int main()
{
ptransforms = new CParamTransforms();
int fail = 0;
fail+=testTransform("exp");
fail+=testTransform("negLogLogit");
fail+=testTransform("sigmoid");
ptransforms->writeMatlabFile("crap.mat", "writtenTransforms");
CParamTransforms* preadTrans = new CParamTransforms();
preadTrans->readMatlabFile("crap.mat", "writtenTransforms");
if(ptransforms->equals(*preadTrans))
cout << "MATLAB Read and write transforms to stream passed"<<endl;
else
{
cout << "FAILURE: Read and write to MATLAB" << endl;
cout << "Written transforms:" << endl;
ptransforms->display(cout);
cout << "Read in transforms: " << endl;
preadTrans->display(cout);
fail++;
}
ptransforms->toFile("crap_paramtransform");
preadTrans->fromFile("crap_paramtransform");
if(ptransforms->equals(*preadTrans))
cout << "Read and write transforms to stream passed"<<endl;
else
{
cout << "FAILURE: Read and write to stream" << endl;
cout << "Written transforms:" << endl;
ptransforms->display(cout);
cout << "Read in transforms: " << endl;
preadTrans->display(cout);
fail++;
}
cout << "Number of failures: " << fail << endl;
}
int main(int argc, char *argv[]) {
initEnsC(argc, argv);
Mapper *mapper = Mapper_new( "rawcontig", "virtualcontig", NULL, NULL );
int nToLoad = loadSGPDump(mapper, 0 );
// loading done successfully
ok(1, nToLoad == 100);
{
// transform a segment entirely within the first rawcontig
int testOutput[][4] = {1, 2, 5, -1};
testTransform (mapper, 627012, 2, 5, -1, "rawcontig", testOutput, NumOutput(testOutput));
}
{
// now a split coord
int testOutput[][4] = {
{314696, 31917, 31937, -1},
{341, 126, 59773, -1},
{315843, 5332, 5963, +1}
};
testTransform (mapper, 1, 383700, 444000, +1, "virtualcontig",testOutput, NumOutput(testOutput));
}
{
// now a simple gap
int testOutput[][4] = {
{ 627011, 7447, 7507, +1 },
{ 1, 273762, 273781, 0 }
};
testTransform (mapper, 1, 273701, 273781, +1, "virtualcontig", testOutput, NumOutput(testOutput));
}
//
// check if the mapper can do merging
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, 1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, 1, 1, 111, 120 );
{
int testOutput[][4] = {{ 1, 105, 125, 1 }};
testTransform(mapper, 1, 5, 25, 1, "asm1", testOutput, NumOutput(testOutput));
}
//
// Slightly differnt merge case
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, 1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 12, 20, 1, 1, 112, 120 );
{
int testOutput[][4] = {
{ 1, 105, 110, 1 },
{ 1, 11, 11, 0 },
{ 1, 112, 125, 1 }
};
testTransform( mapper, 1, 5, 25, 1, "asm1" , testOutput, NumOutput(testOutput));
}
//
// dont merge on wrong orientation
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, 1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, -1, 1, 111, 120 );
{
int testOutput[][4] = {
{ 1, 105, 110, 1 },
{ 1, 111, 120, -1 },
{ 1, 121, 125, 1 }
};
testTransform( mapper, 1, 5, 25, 1, "asm1" , testOutput, NumOutput(testOutput));
}
//
// can reverse strands merge?
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, -1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, -1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, -1, 1, 111, 120 );
{
int testOutput[][4] = {{ 1, 106, 126, -1 } };
testTransform( mapper, 1, 5, 25, 1, "asm1", testOutput, NumOutput(testOutput));
}
//
// normal merge, not three
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, 1, 1, 111, 120 );
Mapper_addMapCoordinates(mapper, 1, 22, 30, 1, 1, 132, 140 );
Mapper_addMapCoordinates(mapper, 1, 51, 70, 1, 1, 161, 180 );
Mapper_addMapCoordinates(mapper, 1, 31, 35, 1, 1, 141, 145 );
{
int testOutput[][4] = {
{ 1, 105, 120, 1 },
{ 1, 21, 21, 0 },
{ 1, 132, 145, 1 },
{ 1, 36, 45, 0 }
};
testTransform( mapper, 1, 5, 45, 1, "asm1" , testOutput, NumOutput(testOutput));
}
//
// test tranformation of 'insertion' coordinates where end = start -1
//
mapper = Mapper_new("asm1", "asm2", NULL, NULL);
Mapper_addMapCoordinates(mapper,1, 1, 10, 1, 2, 101, 110);
Mapper_addMapCoordinates(mapper,1, 11, 20, -1, 3, 1, 10);
{
// boundary insert, expect 2 edge inserts back
int testOutput[][4] = {
{2, 111, 110, 1},
{3, 11, 10, -1}
};
testTransform(mapper, 1, 11, 10, 1, "asm1", testOutput, NumOutput(testOutput));
}
{
// edge insert, negative strand, expect edge insert negative strand
int testOutput[][4] = {{2, 101, 100, -1}};
testTransform(mapper, 1, 1, 0, -1, "asm1", testOutput, NumOutput(testOutput));
}
{
// normal case, expect single insert in middle
int testOutput[][4] = {{2, 102, 101, 1}};
testTransform(mapper, 1, 2, 1, 1, "asm1", testOutput, NumOutput(testOutput));
}
{
// expect a gap
int testOutput[][4] = {{1, 100, 200, 0}};
testTransform(mapper, 1, 100, 200, 1, "asm1", testOutput, NumOutput(testOutput));
}
return 0;
}
