}
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 < MIN_ROUND || (totNum > 0 && ROUND < MAX_ROUND));
//while (ROUND < MAX_ROUND);
if (totNum > 0) fprintf(stderr, "Warning: RSEM reaches %d iterations before meeting the convergence criteria.\n", MAX_ROUND);
//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); }
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(" 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");