static void addToOpenSet (astar_t *astar,
int node,
int nodeFrom)
{
coord_t nodeCoord = getCoord (astar->bounds, node);
coord_t nodeFromCoord = getCoord (astar->bounds, nodeFrom);
if (!exists (astar->open, node)) {
astar->cameFrom[node] = nodeFrom;
astar->gScores[node] = astar->gScores[nodeFrom] +
preciseDistance (nodeFromCoord, nodeCoord);
insert (astar->open, node, astar->gScores[node] +
estimateDistance (nodeCoord,
getCoord (astar->bounds, astar->goal)));
}
else if (astar->gScores[node] >
astar->gScores[nodeFrom] +
preciseDistance (nodeFromCoord, nodeCoord)) {
astar->cameFrom[node] = nodeFrom;
int oldGScore = astar->gScores[node];
astar->gScores[node] = astar->gScores[nodeFrom] +
preciseDistance (nodeFromCoord, nodeCoord);
double newPri = priorityOf (astar->open, node)
- oldGScore
+ astar->gScores[node];
changePriority (astar->open, node, newPri);
}
}
static int init_astar_object (astar_t* astar, const char *grid, int *solLength, int boundX, int boundY, int start, int end)
{
*solLength = -1;
struct coord_t bounds = {boundX, boundY};
int size = bounds.x * bounds.y;
if (start >= size || start < 0 || end >= size || end < 0)
return 0;
struct coord_t startCoord = getCoord (bounds, start);
struct coord_t endCoord = getCoord (bounds, end);
if (!contained (bounds, startCoord) || !contained (bounds, endCoord))
return 0;
astar->solutionLength = solLength;
astar->bounds = bounds;
astar->start = start;
astar->goal = end;
astar->grid = grid;
astar->open = createQueue();
if (!astar->open)
return 0;
astar->closed = (char*)malloc (size);
if (!astar->closed) {
freeQueue (astar->open);
return 0;
}
astar->gScores = (double*)malloc (size * sizeof (double));
if (!astar->gScores) {
freeQueue (astar->open);
free (astar->closed);
return 0;
}
astar->cameFrom = (node*)malloc (size * sizeof (int));
if (!astar->cameFrom) {
freeQueue (astar->open);
free (astar->closed);
free (astar->gScores);
return 0;
}
memset (astar->closed, 0, size);
astar->gScores[start] = 0;
astar->cameFrom[start] = -1;
insert (astar->open, astar->start, estimateDistance (startCoord, endCoord));
return 1;
}
int *astar_unopt_compute (const char *grid,
int *solLength,
int boundX,
int boundY,
int start,
int end)
{
astar_t astar;
coord_t bounds = {boundX, boundY};
int size = bounds.x * bounds.y;
if (start >= size || start < 0 || end >= size || end < 0)
return NULL;
coord_t startCoord = getCoord (bounds, start);
coord_t endCoord = getCoord (bounds, end);
if (!contained (bounds, startCoord) || !contained (bounds, endCoord))
return NULL;
queue *open = createQueue();
char closed [size];
double gScores [size];
int cameFrom [size];
astar.solutionLength = solLength;
*astar.solutionLength = -1;
astar.bounds = bounds;
astar.start = start;
astar.goal = end;
astar.grid = grid;
astar.open = open;
astar.closed = closed;
astar.gScores = gScores;
astar.cameFrom = cameFrom;
memset (closed, 0, sizeof(closed));
gScores[start] = 0;
cameFrom[start] = -1;
insert (open, start, estimateDistance (startCoord, endCoord));
while (open->size) {
int node = findMin (open)->value;
coord_t nodeCoord = getCoord (bounds, node);
if (nodeCoord.x == endCoord.x && nodeCoord.y == endCoord.y) {
freeQueue (open);
return recordSolution (&astar);
}
deleteMin (open);
closed[node] = 1;
for (int dir = 0; dir < 8; dir++)
{
coord_t newCoord = adjustInDirection (nodeCoord, dir);
int newNode = getIndex (bounds, newCoord);
if (!contained (bounds, newCoord) || !grid[newNode])
continue;
if (closed[newNode])
continue;
addToOpenSet (&astar, newNode, node);
}
}
freeQueue (open);
return NULL;
}
int *astar_compute (const char *grid,
int *solLength,
int boundX,
int boundY,
int start,
int end)
{
*solLength = -1;
astar_t astar;
coord_t bounds = {boundX, boundY};
int size = bounds.x * bounds.y;
if (start >= size || start < 0 || end >= size || end < 0)
return NULL;
coord_t startCoord = getCoord (bounds, start);
coord_t endCoord = getCoord (bounds, end);
if (!contained (bounds, startCoord) || !contained (bounds, endCoord))
return NULL;
queue *open = createQueue();
char closed [size];
double gScores [size];
int cameFrom [size];
astar.solutionLength = solLength;
astar.bounds = bounds;
astar.start = start;
astar.goal = end;
astar.grid = grid;
astar.open = open;
astar.closed = closed;
astar.gScores = gScores;
astar.cameFrom = cameFrom;
memset (closed, 0, sizeof(closed));
gScores[start] = 0;
cameFrom[start] = -1;
insert (open, start, estimateDistance (startCoord, endCoord));
while (open->size) {
int node = findMin (open)->value;
coord_t nodeCoord = getCoord (bounds, node);
if (nodeCoord.x == endCoord.x && nodeCoord.y == endCoord.y) {
freeQueue (open);
return recordSolution (&astar);
}
deleteMin (open);
closed[node] = 1;
direction from = directionWeCameFrom (&astar,
node,
cameFrom[node]);
directionset dirs =
forcedNeighbours (&astar, nodeCoord, from)
| naturalNeighbours (from);
for (int dir = nextDirectionInSet (&dirs); dir != NO_DIRECTION; dir = nextDirectionInSet (&dirs))
{
int newNode = jump (&astar, dir, node);
coord_t newCoord = getCoord (bounds, newNode);
// this'll also bail out if jump() returned -1
if (!contained (bounds, newCoord))
continue;
if (closed[newNode])
continue;
addToOpenSet (&astar, newNode, node);
}
}
freeQueue (open);
return NULL;
}
int main(int argc, char* argv[])
{
// parameters that you can set.
string infF = "";
string infR = "";
string infPath = "";
string outI = "oIter.txt";
string outP = "oPar.txt";
string outCorr = "oCorr.txt";
string outCnt = "oCnt.txt";
string outPath = "";
string outStub = "";
//bool useemp = false;
double truncLimit = 0.99;
int verbose = 3;
int lambdaD = 147;
int minD = 130;
int maxD = 180;
int sampleSize = -1;
int burnins = 1000;
int iterations = 10000;
int seed = -1;
// Unknowns
double lambdaF[2];
double lambdaR[2];
double pF[2];
double pR[2];
/*
* Read and check input parameters
*/
string errorLine = "usage " +
string(argv[0]) +
" [parameters] \n" +
"\t-iF <forward reads binary file> \n" +
"\t-iR <reverse reads binary file> \n" +
"\t-iPath <path to forward and reverse reads binary files \n" +
" (overrides iR and iF if set)> \n" +
"\t-oPath <outdirectory, where all output files are put. \n" +
"\t NOT created - needs to exists. Defaults to where \n"+
"\t the program is executed from.>\n" +
"\t-oStub <outfile names stub, \n" +
"\t defaults -oIter to <-oStub_>oIter.txt, \n" +
"\t defaults -oPar to <-oStub_>oPar.txt> \n" +
"\t defaults -oCorr to <-oStub_>oCorr.txt> \n" +
"\t defaults -oCnt to <-oStub_>oCnt.txt> \n" +
"\t-oIter <outfile, where to write MCMC parameter\n" +
"\t estimates for each iteration,default generated from -oStub>\n" +
"\t-oPar <parameter-file, where to write MCMC\n" +
"\t final parameter estimates, default generated from -oStub> \n" +
/*
"\t-oCorr <out-file, lists correlation coefficients between forward\n" +
"\t and reverse reads in [mind,maxd] \n" +
"\t default generated from -oStub> \n" +
*/
"\t-oCnt <out-file, lists forward and reverse read count frequencies\n" +
"\t default generated from -oStub> \n" +
"\t-trunc <truncation limit in (0,1], default 0.99.> \n" +
"\t-size <sample size, default all observations.> \n" +
"\t-burnin <number of MCMC burnin iterations,\n" +
"\t default 1000.> \n" +
"\t-iter <number of MCMC iterations\n" +
"\t (non-burnin iterations), default 10000.> \n" +
"\t-seed <set seed to random number generator.> \n" +
"\t-ld <distance-lambda, default 147 bp.> \n" +
"\t-mind <min distance, default 130 bp.> \n" +
"\t-maxd <max distance, default 180 bp.> \n" +
/*
"\t-useemp <toggle use of data-driven distance distribution, or poisson\n" +
"\t around distance-lambda. default off.>\n" +
*/
"\t-v <verbose level 0-3. default 2>";
bool fail = false;
string failmessage = "";
for (int i = 1; i < argc; i++)
{
if(strcmp(argv[i],"-iF") == 0)
infF.assign(argv[++i]);
else if(strcmp(argv[i],"-iR") == 0)
infR.assign(argv[++i]);
else if(strcmp(argv[i],"-iPath") == 0)
infPath.assign(argv[++i]);
else if(strcmp(argv[i],"-oPath") == 0)
outPath.assign(argv[++i]);
else if(strcmp(argv[i],"-oStub") == 0)
outStub.assign(argv[++i]);
else if(strcmp(argv[i],"-oIter") == 0)
outI.assign(argv[++i]);
else if(strcmp(argv[i],"-oPar") == 0)
outP.assign(argv[++i]);
/*
else if(strcmp(argv[i],"-oCorr") == 0)
outCorr.assign(argv[++i]);
*/
else if(strcmp(argv[i],"-oCnt") == 0)
outCnt.assign(argv[++i]);
/*
else if (strcmp(argv[i],"-useemp") == 0)
useemp = true;
*/
else if (strcmp(argv[i],"-v") == 0)
verbose = atoi(argv[++i]);
else if (strcmp(argv[i],"-seed") == 0)
seed = atoi(argv[++i]);
else if (strcmp(argv[i],"-trunc") == 0)
truncLimit = atof(argv[++i]);
else if (strcmp(argv[i],"-size") == 0)
sampleSize = atoi(argv[++i]);
else if (strcmp(argv[i],"-burnin") == 0)
burnins = atoi(argv[++i]);
else if (strcmp(argv[i],"-iter") == 0)
iterations = atoi(argv[++i]);
else if (strcmp(argv[i],"-ld") == 0)
lambdaD = atoi(argv[++i]);
else if (strcmp(argv[i],"-mind") == 0)
minD = atoi(argv[++i]);
else if (strcmp(argv[i],"-maxd") == 0)
maxD = atoi(argv[++i]);
else
{
failmessage.assign("Unknown argument: ");
failmessage.append(argv[i]);
failmessage.append("\n");
fail = true;
}
}
if (truncLimit <= 0 || truncLimit > 1)
{
failmessage.append("-trunc value does not make sense.\n");
fail = true;
}
bool infPathSpec = false;
if (strcmp(infPath.c_str(), "") != 0)
{
infPathSpec = true;
DIR *d = opendir(infPath.c_str());
if(d)
{
closedir(d);
}
else
{
failmessage.append("-iPath does not exist.\n");
fail = true;
}
}
if (strcmp(infF.c_str(), "") == 0)
{
if (!infPathSpec)
{
failmessage.append("-iF or -iPath must be specified.\n");
fail = true;
}
}
if (strcmp(infR.c_str(), "") == 0)
{
if (!infPathSpec)
{
failmessage.append("-iR or -iPath must be specified.\n");
fail = true;
}
}
if (strcmp(outI.c_str(), "") == 0)
{
failmessage.append("invalid -oIter.\n");
fail = true;
}
if (strcmp(outP.c_str(), "") == 0)
{
failmessage.append("invalid -oPar.\n");
fail = true;
}
if (strcmp(outCorr.c_str(), "") == 0)
{
failmessage.append("invalid -oCorr.\n");
fail = true;
}
if (strcmp(outCnt.c_str(), "") == 0)
{
failmessage.append("invalid -oCnt.\n");
fail = true;
}
if (strcmp(outPath.c_str(), "") != 0)
{
DIR* d = opendir(outPath.c_str());
if(d)
{
closedir(d);
}
else
{
failmessage.append("-oPath does not exist.\n");
fail = true;
}
}
int infFCnt = 1;
if (infPathSpec)
{
infFCnt = countFiles(infPath);
if (infFCnt < 1)
{
failmessage.append("ERROR: infile path \"");
failmessage.append(infPath.c_str());
failmessage.append("\" does not contain a positive number of F and R binary files, aborting.\n");
fail = true;
}
}
if (fail)
{
cerr << endl << failmessage.c_str() << endl << errorLine << endl;
return(-1);
}
if(strcmp(outStub.c_str(),"") != 0)
{
outI = outStub + "_" + outI;
outP = outStub + "_" + outP;
outCorr = outStub + "_" + outCorr;
outCnt = outStub + "_" + outCnt;
}
if(strcmp(outPath.c_str(),"") != 0)
{
outI = outPath + outI;
outP = outPath + outP;
outCorr = outPath + outCorr;
outCnt = outPath + outCnt;
}
if (seed < -1)
seed = -1;
ifstream iff[infFCnt];
ifstream ifr[infFCnt];
string fileNames[infFCnt];
if (infPathSpec)
{
if (openFiles(infPath, iff, ifr, fileNames) != infFCnt)
{
failmessage.append("ERROR: all files in \"");
failmessage.append(infPath.c_str());
failmessage.append("\" could not be opened, aborting.\n");
fail = true;
}
}
else
{
iff[0].open(infF.c_str(),ios::binary);
ifr[0].open(infR.c_str(),ios::binary);
if (iff[0].fail())
{
failmessage.append("ERROR: Forward reads binary file \"");
failmessage.append(infF.c_str());
failmessage.append("\" could not be opened, aborting.\n");
fail = true;
}
if (ifr[0].fail())
{
failmessage.append("ERROR: Reverse reads binary file \"");
failmessage.append(infR.c_str());
failmessage.append("\" could not be opened, aborting.\n");
fail = true;
}
}
/*
iff.open(infF.c_str(),ios::binary);
if (iff.fail())
{
failmessage.append("ERROR: Forward reads binary file \"");
failmessage.append(infF.c_str());
failmessage.append("\" could not be opened, aborting.\n");
fail = true;
}
ifstream ifr;
ifr.open(infR.c_str(),ios::binary);
if (ifr.fail())
{
failmessage.append("ERROR: Reverse reads binary file \"");
failmessage.append(infR.c_str());
failmessage.append("\" could not be opened, aborting.\n");
fail = true;
}
*/
ofstream ofi;
ofi.open(outI.c_str(),ios::trunc);
if (ofi.fail())
{
failmessage.append("ERROR: Output file \"");
failmessage.append(outI.c_str());
failmessage.append("\" could not be created, aborting.\n");
fail = true;
}
ofstream ofc;
ofc.open(outCorr.c_str(),ios::trunc);
if (ofc.fail())
{
failmessage.append("ERROR: Output file \"");
failmessage.append(outCorr.c_str());
failmessage.append("\" could not be created, aborting.\n");
fail = true;
}
ofstream ofcnt;
ofcnt.open(outCnt.c_str(),ios::trunc);
if (ofcnt.fail())
{
failmessage.append("ERROR: Output file \"");
failmessage.append(outCnt.c_str());
failmessage.append("\" could not be created, aborting.\n");
fail = true;
}
ofstream ofp;
int truncValF,truncValR;
int estMinD = minD, estMaxD = maxD, estLambdaD = lambdaD;
double* distDens;
vector<string> distDensV;
ofp.open(outP.c_str(),ios::trunc);
if (ofp.fail())
{
failmessage.append("ERROR: Paramater file \"");
failmessage.append(outP.c_str());
failmessage.append("\" could not be created, aborting.\n");
fail = true;
}
if (fail)
{
cerr << endl << failmessage.c_str() << endl << errorLine << endl;
return(-1);
}
ofi << "! Command:";
for (int i = 0; i < argc; i++)
ofi << " " << argv[i];
ofi << endl;
vlevel = verbose;
/*
* Check file lengths
*/
int minPos[infFCnt], maxPos[infFCnt], minF[infFCnt], maxF[infFCnt], minR[infFCnt], maxR[infFCnt];
checkFileLengths(iff, ifr, minPos, maxPos, minR, minF, maxF, maxR, infFCnt);
/*
* Estimate parameters
*/
ofp << "! Command:";
for (int i = 0; i < argc; i++)
ofp << " " << argv[i];
ofp << endl;
vcerr(1) << "*** Identifying truncation limits and data distributions ***" << endl;
calculateTruncVal(iff,ifr,&ofcnt,
&truncValF, &truncValR, truncLimit,
minPos, maxPos,
minR, minF,
maxF, maxR, infFCnt);
ofcnt.close();
distDens = new double[maxD-minD+1];
if (infFCnt == 1)
{
estimateDistance(&iff[0],&ifr[0],&ofc,
&estMinD, &estMaxD, &estLambdaD,
minD, maxD,
minPos[0], maxPos[0],
minR[0], minF[0],
maxF[0], maxR[0],
truncValF, truncValR,distDens,0.3);
ofc.close();
}
/*
if (useemp)
{
vcerr(2) << "\t* Estimating forward-reverse distance" << endl;
estimateDistance(&iff,&ifr,&ofc,
&estMinD, &estMaxD, &estLambdaD,
minD, maxD,
minPos, maxPos,
minR, minF,
maxF, maxR,
truncValF, truncValR,distDens,0.3);
ofc.close();
}
else
{
*/
for (int dist = minD; dist <= maxD; dist++)
distDens[dist-minD] = gsl_ran_poisson_pdf(dist, lambdaD);
/*
}
*/
vcerr(1) << "*** Parameter estimation ***" << endl;
if (estimateParameters(iff,ifr,&ofi,
estMinD,estMaxD,estLambdaD,
pF, pR, lambdaF, lambdaR,
sampleSize,burnins,iterations,
seed,
minPos, maxPos,
minR, minF,
maxF, maxR,
truncValF, truncValR, infFCnt) < 0)
{
cerr << "ERROR: estimateParameters failed, aborting." << endl;
for (int i=0; i<infFCnt; i++)
{
iff[i].close();
ifr[i].close();
}
ofi.close();
ofp.close();
delete[] distDens;
return(-1);
}
else
{
if (writeParameters(&ofp, pF, pR, lambdaF, lambdaR, lambdaD,
truncValF, truncValR,
minD, maxD, estLambdaD,
estMinD, estMaxD, distDens) < 0)
{
cerr << "WARNING: could not write parameters to file, skipping." << endl;
}
}
ofi.close();
ofp.close();
for (int i=0; i<infFCnt; i++)
{
iff[i].close();
ifr[i].close();
}
delete[] distDens;
vcerr(3) << setprecision(3);
vcerr(3) << endl << "\t\tParameter estimates:" << endl;
vcerr(3) << "\t\tpF: S = " << pF[0] << " NotS = " << pF[1] << endl;
vcerr(3) << "\t\tpR: E = " << pR[0] << " NotE = " << pR[1] << endl;
vcerr(3) << "\t\tlambdaF: S = " << lambdaF[0] << " NotS = " << lambdaF[1] << endl;
vcerr(3) << "\t\tlambdaR: E = " << lambdaR[0] << " NotE = " << lambdaR[1] << endl;
vcerr(3) << "\t\testMinD: = " << estMinD << " estMaxd = " << estMaxD << endl;
}
/** Updates the priority; the lower the fscore the higer the priority
* the fscore is the sum of:
* -path-cost (gscore) (which is the distance from the starting Node to the current Node)
* -heuristic estimate (hscore) (which is an estimate of the distance from the current Node to the destination Node)
*
**/
void Node::updatePriority(const int & xDest, const int & yDest)
{
priority = distance + estimateDistance(xDest,yDest)*10;
}
