#include<pthread.h>
#include "utils.h"
+#include "my_assert.h"
+#include "sampling.h"
#include "Read.h"
#include "SingleRead.h"
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
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));
+
+ 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); }
}
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);
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);
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;
}
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'));
+ fprintf(fo, "%s%c", transcript.getGeneID().c_str(), (i < M ? '\t' : '\n'));
}
fclose(fo);
}
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
//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 (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);
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
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);
+ 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]);
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) {
+ int local_N;
+ int fr, to, len, id;
+ vector<double> arr;
+ uniform01 rg(engine_type(time(NULL)));
+
+ if (verbose) printf("Begin to sample reads from their posteriors.\n");
+ for (int i = 0; i < nThreads; i++) {
+ local_N = hitvs[i]->getN();
+ for (int 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 (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(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");
}
- 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);
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");
+ 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");
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");
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("// model parameters should be in imdName.mparams.\n");
exit(-1);
}
nThreads = 1;
genBamF = false;
+ bamSampling = false;
genGibbsOut = false;
pt_fn_list = pt_chr_list = NULL;
}
if (!strcmp(argv[i], "-q")) { quiet = 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;
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