#include<string>
#include<vector>
#include<algorithm>
+#include<fstream>
+#include<iostream>
#include<pthread.h>
#include "utils.h"
+#include "my_assert.h"
#include "sampling.h"
#include "Read.h"
int read_type;
int m, M; // m genes, M isoforms
-int N0, N1, N2, N_tot;
+READ_INT_TYPE N0, N1, N2, N_tot;
int nThreads;
char refName[STRLEN], outName[STRLEN];
char imdName[STRLEN], statName[STRLEN];
char refF[STRLEN], groupF[STRLEN], cntF[STRLEN], tiF[STRLEN];
-char mparamsF[STRLEN], bmparamsF[STRLEN];
+char mparamsF[STRLEN];
char modelF[STRLEN], thetaF[STRLEN];
char inpSamType;
template<class ReadType, class HitType, class ModelType>
void init(ReadReader<ReadType> **&readers, HitContainer<HitType> **&hitvs, double **&ncpvs, ModelType **&mhps) {
- int nReads, nHits, rt;
- int nrLeft, nhT, curnr; // nrLeft : number of reads left, nhT : hit threshold per thread, curnr: current number of reads
+ READ_INT_TYPE nReads;
+ HIT_INT_TYPE nHits;
+ int rt; // read type
+
+ READ_INT_TYPE nrLeft, curnr; // nrLeft : number of reads left, curnr: current number of reads
+ HIT_INT_TYPE nhT; // nhT : hit threshold per thread
char datF[STRLEN];
int s;
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;
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));
+ HIT_INT_TYPE ntLeft = nThreads - i - 1; // # of threads left
+
+ 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); }
+ if (verbose && nrLeft % 1000000 == 0) { cout<< "DAT "<< nrLeft << " reads left"<< endl; }
}
ncpvs[i] = new double[hitvs[i]->getN()];
memset(ncpvs[i], 0, sizeof(double) * hitvs[i]->getN());
curnr += hitvs[i]->getN();
- if (verbose) { printf("Thread %d : N = %d, NHit = %d\n", i, hitvs[i]->getN(), hitvs[i]->getNHits()); }
+ if (verbose) { cout<<"Thread "<< i<< " : N = "<< hitvs[i]->getN()<< ", NHit = "<< hitvs[i]->getNHits()<< endl; }
}
fin.close();
ReadType read;
- int N = hitv->getN();
+ READ_INT_TYPE N = hitv->getN();
double sum;
vector<double> fracs; //to remove this, do calculation twice
- int fr, to, id;
+ HIT_INT_TYPE fr, to, id;
if (needCalcConPrb || updateModel) { reader->reset(); }
if (updateModel) { mhp->init(); }
memset(countv, 0, sizeof(double) * (M + 1));
- for (int i = 0; i < N; i++) {
+ for (READ_INT_TYPE 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);
fracs[0] = probv[0] * ncpv[i];
if (fracs[0] < EPSILON) fracs[0] = 0.0;
sum += fracs[0];
- for (int j = fr; j < to; j++) {
+ for (HIT_INT_TYPE j = fr; j < to; j++) {
HitType &hit = hitv->getHitAt(j);
if (needCalcConPrb) { hit.setConPrb(model->getConPrb(read, hit)); }
id = j - fr + 1;
countv[0] += fracs[0];
if (updateModel) { mhp->updateNoise(read, fracs[0]); }
if (calcExpectedWeights) { ncpv[i] = fracs[0]; }
- for (int j = fr; j < to; j++) {
+ for (HIT_INT_TYPE j = fr; j < to; j++) {
HitType &hit = hitv->getHitAt(j);
id = j - fr + 1;
fracs[id] /= sum;
}
else if (calcExpectedWeights) {
ncpv[i] = 0.0;
- for (int j = fr; j < to; j++) {
+ for (HIT_INT_TYPE j = fr; j < to; j++) {
HitType &hit = hitv->getHitAt(j);
hit.setConPrb(0.0);
}
double *ncpv = (double*)(params->ncpv);
ReadType read;
- int N = hitv->getN();
- int fr, to;
+ READ_INT_TYPE N = hitv->getN();
+ HIT_INT_TYPE fr, to;
assert(model->getNeedCalcConPrb());
reader->reset();
- for (int i = 0; i < N; i++) {
- if (!reader->next(read)) {
- fprintf(stderr, "Can not load a read!\n");
- exit(-1);
- }
+ for (READ_INT_TYPE i = 0; i < N; i++) {
+ general_assert(reader->next(read), "Can not load a read!");
+
fr = hitv->getSAt(i);
to = hitv->getSAt(i + 1);
ncpv[i] = model->getNoiseConPrb(read);
- for (int j = fr; j < to; j++) {
+ for (HIT_INT_TYPE j = fr; j < to; j++) {
HitType &hit = hitv->getHitAt(j);
hit.setConPrb(model->getConPrb(read, hit));
}
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;
}
//E step
for (int i = 0; i < nThreads; i++) {
rc = pthread_create(&threads[i], &attr, E_STEP<ReadType, HitType, ModelType>, (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);
if (bChange < change) bChange = change;
}
- if (verbose) printf("ROUND = %d, SUM = %.15g, bChange = %f, totNum = %d\n", ROUND, sum, bChange, totNum);
+ if (verbose) { cout<< "ROUND = "<< ROUND<< ", SUM = "<< setprecision(15)<< sum<< ", bChange = " << setprecision(6)<< bChange<< ", totNum = " << totNum<< endl; }
} while (ROUND < MIN_ROUND || (totNum > 0 && ROUND < MAX_ROUND));
- //while (ROUND < MAX_ROUND);
+// } while (ROUND < 1);
- if (totNum > 0) fprintf(stderr, "Warning: RSEM reaches %d iterations before meeting the convergence criteria.\n", MAX_ROUND);
+ if (totNum > 0) { cout<< "Warning: RSEM reaches "<< MAX_ROUND<< " iterations before meeting the convergence criteria."<< endl; }
//generate output file used by Gibbs sampler
if (genGibbsOut) {
if (model.getNeedCalcConPrb()) {
for (int i = 0; i < nThreads; i++) {
rc = pthread_create(&threads[i], &attr, calcConProbs<ReadType, HitType, ModelType>, (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);
sprintf(out_for_gibbs_F, "%s.ofg", imdName);
- fo = fopen(out_for_gibbs_F, "w");
- fprintf(fo, "%d %d\n", M, N0);
+ ofstream fout(out_for_gibbs_F);
+ fout<< M<< " "<< N0<< endl;
for (int i = 0; i < nThreads; i++) {
- int numN = hitvs[i]->getN();
- for (int j = 0; j < numN; j++) {
- int fr = hitvs[i]->getSAt(j);
- int to = hitvs[i]->getSAt(j + 1);
- int totNum = 0;
-
- if (ncpvs[i][j] >= EPSILON) { ++totNum; fprintf(fo, "%d %.15g ", 0, ncpvs[i][j]); }
- for (int k = fr; k < to; k++) {
+ READ_INT_TYPE numN = hitvs[i]->getN();
+ for (READ_INT_TYPE j = 0; j < numN; j++) {
+ HIT_INT_TYPE fr = hitvs[i]->getSAt(j);
+ HIT_INT_TYPE to = hitvs[i]->getSAt(j + 1);
+ HIT_INT_TYPE totNum = 0;
+
+ if (ncpvs[i][j] >= EPSILON) { ++totNum; fout<< "0 "<< setprecision(15)<< ncpvs[i][j]<< " "; }
+ for (HIT_INT_TYPE k = fr; k < to; k++) {
HitType &hit = hitvs[i]->getHitAt(k);
if (hit.getConPrb() >= EPSILON) {
++totNum;
- fprintf(fo, "%d %.15g ", hit.getSid(), hit.getConPrb());
+ fout<< hit.getSid()<< " "<< setprecision(15)<< hit.getConPrb()<< " ";
}
}
- if (totNum > 0) { fprintf(fo, "\n"); }
+ if (totNum > 0) { fout<< endl; }
}
}
- fclose(fo);
+ fout.close();
}
sprintf(thetaF, "%s.theta", statName);
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
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<ReadType, HitType, ModelType>, (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++) {
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]);
sprintf(outBamF, "%s.transcript.bam", outName);
if (bamSampling) {
- int local_N;
- int fr, to, len, id;
+ READ_INT_TYPE local_N;
+ HIT_INT_TYPE fr, to, len, id;
vector<double> arr;
- arr.clear();
+ uniform01 rg(engine_type(time(NULL)));
- if (verbose) printf("Begin to sample reads from their posteriors.\n");
+ if (verbose) cout<< "Begin to sample reads from their posteriors."<< endl;
for (int i = 0; i < nThreads; i++) {
local_N = hitvs[i]->getN();
- for (int j = 0; j < local_N; j++) {
+ for (READ_INT_TYPE j = 0; j < local_N; j++) {
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
- for (int k = fr; k < to; k++) hitvs[i]->getHitAt(k).setConPrb(k - fr + 1 == id ? 1.0 : 0.0);
+ for (HIT_INT_TYPE k = fr; k < to; k++) arr[k - fr + 1] = arr[k - fr] + hitvs[i]->getHitAt(k).getConPrb();
+ id = (arr[len - 1] < EPSILON ? -1 : sample(rg, arr, len)); // if all entries in arr are 0, let id be -1
+ for (HIT_INT_TYPE 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");
+
+ if (verbose) cout<< "Sampling is finished."<< endl;
}
BamWriter writer(inpSamType, inpSamF, pt_fn_list, outBamF, transcripts);
ifstream fin;
bool quiet = false;
- if (argc < 5) {
- printf("Usage : rsem-run-em refName read_type sampleName sampleToken [-p #Threads] [-b samInpType samInpF has_fn_list_? [fn_list]] [-q] [--gibbs-out] [--sampling]\n\n");
+ if (argc < 6) {
+ printf("Usage : rsem-run-em refName read_type sampleName imdName statName [-p #Threads] [-b samInpType samInpF has_fn_list_? [fn_list]] [-q] [--gibbs-out] [--sampling]\n\n");
printf(" refName: reference name\n");
printf(" read_type: 0 single read without quality score; 1 single read with quality score; 2 paired-end read without quality score; 3 paired-end read with quality score.\n");
printf(" sampleName: sample's name, including the path\n");
strcpy(refName, argv[1]);
read_type = atoi(argv[2]);
strcpy(outName, argv[3]);
- sprintf(imdName, "%s.temp/%s", argv[3], argv[4]);
- sprintf(statName, "%s.stat/%s", argv[3], argv[4]);
+ strcpy(imdName, argv[4]);
+ strcpy(statName, argv[5]);
nThreads = 1;
genGibbsOut = false;
pt_fn_list = pt_chr_list = NULL;
- for (int i = 5; i < argc; i++) {
+ for (int i = 6; i < argc; i++) {
if (!strcmp(argv[i], "-p")) { nThreads = atoi(argv[i + 1]); }
if (!strcmp(argv[i], "-b")) {
genBamF = true;
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;
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;
+ if ((READ_INT_TYPE)nThreads > N1) nThreads = N1;
//set model parameters
mparams.M = M;
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;
time_t b = time(NULL);
- printTimeUsed(a, b);
+ printTimeUsed(a, b, "EM.cpp");
return 0;
}
projects / rsem.git / blobdiff