void simulateWorld(long tstart, long tend) {
const static double DT_100MS = 100;
timeTmp += tend - tstart;
if (timeTmp >= DT_100MS) {
for (long ts = timeTmp; timeTmp > 0; timeTmp -= DT_100MS) {
stepSign(centerHansel, angleHansel, DT_100MS / 1000);
stepSign(centerGreta, angleGreta, DT_100MS / 1000);
calcCoverage();
if (isCovered) {
timeCovered += DT_100MS;
}
}
}
}
int main(int argc, char *argv[]) {
DBAdaptor * dba;
StatementHandle *sth;
ResultRow * row;
Vector * slices;
int nSlices;
htsFile * out;
int argNum = 1;
char *inFName = NULL;
char *outFName = NULL;
char *dbUser = "******";
char *dbPass = NULL;
int dbPort = 3306;
char *dbHost = "ens-staging.internal.sanger.ac.uk";
char *dbName = "homo_sapiens_core_71_37";
char *assName = "GRCh37";
char *chrName = "1";
int flags = 0;
int threads = 1;
initEnsC(argc, argv);
while (argNum < argc) {
char *arg = argv[argNum];
char *val;
// Ones without a val go here
if (!strcmp(arg, "-U") || !strcmp(arg,"--ucsc_naming")) {
flags |= M_UCSC_NAMING;
} else {
// Ones with a val go in this block
if (argNum == argc-1) {
Bamcov_usage();
}
val = argv[++argNum];
if (!strcmp(arg, "-i") || !strcmp(arg,"--in_file")) {
StrUtil_copyString(&inFName,val,0);
} else if (!strcmp(arg, "-o") || !strcmp(arg,"--out_file")) {
StrUtil_copyString(&outFName,val,0);
} else if (!strcmp(arg, "-h") || !strcmp(arg,"--host")) {
StrUtil_copyString(&dbHost,val,0);
} else if (!strcmp(arg, "-p") || !strcmp(arg,"--password")) {
StrUtil_copyString(&dbPass,val,0);
} else if (!strcmp(arg, "-P") || !strcmp(arg,"--port")) {
dbPort = atoi(val);
} else if (!strcmp(arg, "-n") || !strcmp(arg,"--name")) {
StrUtil_copyString(&dbName,val,0);
} else if (!strcmp(arg, "-u") || !strcmp(arg,"--user")) {
StrUtil_copyString(&dbUser,val,0);
} else if (!strcmp(arg, "-t") || !strcmp(arg,"--threads")) {
threads = atoi(val);
} else if (!strcmp(arg, "-a") || !strcmp(arg,"--assembly")) {
StrUtil_copyString(&assName,val,0);
} else if (!strcmp(arg, "-v") || !strcmp(arg,"--verbosity")) {
verbosity = atoi(val);
// Temporary
} else if (!strcmp(arg, "-c") || !strcmp(arg,"--chromosome")) {
StrUtil_copyString(&chrName,val,0);
} else {
fprintf(stderr,"Error in command line at %s\n\n",arg);
Bamcov_usage();
}
}
argNum++;
}
if (verbosity > 0) {
printf("Program for calculating read coverage in a BAM file \n"
"Steve M.J. Searle. [email protected] Last update April 2013.\n");
}
if (!inFName || !outFName) {
Bamcov_usage();
}
dba = DBAdaptor_new(dbHost,dbUser,dbPass,dbName,dbPort,NULL);
//nSlices = getSlices(dba, destName);
nSlices = 1;
slices = Vector_new();
SliceAdaptor *sa = DBAdaptor_getSliceAdaptor(dba);
Slice *slice = SliceAdaptor_fetchByRegion(sa,NULL,chrName,POS_UNDEF,POS_UNDEF,1,NULL, 0);
Vector_addElement(slices,slice);
if (Vector_getNumElement(slices) == 0) {
fprintf(stderr, "Error: No slices.\n");
exit(1);
}
htsFile *in = hts_open(inFName, "rb");
if (in == 0) {
fprintf(stderr, "Fail to open BAM file %s\n", inFName);
return 1;
}
hts_set_threads(in, threads);
hts_idx_t *idx;
idx = bam_index_load(inFName); // load BAM index
if (idx == 0) {
fprintf(stderr, "BAM index file is not available.\n");
return 1;
}
int i;
for (i=0; i<Vector_getNumElement(slices); i++) {
Slice *slice = Vector_getElementAt(slices,i);
if (verbosity > 0) printf("Working on '%s'\n",Slice_getName(slice));
// if (verbosity > 0) printf("Stage 1 - retrieving annotation from database\n");
// Vector *genes = getGenes(slice, flags);
if (verbosity > 0) printf("Stage 1 - calculating coverage\n");
calcCoverage(inFName, slice, in, idx, flags);
}
hts_idx_destroy(idx);
hts_close(in);
if (verbosity > 0) printf("Done\n");
return 0;
}
void findCannyCandidates( GradientChain& grad, CandidatePtrVector& cds ) {
// Read canny edge stats from gradient image
IplImage *canny = grad.cannyEdges;
int width = canny->width;
int height = canny->height;
int wstep = canny->widthStep;
float minRad = grad.minRad;
float maxRad = grad.maxRad;
// Single pass through image (sort of) linking edges
vector<cp_circle> iden;
const char EDGE_MARKER = (char)(255);
const char USED_MARKER = (char)(254);
//cout << width << " " << height << endl;
for( int r = 1; r < height-1; r++ ) {
for( int c = 1; c < width-1; c++ ) {
// Check if new Contour exists
if( (canny->imageData+wstep*r)[c] == EDGE_MARKER ) {
stack<cp_point> sq;
cp_point pt(r,c);
vector<cp_point> seq;
sq.push( pt );
while( sq.size() != 0 ) {
pt = sq.top();
int ir = pt.r;
int ic = pt.c;
// Check boundary conditions
if( ir < 1 || ic < 1 || ir > height-1 || ic > width-1 ) {
sq.pop();
continue;
}
// Check label
char* pos = (canny->imageData + wstep*ir)+ic;
if( *pos != EDGE_MARKER ) {
sq.pop();
continue;
}
*pos = USED_MARKER;
seq.push_back( pt );
sq.pop();
// Check 8-connectedness
sq.push( cp_point( ir+1, ic ) );
sq.push( cp_point( ir, ic+1 ) );
sq.push( cp_point( ir-1, ic ) );
sq.push( cp_point( ir, ic-1 ) );
sq.push( cp_point( ir-1, ic+1 ) );
sq.push( cp_point( ir-1, ic-1 ) );
sq.push( cp_point( ir+1, ic+1 ) );
sq.push( cp_point( ir+1, ic-1 ) );
}
// Quickly Analyze Contour
int csize = seq.size();
// Threshold size
if( csize < 8 )
continue;
// If its a very small Contour
if( csize < 16 ) {
int i1 = 1;
int i2 = csize / 2;
int i3 = csize - 2;
cp_circle c1;
bool status = circleFrom3PointsInd( seq, i1, i2, i3, c1 );
if( status && c1.rad > (1.5*minRad) && c1.rad < maxRad ) {
calcMSE( c1, seq );
calcCoverage( c1, seq );
iden.push_back( c1 );
}
continue;
}
// Sampling Indecies
int i1 = 0;
int i2 = 0.2*csize;
int i3 = 0.4*csize;
int i4 = 0.6*csize;
int i5 = 0.8*csize;
int i6 = csize - 1;
// Sample circles
cp_circle c1, c2, c3;
bool s1 = circleFrom3PointsInd( seq, i1, i4, i6, c1 );
bool s2 = circleFrom3PointsInd( seq, i2, i4, i6, c2 );
bool s3 = circleFrom3PointsInd( seq, i1, i3, i5, c3 );
// Filter
if( s1 && c1.rad > minRad && c1.rad < maxRad ) {
calcMSE( c1, seq );
calcCoverage( c1, seq );
iden.push_back( c1 );
}
if( s2 && c2.rad > minRad && c2.rad < maxRad ) {
calcMSE( c2, seq );
calcCoverage( c2, seq );
iden.push_back( c2 );
}
if( s3 && c3.rad > minRad && c3.rad < maxRad ) {
calcMSE( c3, seq );
calcCoverage( c3, seq );
iden.push_back( c3 );
}
}
}
}
// Insert/Adjust IP for scale
const int MAX_CP_IP = 40;
sort( iden.begin(), iden.end(), compareCircles );
for( unsigned int i = 0; i < iden.size(); i++ ) {
// Check max
if( i >= MAX_CP_IP )
break;
// Insert new Candidate point
Candidate* cd1 = new Candidate;
cd1->r = iden[i].r * grad.scale;
cd1->c = iden[i].c * grad.scale;
cd1->major = iden[i].rad * grad.scale;
cd1->minor = iden[i].rad * grad.scale;
cd1->angle = 0.0;
cd1->method = CANNY;
cd1->magnitude = iden[i].normMSE*iden[i].csize;
cds.push_back( cd1 );
}
}