int lassort(libmaus2::util::ArgParser const & arg, libmaus2::util::ArgInfo const &)
{
std::string const outfilename = arg[0];
std::vector<std::string> VI;
for ( uint64_t i = 1 ; i < arg.size(); ++i )
VI.push_back(arg[i]);
int64_t const tspace = libmaus2::dazzler::align::AlignmentFile::getTSpace(VI);
libmaus2::dazzler::align::AlignmentWriter::unique_ptr_type AW(
new libmaus2::dazzler::align::AlignmentWriter(outfilename,tspace,false /* index */, 0 /* expt */)
);
libmaus2::dazzler::align::Overlap OVL;
for ( uint64_t i = 0; i < VI.size(); ++i )
{
libmaus2::dazzler::align::AlignmentFileRegion::unique_ptr_type PIN(libmaus2::dazzler::align::OverlapIndexer::openAlignmentFileWithoutIndex(VI[i]));
std::vector < libmaus2::dazzler::align::Overlap > VOVL;
while ( PIN->getNextOverlap(OVL) )
{
if ( VOVL.size() && VOVL[0].aread != OVL.aread )
handleVector(VOVL,*AW);
VOVL.push_back(OVL);
}
handleVector(VOVL,*AW);
}
AW.reset();
return EXIT_SUCCESS;
}
SBezier SBezier::From(Vector4 p0, Vector4 p1, Vector4 p2, Vector4 p3) {
SBezier ret;
//**walter steffe--begin
Vector pp0=p0.PerspectiveProject();
Vector pp1=p1.PerspectiveProject();
Vector pp2=p2.PerspectiveProject();
Vector pp3=p3.PerspectiveProject();
TColgp_Array1OfPnt AP(0,3);
TColStd_Array1OfReal AW(0,3);
AW.SetValue(0,p0.w);
AW.SetValue(1,p1.w);
AW.SetValue(2,p2.w);
AW.SetValue(3,p3.w);
AP.SetValue(0,gp_Pnt(pp0.x,pp0.y,pp0.z));
AP.SetValue(1,gp_Pnt(pp1.x,pp1.y,pp1.z));
AP.SetValue(2,gp_Pnt(pp2.x,pp2.y,pp2.z));
AP.SetValue(3,gp_Pnt(pp3.x,pp3.y,pp3.z));
ret.hCurve=new Geom_BezierCurve(AP, AW);
//**walter steffe--end
ZERO(&ret);
ret.deg = 3;
ret.weight[0] = p0.w;
ret.ctrl [0] = p0.PerspectiveProject();
ret.weight[1] = p1.w;
ret.ctrl [1] = p1.PerspectiveProject();
ret.weight[2] = p2.w;
ret.ctrl [2] = p2.PerspectiveProject();
ret.weight[3] = p3.w;
ret.ctrl [3] = p3.PerspectiveProject();
return ret;
}
SBezier SBezier::From(Vector4 p0, Vector4 p1) {
SBezier ret;
//**walter steffe--begin
Vector pp0=p0.PerspectiveProject();
Vector pp1=p1.PerspectiveProject();
TColgp_Array1OfPnt AP(0,1);
TColStd_Array1OfReal AW(0,1);
AW.SetValue(0,p0.w);
AW.SetValue(1,p1.w);
AP.SetValue(0,gp_Pnt(pp0.x,pp0.y,pp0.z));
AP.SetValue(1,gp_Pnt(pp1.x,pp1.y,pp1.z));
gp_Pnt P0=AP.Value(0);
gp_Pnt P1=AP.Value(1);
double W0=AW.Value(0);
double W1=AW.Value(1);
Vector dpp=pp0.Minus(pp1);
if(dpp.Magnitude() > 1.e-10)
ret.hCurve=new Geom_BezierCurve(AP, AW);
// ret.hCurve=new Geom_BezierCurve(AP);
//**walter steffe--end
ZERO(&ret);
ret.deg = 1;
ret.weight[0] = p0.w;
ret.ctrl [0] = p0.PerspectiveProject();
ret.weight[1] = p1.w;
ret.ctrl [1] = p1.PerspectiveProject();
return ret;
}
static std::vector<std::string> splitFile(std::string const & aligns, std::string const & prefix, uint64_t const n, bool const tmp)
{
libmaus2::aio::InputStreamInstance algnfile(aligns);
libmaus2::dazzler::align::AlignmentFile algn(algnfile);
libmaus2::dazzler::align::Overlap OVL;
AlignmentSplitWriter AW(algn.tspace,prefix,n,tmp);
// get next overlap
while ( algn.getNextOverlap(algnfile,OVL) )
AW.push(OVL);
return AW.outputfilenames;
}
int lasfilterquality(libmaus2::util::ArgParser const & arg, libmaus2::util::ArgInfo const & /* arginfo */)
{
libmaus2::dazzler::align::AlignmentFileRegion::unique_ptr_type Pfile(libmaus2::dazzler::align::OverlapIndexer::openAlignmentFileWithoutIndex(arg[2]));
int64_t const tspace = Pfile->Palgn->tspace;
libmaus2::dazzler::align::Overlap OVL;
libmaus2::dazzler::align::AlignmentWriter AW(arg[1],tspace,true);
libmaus2::dazzler::db::DatabaseFile DB(arg[0]);
DB.computeTrimVector();
libmaus2::dazzler::db::Track::unique_ptr_type Pqual(DB.readTrack("qual"));
libmaus2::dazzler::db::TrackAnnoInterface const & qualanno = Pqual->getAnno();
libmaus2::autoarray::AutoArray<unsigned char> const & qualdata = *(Pqual->Adata);
unsigned int const defq = 25;
unsigned int const q = arg.argPresent("q") ? arg.getUnsignedNumericArg<uint64_t>("q") : defq;
libmaus2::autoarray::AutoArray < std::pair<uint64_t,uint64_t> > I;
libmaus2::autoarray::AutoArray < std::pair< int32_t,int32_t > > O;
uint64_t Io = 0;
int64_t prevaread = -1;
while ( Pfile->getNextOverlap(OVL) )
{
int64_t const aread = OVL.aread;
if ( aread != prevaread )
{
Io = 0;
int64_t const alow = qualanno[aread];
int64_t const ahigh = qualanno[aread+1];
unsigned char const * ua = qualdata.begin() + alow;
unsigned char const * ue = qualdata.begin() + ahigh;
unsigned char const * up = ua;
while ( up != ue )
{
while ( up != ue && *up > q )
++up;
assert ( up == ue || *up <= q );
unsigned char const * ul = up;
while ( up != ue && *up <= q )
++up;
if ( up != ul )
I.push(Io,std::pair<uint64_t,uint64_t>((ul-ua)*tspace,(up-ua)*tspace));
}
#if 0
std::cerr << aread << "\t";
for ( uint64_t i = 0; i < Io; ++i )
std::cerr << "(" << I[i].first << "," << I[i].second << ")";
std::cerr << std::endl;
#endif
prevaread = aread;
}
OVL.alignToTracePoints(tspace);
uint64_t const o = OVL.filterIntervals(I.begin(),I.begin()+Io,O);
for ( uint64_t i = 0; i < o; ++i )
{
libmaus2::dazzler::align::Overlap fOVL = OVL.filter(O[i],tspace);
assert ( ! fOVL.isEmpty() );
AW.put(fOVL);
}
}
return EXIT_SUCCESS;
}
