#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"
#include "SingleRead.h"
#include "HitWrapper.h"
#include "BamWriter.h"
+#include "WriteResults.h"
+
using namespace std;
const double STOP_CRITERIA = 0.001;
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;
bool genBamF; // If user wants to generate bam file, true; otherwise, false.
+bool bamSampling; // true if sampling from read posterior distribution when bam file is generated
bool updateModel, calcExpectedWeights;
bool genGibbsOut; // generate file for Gibbs sampler
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 refF[STRLEN], cntF[STRLEN], tiF[STRLEN];
+char mparamsF[STRLEN];
char modelF[STRLEN], thetaF[STRLEN];
char inpSamType;
double *probv, **countvs;
Refs refs;
-GroupInfo gi;
Transcripts transcripts;
ModelParams mparams;
+bool hasSeed;
+seedType seed;
+
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;
indices[i] = new ReadIndex(readFs[i]);
}
for (int i = 0; i < nThreads; i++) {
- readers[i] = new ReadReader<ReadType>(s, readFs);
+ readers[i] = new ReadReader<ReadType>(s, readFs, refs.hasPolyA(), mparams.seedLen); // allow calculation of calc_lq() function
readers[i]->setIndices(indices);
}
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));
}
return NULL;
}
-template<class ModelType>
-void calcExpectedEffectiveLengths(ModelType& model) {
- int lb, ub, span;
- double *pdf = NULL, *cdf = NULL, *clen = NULL; // clen[i] = sigma_{j=1}^{i}pdf[i]*(lb+i)
-
- model.getGLD().copyTo(pdf, cdf, lb, ub, span);
- clen = new double[span + 1];
- clen[0] = 0.0;
- for (int i = 1; i <= span; i++) {
- clen[i] = clen[i - 1] + pdf[i] * (lb + i);
- }
-
- eel.clear();
- eel.resize(M + 1, 0.0);
- for (int i = 1; i <= M; i++) {
- int totLen = refs.getRef(i).getTotLen();
- int fullLen = refs.getRef(i).getFullLen();
- int pos1 = max(min(totLen - fullLen + 1, ub) - lb, 0);
- int pos2 = max(min(totLen, ub) - lb, 0);
-
- if (pos2 == 0) { eel[i] = 0.0; continue; }
-
- eel[i] = fullLen * cdf[pos1] + ((cdf[pos2] - cdf[pos1]) * (totLen + 1) - (clen[pos2] - clen[pos1]));
- assert(eel[i] >= 0);
- if (eel[i] < MINEEL) { eel[i] = 0.0; }
- }
-
- delete[] pdf;
- delete[] cdf;
- delete[] clen;
-}
-
template<class ModelType>
void writeResults(ModelType& model, double* counts) {
- double denom;
- char outF[STRLEN];
- FILE *fo;
-
- sprintf(modelF, "%s.model", statName);
- model.write(modelF);
-
- //calculate tau values
- double *tau = new double[M + 1];
- memset(tau, 0, sizeof(double) * (M + 1));
-
- denom = 0.0;
- for (int i = 1; i <= M; i++)
- if (eel[i] >= EPSILON) {
- tau[i] = theta[i] / eel[i];
- denom += tau[i];
- }
- if (denom <= 0) { fprintf(stderr, "No alignable reads?!\n"); exit(-1); }
- //assert(denom > 0);
- for (int i = 1; i <= M; i++) {
- tau[i] /= denom;
- }
-
- //isoform level results
- sprintf(outF, "%s.iso_res", imdName);
- fo = fopen(outF, "w");
- for (int i = 1; i <= M; i++) {
- const Transcript& transcript = transcripts.getTranscriptAt(i);
- fprintf(fo, "%s%c", transcript.getTranscriptID().c_str(), (i < M ? '\t' : '\n'));
- }
- for (int i = 1; i <= M; i++)
- fprintf(fo, "%.2f%c", counts[i], (i < M ? '\t' : '\n'));
- for (int i = 1; i <= M; i++)
- fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
- for (int i = 1; i <= M; i++) {
- const Transcript& transcript = transcripts.getTranscriptAt(i);
- fprintf(fo, "%s%c", transcript.getLeft().c_str(), (i < M ? '\t' : '\n'));
- }
- fclose(fo);
-
- //gene level results
- sprintf(outF, "%s.gene_res", imdName);
- fo = fopen(outF, "w");
- for (int i = 0; i < m; i++) {
- const string& gene_id = transcripts.getTranscriptAt(gi.spAt(i)).getGeneID();
- fprintf(fo, "%s%c", gene_id.c_str(), (i < m - 1 ? '\t' : '\n'));
- }
- for (int i = 0; i < m; i++) {
- double sumC = 0.0; // sum of counts
- int b = gi.spAt(i), e = gi.spAt(i + 1);
- for (int j = b; j < e; j++) sumC += counts[j];
- fprintf(fo, "%.2f%c", sumC, (i < m - 1 ? '\t' : '\n'));
- }
- for (int i = 0; i < m; i++) {
- double sumT = 0.0; // sum of tau values
- int b = gi.spAt(i), e = gi.spAt(i + 1);
- for (int j = b; j < e; j++) sumT += tau[j];
- fprintf(fo, "%.15g%c", sumT, (i < m - 1 ? '\t' : '\n'));
- }
- for (int i = 0; i < m; i++) {
- int b = gi.spAt(i), e = gi.spAt(i + 1);
- for (int j = b; j < e; j++) {
- fprintf(fo, "%s%c", transcripts.getTranscriptAt(j).getTranscriptID().c_str(), (j < e - 1 ? ',' : (i < m - 1 ? '\t' :'\n')));
- }
- }
- fclose(fo);
-
- delete[] tau;
-
- if (verbose) { printf("Expression Results are written!\n"); }
+ sprintf(modelF, "%s.model", statName);
+ model.write(modelF);
+ writeResultsEM(M, refName, imdName, transcripts, theta, eel, countvs[0]);
}
template<class ReadType, class HitType, class ModelType>
}
inline bool doesUpdateModel(int ROUND) {
- //return false; // never update, for debugging only
- return ROUND <= 20 || ROUND % 100 == 0;
+ // return ROUND <= 20 || ROUND % 100 == 0;
+ return ROUND <= 10;
}
//Including initialize, algorithm and results saving
Params fparams[nThreads];
pthread_t threads[nThreads];
pthread_attr_t attr;
- void *status;
int rc;
//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);
+ rc = pthread_join(threads[i], NULL);
+ 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);
- } while (ROUND < MIN_ROUND || totNum > 0 && ROUND < MAX_ROUND);
- //while (ROUND < MAX_ROUND);
+ 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 < 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); }
+ rc = pthread_join(threads[i], NULL);
+ 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);
- fo = fopen(thetaF, "w");
- fprintf(fo, "%d\n", M + 1);
-
- // output theta'
- for (int i = 0; i < M; i++) fprintf(fo, "%.15g ", theta[i]);
- fprintf(fo, "%.15g\n", theta[M]);
-
- //calculate expected effective lengths for each isoform
- calcExpectedEffectiveLengths<ModelType>(model);
-
- //correct theta vector
- sum = theta[0];
- 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); }
- for (int i = 0; i <= M; i++) theta[i] /= sum;
-
//calculate expected weights and counts using learned parameters
+ //just use the raw theta learned from the data, do not correct for eel or mw
updateModel = false; calcExpectedWeights = true;
+ 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);
+ rc = pthread_join(threads[i], NULL);
+ 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++) {
/* destroy attribute */
pthread_attr_destroy(&attr);
- //convert theta' to theta
- 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]);
- sum += theta[i];
- }
- assert(sum >= EPSILON);
- for (int i = 0; i <= M; i++) theta[i] /= sum;
+
+ sprintf(thetaF, "%s.theta", statName);
+ fo = fopen(thetaF, "w");
+ fprintf(fo, "%d\n", M + 1);
+
+ // output theta'
+ for (int i = 0; i < M; i++) fprintf(fo, "%.15g ", theta[i]);
+ fprintf(fo, "%.15g\n", theta[M]);
+
+ //calculate expected effective lengths for each isoform
+ calcExpectedEffectiveLengths<ModelType>(M, refs, model, eel);
+ polishTheta(M, theta, eel, model.getMW());
// output theta
for (int i = 0; i < M; i++) fprintf(fo, "%.15g ", theta[i]);
writeResults<ModelType>(model, countvs[0]);
if (genBamF) {
- sprintf(outBamF, "%s.bam", outName);
- if (transcripts.getType() == 0) {
- sprintf(chr_list, "%s.chrlist", refName);
- pt_chr_list = (char*)(&chr_list);
+ sprintf(outBamF, "%s.transcript.bam", outName);
+
+ if (bamSampling) {
+ READ_INT_TYPE local_N;
+ HIT_INT_TYPE fr, to, len, id;
+ vector<double> arr;
+ engine_type engine(hasSeed ? seed : time(NULL));
+ uniform_01_dist uniform_01;
+ uniform_01_generator rg(engine, uniform_01);
+
+ if (verbose) cout<< "Begin to sample reads from their posteriors."<< endl;
+ for (int i = 0; i < nThreads; i++) {
+ local_N = hitvs[i]->getN();
+ 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.assign(len, 0);
+ arr[0] = ncpvs[i][j];
+ 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) cout<< "Sampling is finished."<< endl;
}
- BamWriter writer(inpSamType, inpSamF, pt_fn_list, outBamF, pt_chr_list);
+ BamWriter writer(inpSamType, inpSamF, pt_fn_list, outBamF, transcripts);
HitWrapper<HitType> wrapper(nThreads, hitvs);
- writer.work(wrapper, transcripts);
+ writer.work(wrapper);
}
release<ReadType, HitType, ModelType>(readers, hitvs, ncpvs, mhps);
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]\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] [--seed seed]\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(" samplePath: sample path.\n");
- printf(" sampleName: sample name.\n");
+ printf(" sampleName: sample's name, including the path\n");
+ printf(" sampleToken: sampleName excludes the path\n");
printf(" -p: number of threads which user wants to use. (default: 1)\n");
printf(" -b: produce bam format output file. (default: off)\n");
printf(" -q: set it quiet\n");
- printf(" --gibbs-out: generate output file use by Gibbs sampler. (default: off)\n");
+ printf(" --gibbs-out: generate output file used by Gibbs sampler. (default: off)\n");
+ printf(" --sampling: sample each read from its posterior distribution when bam file is generated. (default: off)\n");
+ printf(" --seed uint32: the seed used for the BAM sampling. (default: off)\n");
printf("// model parameters should be in imdName.mparams.\n");
exit(-1);
}
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;
genBamF = false;
+ bamSampling = false;
genGibbsOut = false;
pt_fn_list = pt_chr_list = NULL;
+ hasSeed = false;
- 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], "-q")) { quiet = true; }
if (!strcmp(argv[i], "--gibbs-out")) { genGibbsOut = true; }
+ if (!strcmp(argv[i], "--sampling")) { bamSampling = true; }
+ if (!strcmp(argv[i], "--seed")) {
+ hasSeed = true;
+ int len = strlen(argv[i + 1]);
+ seed = 0;
+ for (int k = 0; k < len; k++) seed = seed * 10 + (argv[i + 1][k] - '0');
+ }
}
- 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(refF, "%s.seq", refName);
refs.loadRefs(refF);
M = refs.getM();
- sprintf(groupF, "%s.grp", refName);
- gi.load(groupF);
- m = gi.getm();
sprintf(tiF, "%s.ti", refName);
transcripts.readFrom(tiF);
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