int main(int argc, char* argv[]) {
bool quiet = false;
if (argc < 6) {
printf("Usage : rsem-parse-alignments refName imdName statName alignFType('s' for sam, 'b' for bam) alignF [-t Type] [-l fn_list] [-tag tagName] [-q]\n");
exit(-1);
}
strcpy(fn_list, "");
read_type = 0;
if (argc > 6) {
for (int i = 6; i < argc; i++) {
if (!strcmp(argv[i], "-t")) {
read_type = atoi(argv[i + 1]);
}
if (!strcmp(argv[i], "-l")) {
strcpy(fn_list, argv[i + 1]);
}
if (!strcmp(argv[i], "-tag")) {
SamParser::setReadTypeTag(argv[i + 1]);
}
if (!strcmp(argv[i], "-q")) { quiet = true; }
}
}
verbose = !quiet;
sprintf(groupF, "%s.grp", argv[1]);
gi.load(groupF);
sprintf(tiF, "%s.ti", argv[1]);
transcripts.readFrom(tiF);
sprintf(datF, "%s.dat", argv[2]);
sprintf(cntF, "%s.cnt", argv[3]);
init(argv[2], argv[4][0], argv[5]);
hit_out.open(datF);
string firstLine(99, ' ');
firstLine.append(1, '\n'); //May be dangerous!
hit_out<<firstLine;
switch(read_type) {
case 0 : parseIt<SingleRead, SingleHit>(parser); break;
case 1 : parseIt<SingleReadQ, SingleHit>(parser); break;
case 2 : parseIt<PairedEndRead, PairedEndHit>(parser); break;
case 3 : parseIt<PairedEndReadQ, PairedEndHit>(parser); break;
}
hit_out.seekp(0, ios_base::beg);
hit_out<<N[1]<<" "<<nHits<<" "<<read_type;
hit_out.close();
//cntF for statistics of alignments file
ofstream fout(cntF);
fout<<N[0]<<" "<<N[1]<<" "<<N[2]<<" "<<(N[0] + N[1] + N[2])<<endl;
fout<<nUnique<<" "<<nMulti<<" "<<nIsoMulti<<endl;
fout<<nHits<<" "<<read_type<<endl;
fout<<"0\t"<<N[0]<<endl;
for (iter = counter.begin(); iter != counter.end(); iter++) {
fout<<iter->first<<'\t'<<iter->second<<endl;
}
fout<<"Inf\t"<<N[2]<<endl;
fout.close();
release();
if (verbose) { printf("Done!\n"); }
return 0;
}
int main(int argc, char* argv[]) {
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");
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(" 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 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);
}
time_t a = time(NULL);
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]);
nThreads = 1;
genBamF = false;
bamSampling = false;
genGibbsOut = false;
pt_fn_list = pt_chr_list = NULL;
for (int i = 5; i < argc; i++) {
if (!strcmp(argv[i], "-p")) { nThreads = atoi(argv[i + 1]); }
if (!strcmp(argv[i], "-b")) {
genBamF = true;
inpSamType = argv[i + 1][0];
strcpy(inpSamF, argv[i + 2]);
if (atoi(argv[i + 3]) == 1) {
strcpy(fn_list, argv[i + 4]);
pt_fn_list = (char*)(&fn_list);
}
}
if (!strcmp(argv[i], "-q")) { quiet = true; }
if (!strcmp(argv[i], "--gibbs-out")) { genGibbsOut = true; }
if (!strcmp(argv[i], "--sampling")) { bamSampling = true; }
}
general_assert(nThreads > 0, "Number of threads should be bigger than 0!");
verbose = !quiet;
//basic info loading
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);
general_assert(fin.is_open(), "Cannot open " + cstrtos(cntF) + "! It may not exist.");
fin>>N0>>N1>>N2>>N_tot;
fin.close();
general_assert(N1 > 0, "There are no alignable reads!");
if ((READ_INT_TYPE)nThreads > N1) nThreads = N1;
//set model parameters
mparams.M = M;
mparams.N[0] = N0; mparams.N[1] = N1; mparams.N[2] = N2;
mparams.refs = &refs;
sprintf(mparamsF, "%s.mparams", imdName);
fin.open(mparamsF);
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;
mparams.estRSPD = (val != 0);
fin>> mparams.B>> mparams.mate_minL>> mparams.mate_maxL>> mparams.mean>> mparams.sd;
fin>> mparams.seedLen;
fin.close();
//run EM
switch(read_type) {
case 0 : EM<SingleRead, SingleHit, SingleModel>(); break;
case 1 : EM<SingleReadQ, SingleHit, SingleQModel>(); break;
case 2 : EM<PairedEndRead, PairedEndHit, PairedEndModel>(); break;
case 3 : EM<PairedEndReadQ, PairedEndHit, PairedEndQModel>(); break;
default : fprintf(stderr, "Unknown Read Type!\n"); exit(-1);
}
time_t b = time(NULL);
printTimeUsed(a, b, "EM.cpp");
return 0;
}
int main(int argc, char* argv[]) {
ifstream fin;
bool quiet = false;
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] [--calc-evaluation-score nb_r nb_p L w]\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(" 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(" --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(" --calc-evaluation-score nb_r nb_p L w: "
"nb_r and nb_p are parameters for the true transcript length distribution, which is modeled by a negative binomial distribution; "
"L is the read length and w is the mininum overlap required for joining two contigs.\n");
printf("// model parameters should be in imdName.mparams.\n");
exit(-1);
}
time_t a = time(NULL);
strcpy(refName, argv[1]);
read_type = atoi(argv[2]);
strcpy(outName, argv[3]);
strcpy(imdName, argv[4]);
strcpy(statName, argv[5]);
nThreads = 1;
genBamF = false;
bamSampling = false;
genGibbsOut = false;
calcEvalScore = false;
pt_fn_list = NULL;
hasSeed = false;
for (int i = 6; i < argc; i++) {
if (!strcmp(argv[i], "-p")) { nThreads = atoi(argv[i + 1]); }
if (!strcmp(argv[i], "-b")) {
genBamF = true;
inpSamType = argv[i + 1][0];
strcpy(inpSamF, argv[i + 2]);
if (atoi(argv[i + 3]) == 1) {
strcpy(fn_list, argv[i + 4]);
pt_fn_list = (char*)(&fn_list);
}
}
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 (!strcmp(argv[i], "--calc-evaluation-score")) {
calcEvalScore = true;
nb_r = atof(argv[i + 1]);
nb_p = atof(argv[i + 2]);
L = atoi(argv[i + 3]);
w = atoi(argv[i + 4]);
}
}
general_assert(nThreads > 0, "Number of threads should be bigger than 0!");
verbose = !quiet;
//basic info loading
sprintf(refF, "%s.seq", refName);
refs.loadRefs(refF);
M = refs.getM();
sprintf(tiF, "%s.ti", refName);
transcripts.readFrom(tiF);
sprintf(cntF, "%s.cnt", statName);
fin.open(cntF);
general_assert(fin.is_open(), "Cannot open " + cstrtos(cntF) + "! It may not exist.");
fin>>N0>>N1>>N2>>N_tot;
fin.close();
general_assert(N1 > 0, "There are no alignable reads!");
if ((READ_INT_TYPE)nThreads > N1) nThreads = N1;
//set model parameters
mparams.M = M;
mparams.N[0] = N0; mparams.N[1] = N1; mparams.N[2] = N2;
mparams.refs = &refs;
sprintf(mparamsF, "%s.mparams", imdName);
fin.open(mparamsF);
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;
mparams.estRSPD = (val != 0);
fin>> mparams.B>> mparams.mate_minL>> mparams.mate_maxL>> mparams.mean>> mparams.sd;
fin>> mparams.seedLen;
fin.close();
//run EM
switch(read_type) {
case 0 : EM<SingleRead, SingleHit, SingleModel>(); break;
case 1 : EM<SingleReadQ, SingleHit, SingleQModel>(); break;
case 2 : EM<PairedEndRead, PairedEndHit, PairedEndModel>(); break;
case 3 : EM<PairedEndReadQ, PairedEndHit, PairedEndQModel>(); break;
default : fprintf(stderr, "Unknown Read Type!\n"); exit(-1);
}
if (calcEvalScore) {
CalcEvalScore ces(refs, nb_r, nb_p, L, w, statName);
sprintf(scoreF, "%s.score", outName);
ces.writeScoresTo(scoreF);
char groupF[STRLEN];
GroupInfo gi;
sprintf(groupF, "%s.grp", argv[1]);
gi.load(groupF);
ces.generateExpressionFiles(gi, transcripts, scoreF);
}
time_t b = time(NULL);
printTimeUsed(a, b, "EM.cpp");
return 0;
}