16 #include "SingleRead.h"
17 #include "SingleReadQ.h"
18 #include "PairedEndRead.h"
19 #include "PairedEndReadQ.h"
21 #include "SingleHit.h"
22 #include "PairedEndHit.h"
25 #include "SingleModel.h"
26 #include "SingleQModel.h"
27 #include "PairedEndModel.h"
28 #include "PairedEndQModel.h"
30 #include "Transcript.h"
31 #include "Transcripts.h"
34 #include "GroupInfo.h"
35 #include "HitContainer.h"
36 #include "ReadIndex.h"
37 #include "ReadReader.h"
39 #include "ModelParams.h"
41 #include "HitWrapper.h"
42 #include "BamWriter.h"
46 const double STOP_CRITERIA = 0.001;
47 const int MAX_ROUND = 10000;
48 const int MIN_ROUND = 20;
52 void *reader, *hitv, *ncpv, *mhp, *countv;
56 int m, M; // m genes, M isoforms
57 int N0, N1, N2, N_tot;
61 bool genBamF; // If user wants to generate bam file, true; otherwise, false.
62 bool bamSampling; // true if sampling from read posterior distribution when bam file is generated
63 bool updateModel, calcExpectedWeights;
64 bool genGibbsOut; // generate file for Gibbs sampler
66 char refName[STRLEN], outName[STRLEN];
67 char imdName[STRLEN], statName[STRLEN];
68 char refF[STRLEN], groupF[STRLEN], cntF[STRLEN], tiF[STRLEN];
69 char mparamsF[STRLEN], bmparamsF[STRLEN];
70 char modelF[STRLEN], thetaF[STRLEN];
73 char *pt_fn_list, *pt_chr_list;
74 char inpSamF[STRLEN], outBamF[STRLEN], fn_list[STRLEN], chr_list[STRLEN];
76 char out_for_gibbs_F[STRLEN];
78 vector<double> theta, eel; // eel : expected effective length
80 double *probv, **countvs;
84 Transcripts transcripts;
88 template<class ReadType, class HitType, class ModelType>
89 void init(ReadReader<ReadType> **&readers, HitContainer<HitType> **&hitvs, double **&ncpvs, ModelType **&mhps) {
90 int nReads, nHits, rt;
91 int nrLeft, nhT, curnr; // nrLeft : number of reads left, nhT : hit threshold per thread, curnr: current number of reads
95 char readFs[2][STRLEN];
96 ReadIndex *indices[2];
99 readers = new ReadReader<ReadType>*[nThreads];
100 genReadFileNames(imdName, 1, read_type, s, readFs);
101 for (int i = 0; i < s; i++) {
102 indices[i] = new ReadIndex(readFs[i]);
104 for (int i = 0; i < nThreads; i++) {
105 readers[i] = new ReadReader<ReadType>(s, readFs, refs.hasPolyA(), mparams.seedLen); // allow calculation of calc_lq() function
106 readers[i]->setIndices(indices);
109 hitvs = new HitContainer<HitType>*[nThreads];
110 for (int i = 0; i < nThreads; i++) {
111 hitvs[i] = new HitContainer<HitType>();
114 sprintf(datF, "%s.dat", imdName);
116 if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", datF); exit(-1); }
117 fin>>nReads>>nHits>>rt;
118 if (nReads != N1) { fprintf(stderr, "Number of alignable reads does not match!\n"); exit(-1); }
119 //assert(nReads == N1);
120 if (rt != read_type) { fprintf(stderr, "Data file (.dat) does not have the right read type!\n"); exit(-1); }
121 //assert(rt == read_type);
123 //A just so so strategy for paralleling
124 nhT = nHits / nThreads;
128 ncpvs = new double*[nThreads];
129 for (int i = 0; i < nThreads; i++) {
130 int ntLeft = nThreads - i - 1; // # of threads left
131 if (!readers[i]->locate(curnr)) { fprintf(stderr, "Read indices files do not match!\n"); exit(-1); }
132 //assert(readers[i]->locate(curnr));
134 while (nrLeft > ntLeft && (i == nThreads - 1 || hitvs[i]->getNHits() < nhT)) {
135 if (!hitvs[i]->read(fin)) { fprintf(stderr, "Cannot read alignments from .dat file!\n"); exit(-1); }
136 //assert(hitvs[i]->read(fin));
138 if (verbose && nrLeft % 1000000 == 0) { printf("DAT %d reads left!\n", nrLeft); }
140 ncpvs[i] = new double[hitvs[i]->getN()];
141 memset(ncpvs[i], 0, sizeof(double) * hitvs[i]->getN());
142 curnr += hitvs[i]->getN();
144 if (verbose) { printf("Thread %d : N = %d, NHit = %d\n", i, hitvs[i]->getN(), hitvs[i]->getNHits()); }
149 mhps = new ModelType*[nThreads];
150 for (int i = 0; i < nThreads; i++) {
151 mhps[i] = new ModelType(mparams, false); // just model helper
154 probv = new double[M + 1];
155 countvs = new double*[nThreads];
156 for (int i = 0; i < nThreads; i++) {
157 countvs[i] = new double[M + 1];
161 if (verbose) { printf("EM_init finished!\n"); }
164 template<class ReadType, class HitType, class ModelType>
165 void* E_STEP(void* arg) {
166 Params *params = (Params*)arg;
167 ModelType *model = (ModelType*)(params->model);
168 ReadReader<ReadType> *reader = (ReadReader<ReadType>*)(params->reader);
169 HitContainer<HitType> *hitv = (HitContainer<HitType>*)(params->hitv);
170 double *ncpv = (double*)(params->ncpv);
171 ModelType *mhp = (ModelType*)(params->mhp);
172 double *countv = (double*)(params->countv);
174 bool needCalcConPrb = model->getNeedCalcConPrb();
178 int N = hitv->getN();
180 vector<double> fracs; //to remove this, do calculation twice
183 if (needCalcConPrb || updateModel) { reader->reset(); }
184 if (updateModel) { mhp->init(); }
186 memset(countv, 0, sizeof(double) * (M + 1));
187 for (int i = 0; i < N; i++) {
188 if (needCalcConPrb || updateModel) {
189 if (!reader->next(read)) {
190 fprintf(stderr, "Can not load a read!\n");
193 //assert(reader->next(read));
195 fr = hitv->getSAt(i);
196 to = hitv->getSAt(i + 1);
197 fracs.resize(to - fr + 1);
201 if (needCalcConPrb) { ncpv[i] = model->getNoiseConPrb(read); }
202 fracs[0] = probv[0] * ncpv[i];
203 if (fracs[0] < EPSILON) fracs[0] = 0.0;
205 for (int j = fr; j < to; j++) {
206 HitType &hit = hitv->getHitAt(j);
207 if (needCalcConPrb) { hit.setConPrb(model->getConPrb(read, hit)); }
209 fracs[id] = probv[hit.getSid()] * hit.getConPrb();
210 if (fracs[id] < EPSILON) fracs[id] = 0.0;
214 if (sum >= EPSILON) {
216 countv[0] += fracs[0];
217 if (updateModel) { mhp->updateNoise(read, fracs[0]); }
218 if (calcExpectedWeights) { ncpv[i] = fracs[0]; }
219 for (int j = fr; j < to; j++) {
220 HitType &hit = hitv->getHitAt(j);
223 countv[hit.getSid()] += fracs[id];
224 if (updateModel) { mhp->update(read, hit, fracs[id]); }
225 if (calcExpectedWeights) { hit.setConPrb(fracs[id]); }
228 else if (calcExpectedWeights) {
230 for (int j = fr; j < to; j++) {
231 HitType &hit = hitv->getHitAt(j);
240 template<class ReadType, class HitType, class ModelType>
241 void* calcConProbs(void* arg) {
242 Params *params = (Params*)arg;
243 ModelType *model = (ModelType*)(params->model);
244 ReadReader<ReadType> *reader = (ReadReader<ReadType>*)(params->reader);
245 HitContainer<HitType> *hitv = (HitContainer<HitType>*)(params->hitv);
246 double *ncpv = (double*)(params->ncpv);
249 int N = hitv->getN();
252 assert(model->getNeedCalcConPrb());
255 for (int i = 0; i < N; i++) {
256 if (!reader->next(read)) {
257 fprintf(stderr, "Can not load a read!\n");
260 fr = hitv->getSAt(i);
261 to = hitv->getSAt(i + 1);
263 ncpv[i] = model->getNoiseConPrb(read);
264 for (int j = fr; j < to; j++) {
265 HitType &hit = hitv->getHitAt(j);
266 hit.setConPrb(model->getConPrb(read, hit));
273 template<class ModelType>
274 void calcExpectedEffectiveLengths(ModelType& model) {
276 double *pdf = NULL, *cdf = NULL, *clen = NULL; // clen[i] = sigma_{j=1}^{i}pdf[i]*(lb+i)
278 model.getGLD().copyTo(pdf, cdf, lb, ub, span);
279 clen = new double[span + 1];
281 for (int i = 1; i <= span; i++) {
282 clen[i] = clen[i - 1] + pdf[i] * (lb + i);
286 eel.resize(M + 1, 0.0);
287 for (int i = 1; i <= M; i++) {
288 int totLen = refs.getRef(i).getTotLen();
289 int fullLen = refs.getRef(i).getFullLen();
290 int pos1 = max(min(totLen - fullLen + 1, ub) - lb, 0);
291 int pos2 = max(min(totLen, ub) - lb, 0);
293 if (pos2 == 0) { eel[i] = 0.0; continue; }
295 eel[i] = fullLen * cdf[pos1] + ((cdf[pos2] - cdf[pos1]) * (totLen + 1) - (clen[pos2] - clen[pos1]));
297 if (eel[i] < MINEEL) { eel[i] = 0.0; }
305 template<class ModelType>
306 void writeResults(ModelType& model, double* counts) {
311 sprintf(modelF, "%s.model", statName);
314 //calculate tau values
315 double *tau = new double[M + 1];
316 memset(tau, 0, sizeof(double) * (M + 1));
319 for (int i = 1; i <= M; i++)
320 if (eel[i] >= EPSILON) {
321 tau[i] = theta[i] / eel[i];
324 if (denom <= 0) { fprintf(stderr, "No alignable reads?!\n"); exit(-1); }
326 for (int i = 1; i <= M; i++) {
330 //isoform level results
331 sprintf(outF, "%s.iso_res", imdName);
332 fo = fopen(outF, "w");
333 for (int i = 1; i <= M; i++) {
334 const Transcript& transcript = transcripts.getTranscriptAt(i);
335 fprintf(fo, "%s%c", transcript.getTranscriptID().c_str(), (i < M ? '\t' : '\n'));
337 for (int i = 1; i <= M; i++)
338 fprintf(fo, "%.2f%c", counts[i], (i < M ? '\t' : '\n'));
339 for (int i = 1; i <= M; i++)
340 fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
341 for (int i = 1; i <= M; i++) {
342 const Transcript& transcript = transcripts.getTranscriptAt(i);
343 fprintf(fo, "%s%c", transcript.getGeneID().c_str(), (i < M ? '\t' : '\n'));
348 sprintf(outF, "%s.gene_res", imdName);
349 fo = fopen(outF, "w");
350 for (int i = 0; i < m; i++) {
351 const string& gene_id = transcripts.getTranscriptAt(gi.spAt(i)).getGeneID();
352 fprintf(fo, "%s%c", gene_id.c_str(), (i < m - 1 ? '\t' : '\n'));
354 for (int i = 0; i < m; i++) {
355 double sumC = 0.0; // sum of counts
356 int b = gi.spAt(i), e = gi.spAt(i + 1);
357 for (int j = b; j < e; j++) sumC += counts[j];
358 fprintf(fo, "%.2f%c", sumC, (i < m - 1 ? '\t' : '\n'));
360 for (int i = 0; i < m; i++) {
361 double sumT = 0.0; // sum of tau values
362 int b = gi.spAt(i), e = gi.spAt(i + 1);
363 for (int j = b; j < e; j++) sumT += tau[j];
364 fprintf(fo, "%.15g%c", sumT, (i < m - 1 ? '\t' : '\n'));
366 for (int i = 0; i < m; i++) {
367 int b = gi.spAt(i), e = gi.spAt(i + 1);
368 for (int j = b; j < e; j++) {
369 fprintf(fo, "%s%c", transcripts.getTranscriptAt(j).getTranscriptID().c_str(), (j < e - 1 ? ',' : (i < m - 1 ? '\t' :'\n')));
376 if (verbose) { printf("Expression Results are written!\n"); }
379 template<class ReadType, class HitType, class ModelType>
380 void release(ReadReader<ReadType> **readers, HitContainer<HitType> **hitvs, double **ncpvs, ModelType **mhps) {
382 for (int i = 0; i < nThreads; i++) {
387 for (int i = 0; i < nThreads; i++) {
399 inline bool doesUpdateModel(int ROUND) {
400 // return ROUND <= 20 || ROUND % 100 == 0;
404 //Including initialize, algorithm and results saving
405 template<class ReadType, class HitType, class ModelType>
412 double bChange = 0.0, change = 0.0; // bChange : biggest change
415 ModelType model(mparams); //master model
416 ReadReader<ReadType> **readers;
417 HitContainer<HitType> **hitvs;
419 ModelType **mhps; //model helpers
421 Params fparams[nThreads];
422 pthread_t threads[nThreads];
428 //initialize boolean variables
429 updateModel = calcExpectedWeights = false;
432 theta.resize(M + 1, 0.0);
433 init<ReadType, HitType, ModelType>(readers, hitvs, ncpvs, mhps);
435 //set initial parameters
437 theta[0] = max(N0 * 1.0 / (N_tot - N2), 1e-8);
438 double val = (1.0 - theta[0]) / M;
439 for (int i = 1; i <= M; i++) theta[i] = val;
441 model.estimateFromReads(imdName);
443 for (int i = 0; i < nThreads; i++) {
444 fparams[i].model = (void*)(&model);
446 fparams[i].reader = (void*)readers[i];
447 fparams[i].hitv = (void*)hitvs[i];
448 fparams[i].ncpv = (void*)ncpvs[i];
449 fparams[i].mhp = (void*)mhps[i];
450 fparams[i].countv = (void*)countvs[i];
453 /* set thread attribute to be joinable */
454 pthread_attr_init(&attr);
455 pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
461 updateModel = doesUpdateModel(ROUND);
463 for (int i = 0; i <= M; i++) probv[i] = theta[i];
466 for (int i = 0; i < nThreads; i++) {
467 rc = pthread_create(&threads[i], &attr, E_STEP<ReadType, HitType, ModelType>, (void*)(&fparams[i]));
468 if (rc != 0) { fprintf(stderr, "Cannot create thread %d at ROUND %d! (numbered from 0)\n", i, ROUND); exit(-1); }
472 for (int i = 0; i < nThreads; i++) {
473 rc = pthread_join(threads[i], &status);
474 if (rc != 0) { fprintf(stderr, "Cannot join thread %d at ROUND %d! (numbered from 0)\n", i, ROUND); exit(-1); }
478 model.setNeedCalcConPrb(false);
480 for (int i = 1; i < nThreads; i++) {
481 for (int j = 0; j <= M; j++) {
482 countvs[0][j] += countvs[i][j];
491 for (int i = 0; i <= M; i++) sum += countvs[0][i];
492 assert(sum >= EPSILON);
493 for (int i = 0; i <= M; i++) theta[i] = countvs[0][i] / sum;
497 for (int i = 0; i < nThreads; i++) { model.collect(*mhps[i]); }
502 bChange = 0.0; totNum = 0;
503 for (int i = 0; i <= M; i++)
504 if (probv[i] >= 1e-7) {
505 change = fabs(theta[i] - probv[i]) / probv[i];
506 if (change >= STOP_CRITERIA) ++totNum;
507 if (bChange < change) bChange = change;
510 if (verbose) printf("ROUND = %d, SUM = %.15g, bChange = %f, totNum = %d\n", ROUND, sum, bChange, totNum);
511 } while (ROUND < MIN_ROUND || (totNum > 0 && ROUND < MAX_ROUND));
512 //while (ROUND < MAX_ROUND);
514 if (totNum > 0) fprintf(stderr, "Warning: RSEM reaches %d iterations before meeting the convergence criteria.\n", MAX_ROUND);
516 //generate output file used by Gibbs sampler
518 if (model.getNeedCalcConPrb()) {
519 for (int i = 0; i < nThreads; i++) {
520 rc = pthread_create(&threads[i], &attr, calcConProbs<ReadType, HitType, ModelType>, (void*)(&fparams[i]));
521 if (rc != 0) { fprintf(stderr, "Cannot create thread %d when generate files for Gibbs sampler! (numbered from 0)\n", i); exit(-1); }
523 for (int i = 0; i < nThreads; i++) {
524 rc = pthread_join(threads[i], &status);
525 if (rc != 0) { fprintf(stderr, "Cannot join thread %d when generate files for Gibbs sampler! (numbered from 0)\n", i); exit(-1); }
528 model.setNeedCalcConPrb(false);
530 sprintf(out_for_gibbs_F, "%s.ofg", imdName);
531 fo = fopen(out_for_gibbs_F, "w");
532 fprintf(fo, "%d %d\n", M, N0);
533 for (int i = 0; i < nThreads; i++) {
534 int numN = hitvs[i]->getN();
535 for (int j = 0; j < numN; j++) {
536 int fr = hitvs[i]->getSAt(j);
537 int to = hitvs[i]->getSAt(j + 1);
540 if (ncpvs[i][j] >= EPSILON) { ++totNum; fprintf(fo, "%d %.15g ", 0, ncpvs[i][j]); }
541 for (int k = fr; k < to; k++) {
542 HitType &hit = hitvs[i]->getHitAt(k);
543 if (hit.getConPrb() >= EPSILON) {
545 fprintf(fo, "%d %.15g ", hit.getSid(), hit.getConPrb());
549 if (totNum > 0) { fprintf(fo, "\n"); }
555 sprintf(thetaF, "%s.theta", statName);
556 fo = fopen(thetaF, "w");
557 fprintf(fo, "%d\n", M + 1);
560 for (int i = 0; i < M; i++) fprintf(fo, "%.15g ", theta[i]);
561 fprintf(fo, "%.15g\n", theta[M]);
563 //calculate expected effective lengths for each isoform
564 calcExpectedEffectiveLengths<ModelType>(model);
566 //correct theta vector
568 for (int i = 1; i <= M; i++)
569 if (eel[i] < EPSILON) { theta[i] = 0.0; }
570 else sum += theta[i];
571 if (sum < EPSILON) { fprintf(stderr, "No Expected Effective Length is no less than %.6g?!\n", MINEEL); exit(-1); }
572 for (int i = 0; i <= M; i++) theta[i] /= sum;
574 //calculate expected weights and counts using learned parameters
575 updateModel = false; calcExpectedWeights = true;
576 for (int i = 0; i <= M; i++) probv[i] = theta[i];
577 for (int i = 0; i < nThreads; i++) {
578 rc = pthread_create(&threads[i], &attr, E_STEP<ReadType, HitType, ModelType>, (void*)(&fparams[i]));
579 if (rc != 0) { fprintf(stderr, "Cannot create thread %d when calculate expected weights! (numbered from 0)\n", i); exit(-1); }
582 for (int i = 0; i < nThreads; i++) {
583 rc = pthread_join(threads[i], &status);
584 if (rc != 0) { fprintf(stderr, "Cannot join thread %d! (numbered from 0) when calculate expected weights!\n", i); exit(-1); }
587 model.setNeedCalcConPrb(false);
588 for (int i = 1; i < nThreads; i++) {
589 for (int j = 0; j <= M; j++) {
590 countvs[0][j] += countvs[i][j];
595 /* destroy attribute */
596 pthread_attr_destroy(&attr);
598 //convert theta' to theta
599 double *mw = model.getMW();
601 for (int i = 0; i <= M; i++) {
602 theta[i] = (mw[i] < EPSILON ? 0.0 : theta[i] / mw[i]);
605 assert(sum >= EPSILON);
606 for (int i = 0; i <= M; i++) theta[i] /= sum;
609 for (int i = 0; i < M; i++) fprintf(fo, "%.15g ", theta[i]);
610 fprintf(fo, "%.15g\n", theta[M]);
614 writeResults<ModelType>(model, countvs[0]);
617 sprintf(outBamF, "%s.transcript.bam", outName);
625 if (verbose) printf("Begin to sample reads from their posteriors.\n");
626 for (int i = 0; i < nThreads; i++) {
627 local_N = hitvs[i]->getN();
628 for (int j = 0; j < local_N; j++) {
629 fr = hitvs[i]->getSAt(j);
630 to = hitvs[i]->getSAt(j + 1);
633 arr[0] = ncpvs[i][j];
634 for (int k = fr; k < to; k++) arr[k - fr + 1] = arr[k - fr] + hitvs[i]->getHitAt(k).getConPrb();
635 id = (arr[len - 1] < EPSILON ? -1 : sample(arr, len)); // if all entries in arr are 0, let id be -1
636 for (int k = fr; k < to; k++) hitvs[i]->getHitAt(k).setConPrb(k - fr + 1 == id ? 1.0 : 0.0);
639 if (verbose) printf("Sampling is finished.\n");
642 BamWriter writer(inpSamType, inpSamF, pt_fn_list, outBamF, transcripts);
643 HitWrapper<HitType> wrapper(nThreads, hitvs);
644 writer.work(wrapper);
647 release<ReadType, HitType, ModelType>(readers, hitvs, ncpvs, mhps);
650 int main(int argc, char* argv[]) {
655 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");
656 printf(" refName: reference name\n");
657 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");
658 printf(" sampleName: sample's name, including the path\n");
659 printf(" sampleToken: sampleName excludes the path\n");
660 printf(" -p: number of threads which user wants to use. (default: 1)\n");
661 printf(" -b: produce bam format output file. (default: off)\n");
662 printf(" -q: set it quiet\n");
663 printf(" --gibbs-out: generate output file used by Gibbs sampler. (default: off)\n");
664 printf(" --sampling: sample each read from its posterior distribution when bam file is generated. (default: off)\n");
665 printf("// model parameters should be in imdName.mparams.\n");
669 time_t a = time(NULL);
671 strcpy(refName, argv[1]);
672 read_type = atoi(argv[2]);
673 strcpy(outName, argv[3]);
674 sprintf(imdName, "%s.temp/%s", argv[3], argv[4]);
675 sprintf(statName, "%s.stat/%s", argv[3], argv[4]);
682 pt_fn_list = pt_chr_list = NULL;
684 for (int i = 5; i < argc; i++) {
685 if (!strcmp(argv[i], "-p")) { nThreads = atoi(argv[i + 1]); }
686 if (!strcmp(argv[i], "-b")) {
688 inpSamType = argv[i + 1][0];
689 strcpy(inpSamF, argv[i + 2]);
690 if (atoi(argv[i + 3]) == 1) {
691 strcpy(fn_list, argv[i + 4]);
692 pt_fn_list = (char*)(&fn_list);
695 if (!strcmp(argv[i], "-q")) { quiet = true; }
696 if (!strcmp(argv[i], "--gibbs-out")) { genGibbsOut = true; }
697 if (!strcmp(argv[i], "--sampling")) { bamSampling = true; }
699 if (nThreads <= 0) { fprintf(stderr, "Number of threads should be bigger than 0!\n"); exit(-1); }
700 //assert(nThreads > 0);
705 sprintf(refF, "%s.seq", refName);
708 sprintf(groupF, "%s.grp", refName);
712 sprintf(tiF, "%s.ti", refName);
713 transcripts.readFrom(tiF);
715 sprintf(cntF, "%s.cnt", statName);
717 if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", cntF); exit(-1); }
718 fin>>N0>>N1>>N2>>N_tot;
721 if (N1 <= 0) { fprintf(stderr, "There are no alignable reads!\n"); exit(-1); }
723 if (nThreads > N1) nThreads = N1;
725 //set model parameters
727 mparams.N[0] = N0; mparams.N[1] = N1; mparams.N[2] = N2;
728 mparams.refs = &refs;
730 sprintf(mparamsF, "%s.mparams", imdName);
732 if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", mparamsF); exit(-1); }
733 fin>> mparams.minL>> mparams.maxL>> mparams.probF;
734 int val; // 0 or 1 , for estRSPD
736 mparams.estRSPD = (val != 0);
737 fin>> mparams.B>> mparams.mate_minL>> mparams.mate_maxL>> mparams.mean>> mparams.sd;
738 fin>> mparams.seedLen;
743 case 0 : EM<SingleRead, SingleHit, SingleModel>(); break;
744 case 1 : EM<SingleReadQ, SingleHit, SingleQModel>(); break;
745 case 2 : EM<PairedEndRead, PairedEndHit, PairedEndModel>(); break;
746 case 3 : EM<PairedEndReadQ, PairedEndHit, PairedEndQModel>(); break;
747 default : fprintf(stderr, "Unknown Read Type!\n"); exit(-1);
750 time_t b = time(NULL);