If a target file was provided,
// use the index of the target reads
std::string indexPrefix;
if(!opt::targetFile.empty())
indexPrefix = stripFilename(opt::targetFile);
else
indexPrefix = stripFilename(opt::readsFile);
BWT* pBWT = new BWT(indexPrefix + BWT_EXT, opt::sampleRate);
SampledSuffixArray* pSSA = new SampledSuffixArray(indexPrefix + SAI_EXT, SSA_FT_SAI);
Timer* pTimer = new Timer(PROGRAM_IDENT);
pBWT->printInfo();
// Read the sequence file and write vertex records for each
// Also store the read names in a vector of strings
ReadTable reads;
SeqReader* pReader = new SeqReader(opt::readsFile, SRF_NO_VALIDATION);
SeqRecord record;
while(pReader->get(record))
{
reads.addRead(record.toSeqItem());
ASQG::VertexRecord vr(record.id, record.seq.toString());
vr.write(*pASQGWriter);
if(reads.getCount() % 100000 == 0)
printf("Read %zu sequences\n", reads.getCount());
}
delete pReader;
pReader = NULL;
BWTIndexSet index;
index.pBWT = pBWT;
index.pSSA = pSSA;
index.pReadTable = &reads;
// Make a prefix for the temporary hits files
size_t n_reads = reads.getCount();
omp_set_num_threads(opt::numThreads);
#pragma omp parallel for
for(size_t read_idx = 0; read_idx < n_reads; ++read_idx)
{
const SeqItem& curr_read = reads.getRead(read_idx);
printf("read %s %zubp\n", curr_read.id.c_str(), curr_read.seq.length());
SequenceOverlapPairVector sopv =
KmerOverlaps::retrieveMatches(curr_read.seq.toString(),
opt::seedLength,
opt::minOverlap,
1 - opt::errorRate,
100,
index);
printf("Found %zu matches\n", sopv.size());
for(size_t i = 0; i < sopv.size(); ++i)
{
std::string match_id = reads.getRead(sopv[i].match_idx).id;
// We only want to output each edge once so skip this overlap
// if the matched read has a lexicographically lower ID
if(curr_read.id > match_id)
continue;
std::string ao = ascii_overlap(sopv[i].sequence[0], sopv[i].sequence[1], sopv[i].overlap, 50);
printf("\t%s\t[%d %d] ID=%s OL=%d PI:%.2lf C=%s\n", ao.c_str(),
sopv[i].overlap.match[0].start,
sopv[i].overlap.match[0].end,
match_id.c_str(),
sopv[i].overlap.getOverlapLength(),
sopv[i].overlap.getPercentIdentity(),
sopv[i].overlap.cigar.c_str());
// Convert to ASQG
SeqCoord sc1(sopv[i].overlap.match[0].start, sopv[i].overlap.match[0].end, sopv[i].overlap.length[0]);
SeqCoord sc2(sopv[i].overlap.match[1].start, sopv[i].overlap.match[1].end, sopv[i].overlap.length[1]);
// KmerOverlaps returns the coordinates of the overlap after flipping the reads
// to ensure the strand matches. The ASQG file wants the coordinate of the original
// sequencing strand. Flip here if necessary
if(sopv[i].is_reversed)
sc2.flip();
// Convert the SequenceOverlap the ASQG's overlap format
Overlap ovr(curr_read.id, sc1, match_id, sc2, sopv[i].is_reversed, -1);
ASQG::EdgeRecord er(ovr);
er.setCigarTag(sopv[i].overlap.cigar);
er.setPercentIdentityTag(sopv[i].overlap.getPercentIdentity());
#pragma omp critical
{
er.write(*pASQGWriter);
}
}
}
// Cleanup
delete pReader;
delete pBWT;
delete pSSA;
delete pASQGWriter;
delete pTimer;
if(opt::numThreads > 1)
pthread_exit(NULL);
return 0;
}
