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Fix memory issues #59

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Fix memory issues #59

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34 changes: 6 additions & 28 deletions cmd_cram_demuxlet.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -535,30 +535,6 @@ int32_t main(int32_t argc, char** argv) {
if ( ( writePair && wpair == NULL ) || ( wsingle == NULL ) )
error("[E:%s:%d %s] Cannot create %s.single, %s.pair files",__FILE__,__LINE__,__FUNCTION__,outPrefix.c_str(), outPrefix.c_str());


// start finding the next-best matching individual
// here we iterate each cell separately.
// pre-calculate nsnp*nv*nv*9, nv*1*9, 1*nv*9, 1*9
double* gpAB = new double[scl.nsnps * nv * nv * 9];
double* gpA0 = new double[scl.nsnps * nv * 9];
double* gp00 = new double[scl.nsnps * 9];

int32_t j, k, l, m, n;
for(i=0; i < scl.nsnps; ++i) {
for(j=0; j < nv; ++j) {
for(k=0; k < nv; ++k) {
gps = scl.snps[i].gps;
for(l=0; l < 3; ++l) {
for(m=0; m < 3; ++m) {
gpAB[i*nv*nv*9 + j*nv*9 + k*9 + l*3 + m] = gps[j*3+l] * gps[k*3+m];
gpA0[i*nv*9 + j*9 + l*3 + m] = gps[j*3+l] * gp0s[i*3+m];
gp00[i*9 + l*3 + m] = gp0s[i*3+l] * gp0s[i*3+m];
}
}
}
}
}

// iterate each barcode
int32_t n1 = nv;
double* llksAB = new double[n1 * nv * nAlpha];
Expand Down Expand Up @@ -668,13 +644,14 @@ int32_t main(int32_t argc, char** argv) {
double p;
int32_t j, k, l, m, n;

for(j=jbeg; j < jend; ++j) {
gps = scl.snps[isnp].gps;
for(j=jbeg; j < jend; ++j) {
// pairwise LLK
for(k=0; k < nv; ++k) {
std::fill(sumPs.begin(), sumPs.end(), 0);
for(l=0; l < 3; ++l) {
for(m=0; m < 3; ++m) {
p = gpAB[isnp*nv*nv*9 + j*nv*9 + k*9 + l*3 + m];
p = gps[j*3+l] * gps[k*3+m]; // Compute this on the go for avoiding explosion of the RAM
for(n=0; n < nAlpha; ++n)
sumPs[n] += (p * pGs[n*9+l*3+m]);
}
Expand All @@ -687,7 +664,7 @@ int32_t main(int32_t argc, char** argv) {
std::fill(sumPs.begin(), sumPs.end(), 0);
for(l=0; l < 3; ++l) {
for(m=0; m < 3; ++m) {
p = gpA0[isnp*nv*9 + j*9 + l*3 + m];
p = gps[j*3+l] * gp0s[isnp*3+m]; // Compute this on the go for avoiding explosion of the RAM
for(n=0; n < nAlpha; ++n)
sumPs[n] += (p * pGs[n*9+l*3+m]);
}
Expand All @@ -700,7 +677,7 @@ int32_t main(int32_t argc, char** argv) {
std::fill(sumPs.begin(), sumPs.end(), 0);
for(l=0; l < 3; ++l) {
for(m=0; m < 3; ++m) {
p = gp00[isnp*9 + l*3 + m];
p = gp0s[isnp*3+l] * gp0s[isnp*3+m]; // Compute this on the go for avoiding explosion of the RAM
for(n=0; n < nAlpha; ++n)
sumPs[n] += (p * pGs[n*9+l*3+m]);
}
Expand All @@ -709,6 +686,7 @@ int32_t main(int32_t argc, char** argv) {
llks00[n] += log(sumPs[n]);
}

int32_t j, k, n;
// normalize by max likelihood
double maxLLK = -1e300;
for(j=jbeg; j < jend; ++j) {
Expand Down