X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=EM.cpp;h=b2493b2fa21982125b0cba196325ca86487848c6;hb=cb94fd597b180aa7cb01ae84c9d1025201b98d8e;hp=f9449a85cd3226a3f29356f10fa018e4ca908cba;hpb=fc69cf6af24c0550e55447fc82f01cb6f90c1c42;p=rsem.git diff --git a/EM.cpp b/EM.cpp index f9449a8..b2493b2 100644 --- a/EM.cpp +++ b/EM.cpp @@ -10,6 +10,7 @@ #include #include "utils.h" +#include "my_assert.h" #include "sampling.h" #include "Read.h" @@ -113,12 +114,11 @@ void init(ReadReader **&readers, HitContainer **&hitvs, doubl sprintf(datF, "%s.dat", imdName); fin.open(datF); - if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", datF); exit(-1); } + general_assert(fin.is_open(), "Cannot open " + cstrtos(datF) + "! It may not exist."); fin>>nReads>>nHits>>rt; - if (nReads != N1) { fprintf(stderr, "Number of alignable reads does not match!\n"); exit(-1); } - //assert(nReads == N1); - if (rt != read_type) { fprintf(stderr, "Data file (.dat) does not have the right read type!\n"); exit(-1); } - //assert(rt == read_type); + general_assert(nReads == N1, "Number of alignable reads does not match!"); + general_assert(rt == read_type, "Data file (.dat) does not have the right read type!"); + //A just so so strategy for paralleling nhT = nHits / nThreads; @@ -128,12 +128,12 @@ void init(ReadReader **&readers, HitContainer **&hitvs, doubl ncpvs = new double*[nThreads]; for (int i = 0; i < nThreads; i++) { int ntLeft = nThreads - i - 1; // # of threads left - if (!readers[i]->locate(curnr)) { fprintf(stderr, "Read indices files do not match!\n"); exit(-1); } - //assert(readers[i]->locate(curnr)); + + general_assert(readers[i]->locate(curnr), "Read indices files do not match!"); while (nrLeft > ntLeft && (i == nThreads - 1 || hitvs[i]->getNHits() < nhT)) { - if (!hitvs[i]->read(fin)) { fprintf(stderr, "Cannot read alignments from .dat file!\n"); exit(-1); } - //assert(hitvs[i]->read(fin)); + general_assert(hitvs[i]->read(fin), "Cannot read alignments from .dat file!"); + --nrLeft; if (verbose && nrLeft % 1000000 == 0) { printf("DAT %d reads left!\n", nrLeft); } } @@ -186,12 +186,9 @@ void* E_STEP(void* arg) { memset(countv, 0, sizeof(double) * (M + 1)); for (int i = 0; i < N; i++) { if (needCalcConPrb || updateModel) { - if (!reader->next(read)) { - fprintf(stderr, "Can not load a read!\n"); - exit(-1); - } - //assert(reader->next(read)); + general_assert(reader->next(read), "Can not load a read!"); } + fr = hitv->getSAt(i); to = hitv->getSAt(i + 1); fracs.resize(to - fr + 1); @@ -253,10 +250,8 @@ void* calcConProbs(void* arg) { reader->reset(); for (int i = 0; i < N; i++) { - if (!reader->next(read)) { - fprintf(stderr, "Can not load a read!\n"); - exit(-1); - } + general_assert(reader->next(read), "Can not load a read!"); + fr = hitv->getSAt(i); to = hitv->getSAt(i + 1); @@ -321,8 +316,9 @@ void writeResults(ModelType& model, double* counts) { tau[i] = theta[i] / eel[i]; denom += tau[i]; } - if (denom <= 0) { fprintf(stderr, "No alignable reads?!\n"); exit(-1); } - //assert(denom > 0); + + general_assert(denom > 0, "No alignable reads?!"); + for (int i = 1; i <= M; i++) { tau[i] /= denom; } @@ -465,14 +461,12 @@ void EM() { //E step for (int i = 0; i < nThreads; i++) { rc = pthread_create(&threads[i], &attr, E_STEP, (void*)(&fparams[i])); - if (rc != 0) { fprintf(stderr, "Cannot create thread %d at ROUND %d! (numbered from 0)\n", i, ROUND); exit(-1); } - //assert(rc == 0); + pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0) at ROUND " + itos(ROUND) + "!"); } for (int i = 0; i < nThreads; i++) { rc = pthread_join(threads[i], &status); - if (rc != 0) { fprintf(stderr, "Cannot join thread %d at ROUND %d! (numbered from 0)\n", i, ROUND); exit(-1); } - //assert(rc == 0); + pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0) at ROUND " + itos(ROUND) + "!"); } model.setNeedCalcConPrb(false); @@ -518,11 +512,11 @@ void EM() { if (model.getNeedCalcConPrb()) { for (int i = 0; i < nThreads; i++) { rc = pthread_create(&threads[i], &attr, calcConProbs, (void*)(&fparams[i])); - if (rc != 0) { fprintf(stderr, "Cannot create thread %d when generate files for Gibbs sampler! (numbered from 0)\n", i); exit(-1); } + pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0) when generating files for Gibbs sampler!"); } for (int i = 0; i < nThreads; i++) { rc = pthread_join(threads[i], &status); - if (rc != 0) { fprintf(stderr, "Cannot join thread %d when generate files for Gibbs sampler! (numbered from 0)\n", i); exit(-1); } + pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0) when generating files for Gibbs sampler!"); } } model.setNeedCalcConPrb(false); @@ -568,7 +562,9 @@ void EM() { for (int i = 1; i <= M; i++) if (eel[i] < EPSILON) { theta[i] = 0.0; } else sum += theta[i]; - if (sum < EPSILON) { fprintf(stderr, "No Expected Effective Length is no less than %.6g?!\n", MINEEL); exit(-1); } + + general_assert(sum >= EPSILON, "No Expected Effective Length is no less than" + ftos(MINEEL, 6) + "?!"); + for (int i = 0; i <= M; i++) theta[i] /= sum; //calculate expected weights and counts using learned parameters @@ -576,13 +572,11 @@ void EM() { for (int i = 0; i <= M; i++) probv[i] = theta[i]; for (int i = 0; i < nThreads; i++) { rc = pthread_create(&threads[i], &attr, E_STEP, (void*)(&fparams[i])); - if (rc != 0) { fprintf(stderr, "Cannot create thread %d when calculate expected weights! (numbered from 0)\n", i); exit(-1); } - //assert(rc == 0); + pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0) when calculating expected weights!"); } for (int i = 0; i < nThreads; i++) { rc = pthread_join(threads[i], &status); - if (rc != 0) { fprintf(stderr, "Cannot join thread %d! (numbered from 0) when calculate expected weights!\n", i); exit(-1); } - //assert(rc == 0); + pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0) when calculating expected weights!"); } model.setNeedCalcConPrb(false); for (int i = 1; i < nThreads; i++) { @@ -596,7 +590,7 @@ void EM() { pthread_attr_destroy(&attr); //convert theta' to theta - double *mw = model.getMW(); + double *mw = model.getMW(); sum = 0.0; for (int i = 0; i <= M; i++) { theta[i] = (mw[i] < EPSILON ? 0.0 : theta[i] / mw[i]); @@ -620,7 +614,7 @@ void EM() { int local_N; int fr, to, len, id; vector arr; - arr.clear(); + uniform01 rg(engine_type(time(NULL))); if (verbose) printf("Begin to sample reads from their posteriors.\n"); for (int i = 0; i < nThreads; i++) { @@ -629,13 +623,14 @@ void EM() { fr = hitvs[i]->getSAt(j); to = hitvs[i]->getSAt(j + 1); len = to - fr + 1; - arr.resize(len); + arr.assign(len, 0); arr[0] = ncpvs[i][j]; for (int k = fr; k < to; k++) arr[k - fr + 1] = arr[k - fr] + hitvs[i]->getHitAt(k).getConPrb(); - id = (arr[len - 1] < EPSILON ? -1 : sample(arr, len)); // if all entries in arr are 0, let id be -1 + id = (arr[len - 1] < EPSILON ? -1 : sample(rg, arr, len)); // if all entries in arr are 0, let id be -1 for (int k = fr; k < to; k++) hitvs[i]->getHitAt(k).setConPrb(k - fr + 1 == id ? 1.0 : 0.0); } } + if (verbose) printf("Sampling is finished.\n"); } @@ -696,8 +691,8 @@ int main(int argc, char* argv[]) { if (!strcmp(argv[i], "--gibbs-out")) { genGibbsOut = true; } if (!strcmp(argv[i], "--sampling")) { bamSampling = true; } } - if (nThreads <= 0) { fprintf(stderr, "Number of threads should be bigger than 0!\n"); exit(-1); } - //assert(nThreads > 0); + + general_assert(nThreads > 0, "Number of threads should be bigger than 0!"); verbose = !quiet; @@ -714,11 +709,13 @@ int main(int argc, char* argv[]) { sprintf(cntF, "%s.cnt", statName); fin.open(cntF); - if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", cntF); exit(-1); } + + general_assert(fin.is_open(), "Cannot open " + cstrtos(cntF) + "! It may not exist."); + fin>>N0>>N1>>N2>>N_tot; fin.close(); - if (N1 <= 0) { fprintf(stderr, "There are no alignable reads!\n"); exit(-1); } + general_assert(N1 > 0, "There are no alignable reads!"); if (nThreads > N1) nThreads = N1; @@ -729,7 +726,9 @@ int main(int argc, char* argv[]) { sprintf(mparamsF, "%s.mparams", imdName); fin.open(mparamsF); - if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", mparamsF); exit(-1); } + + general_assert(fin.is_open(), "Cannot open " + cstrtos(mparamsF) + "It may not exist."); + fin>> mparams.minL>> mparams.maxL>> mparams.probF; int val; // 0 or 1 , for estRSPD fin>>val;