void TwoBitFile::populateSequenceMeta(TwoBitSequenceMeta& meta)
{
// seek to offset and read actual sequence meta data.
file_.seekg(meta.offset_);
meta.dnaSize_ = nextInt(); // length of sequence
meta.dnaBytes_ = meta.dnaSize_ / 4 + (meta.dnaSize_ % 4 > 0);
// read nRegions.
readRegions(meta.nRegions); // N-regions
readRegions(meta.mRegions); // mask regions
// check. this number should be zero as per the spec.
if (0 != nextInt()) {
throw Exception(__PRETTY_FUNCTION__, "Unexpected data. Bad 2-bit file.");
}
// store start of packed data
meta.packedPos_ = file_.tellg();
}
bool World::load(const std::string& dir) {
fs::path world_dir(dir);
fs::path region_dir = world_dir / "region";
if(!fs::exists(world_dir)) {
std::cerr << "Error: World directory " << world_dir << " does not exist!" << std::endl;
} else if(!fs::exists(region_dir)) {
std::cerr << "Error: Region directory " << region_dir << " does not exist!" << std::endl;
} else {
return readRegions(region_dir.string());
}
return false;
}
/**
* Loads a world from a directory.
*/
bool World::load(const std::string& dir, int rotation) {
this->rotation = rotation;
fs::path world_dir(dir);
fs::path region_dir = world_dir / "region";
if(!fs::exists(world_dir)) {
std::cerr << "World directory " << world_dir << " does not exists!" << std::endl;
} else if(!fs::exists(region_dir)) {
std::cerr << "Region directory " << region_dir << " does not exists!" << std::endl;
} else {
return readRegions(region_dir.string());
}
return false;
}
int main(int argc, char* argv[]){
if (argc != 3)
printErrorAndDie("Script requires exactly 2 arguments");
std::string region_file = std::string(argv[1]);
std::string vcf_file = std::string(argv[2]);
// Read list of regions
std::vector<Region> regions;
readRegions(region_file, regions, 1000, "", std::cerr);
vcflib::VariantCallFile ref_vcf;
if(!ref_vcf.open(vcf_file))
printErrorAndDie("Failed to open VCF");
// Populate map with samples in VCF header
std::map<std::string, int> sample_indices;
for (unsigned int i = 0; i < ref_vcf.sampleNames.size(); i++)
sample_indices[ref_vcf.sampleNames[i]] = i;
std::vector<std::string> alleles;
std::vector<bool> got_priors;
int32_t pos;
for (unsigned int i = 0; i < regions.size(); i++){
bool success;
double* priors = extract_vcf_alleles_and_log_priors(&ref_vcf, &(regions[i]), sample_indices, alleles, got_priors, pos, success, std::cerr);
if (success){
std::cerr << "Position=" << pos << std::endl;
std::cerr << "Alleles:" << std::endl;
for (unsigned int j = 0; j < alleles.size(); j++)
std::cerr << alleles[j] << std::endl;
}
else {
std::cerr << "Failed to read alleles and priors for region " << regions[i].str() << std::endl;
}
alleles.clear();
got_priors.clear();
delete [] priors;
}
}
int main (int argc, char **argv)
{
Options mergetr = readParameters (argc, argv);
char filename_mesh_node[FILENAME_MAX];
char filename_mesh_ele[FILENAME_MAX];
char filename_otoczka[FILENAME_MAX];
char filename_output_node[FILENAME_MAX];
char filename_output_ele[FILENAME_MAX];
int no_of_meshes = argc-mergetr.args_start;
strcpy (filename_otoczka, mergetr.input);
if ( strstr (filename_otoczka, ".poly") == NULL)
strcat (filename_otoczka, ".poly");
strcpy (filename_output_node, mergetr.output);
strcat (filename_output_node, ".node");
strcpy (filename_output_ele, mergetr.output);
strcat (filename_output_ele, ".ele");
fprintf(stdout, "************************************\n");
fprintf(stdout, "***** M * E * R * G * E * T * R ****\n");
fprintf(stdout, "************************************\n");
fprintf(stdout, "* Otoczka filename: %s\n", filename_otoczka);
fprintf(stdout, "* Output filenames: %s & %s\n", filename_output_node, filename_output_ele);
fprintf(stdout, "* Triangle options: %s\n", mergetr.tr_opt);
fprintf(stdout, "************************************\n");
struct triangulateio *siatka;
struct triangulateio otoczka;
struct triangulateio out;
EdgeList **v;
PointList **p;
int i;
siatka = malloc ( no_of_meshes * sizeof *siatka);
v = malloc ( no_of_meshes * sizeof **v );
p = malloc ( no_of_meshes * sizeof **p );
if (siatka == NULL || v == NULL || p == NULL) {
fprintf (stderr, "** Error! Not enough memory!");
return -1;
}
initTriangulation (&otoczka);
/* OTOCZKA */
FILE *file_otoczka = fopen( filename_otoczka, "r");
if (file_otoczka == NULL) {
fprintf(stderr, "** Error while opening %s\n", filename_otoczka);
return -100;
}
readPoints (file_otoczka, &otoczka);
readSegments (file_otoczka, &otoczka);
readHoles (file_otoczka, &otoczka);
readRegions (file_otoczka, &otoczka);
fclose (file_otoczka);
/* MESHES */
for (i = 0; i < (argc - mergetr.args_start); i++) {
strcpy (filename_mesh_node, argv[mergetr.args_start+i]);
strcat (filename_mesh_node, ".node");
strcpy (filename_mesh_ele, argv[mergetr.args_start+i]);
strcat (filename_mesh_ele, ".ele");
fprintf(stdout, "************************************\n");
fprintf(stdout, "* Mesh filenames: %s & %s\n", filename_mesh_node, filename_mesh_ele);
fprintf(stdout, "************************************\n");
FILE *file_mesh_node = fopen( filename_mesh_node, "r");
FILE *file_mesh_ele = fopen( filename_mesh_ele, "r");
if (file_mesh_node == NULL) {
fprintf(stderr, "** Error while opening %s\n", filename_mesh_node);
return -101;
}
if (file_mesh_node == NULL) {
fprintf(stderr, "** Error while opening %s\n", filename_mesh_ele);
return -102;
}
initTriangulation (&siatka[i]);
readPoints (file_mesh_node, &siatka[i]);
readTriangles (file_mesh_ele, &siatka[i]);
fclose (file_mesh_node);
fclose (file_mesh_ele);
v[i] = createEdgeList(siatka[i]);
markBndEdges (siatka[i], v[i]);
p[i] = makePointList (otoczka, siatka[i], v[i]);
updatePoints (&otoczka, siatka[i], v[i], p[i]);
updateSegments (&otoczka, siatka[i], v[i], p[i]);
updateHoles (&otoczka, siatka[i]);
}
fprintf(stdout, "************************************\n");
/* TRIANGULAtE */
initTriangulation (&out);
strcat (mergetr.tr_opt, "pYYQ");
triangulate (mergetr.tr_opt, &otoczka, &out, (struct triangulateio *) NULL);
/* GLUE HOLES */
/* markNotBndEdges (siatka1, v); */
for (i = 0; i < no_of_meshes; i++) {
glueNotBndPoints (&out, siatka[i], p[i]); /* DOKLEJANIE DO OUT */
fixPointListNumbers (&out, &siatka[i], p[i]);
glueInteriorTriangles (&out, siatka[i], p[i]);
removeHole (&out);
}
FILE *file_output_node = fopen (filename_output_node, "w");
FILE *file_output_ele = fopen (filename_output_ele, "w");
writePoints (file_output_node, out);
writeTriangles (file_output_ele, out);
fclose (file_output_node);
fclose (file_output_ele);
fprintf(stdout, "************************************\n");
free (p);
free (v);
freeTriangulation (&otoczka);
freeTriangulation (&out);
for (i = 0; i < no_of_meshes; i++)
freeTriangulation (&siatka[i]);
return 0;
}