diff --git a/src/Makefile b/src/Makefile index 5e98c91..ba83dc4 100755 --- a/src/Makefile +++ b/src/Makefile @@ -4,6 +4,13 @@ CFLAGS= -I. -O2 -ffast-math -O3 -fopenmp -std=c++11 Sanity: calc_true_variation_parallel_prior_mu_sigma.o ReadInputFiles.o FitFrac.o FukushimaLambertW.o Digamma_Trigamma.o $(CC) $(CFLAGS) -o ../bin/Sanity calc_true_variation_parallel_prior_mu_sigma.o ReadInputFiles.o FitFrac.o FukushimaLambertW.o Digamma_Trigamma.o +Sanity_lib: CFLAGS += -fPIC +Sanity_lib: libSanity.a + +libSanity.a: calc_true_variation_parallel_prior_mu_sigma.o ReadInputFiles.o FitFrac.o FukushimaLambertW.o Digamma_Trigamma.o + ar rcs libSanity.a calc_true_variation_parallel_prior_mu_sigma.o ReadInputFiles.o FitFrac.o FukushimaLambertW.o Digamma_Trigamma.o + cp libSanity.a ../../ + calc_true_variation_parallel_prior_mu_sigma.o: calc_true_variation_parallel_prior_mu_sigma.cpp ReadInputFiles.h FitFrac.h FukushimaLambertW.h Digamma_Trigamma.h $(CC) $(CFLAGS) -c calc_true_variation_parallel_prior_mu_sigma.cpp diff --git a/src/calc_true_variation_parallel_prior_mu_sigma.cpp b/src/calc_true_variation_parallel_prior_mu_sigma.cpp index 8975d08..156548d 100644 --- a/src/calc_true_variation_parallel_prior_mu_sigma.cpp +++ b/src/calc_true_variation_parallel_prior_mu_sigma.cpp @@ -755,7 +755,7 @@ void parse_argv(int argc,char** argv, string &in_file, string &gene_name_file, s int N_param(11); string extended_output("false"); string no_norm_str("false"); - string max_v_str("true"); + string max_v_str("false"); string to_find[11][2] = {{"-f", "--file"}, {"-d", "--destination"}, {"-n", "--n_threads"}, diff --git a/src/calc_true_variation_parallel_prior_mu_sigma.h b/src/calc_true_variation_parallel_prior_mu_sigma.h new file mode 100644 index 0000000..4ef13ef --- /dev/null +++ b/src/calc_true_variation_parallel_prior_mu_sigma.h @@ -0,0 +1,11 @@ +/* NOTES: + - this function gets posterior estimates for a single gene + - mu/var_mu is library-corrected log mean expression + - delta/var_delta is library-corrected guassian noise for log mean expression (e.g. gaussian noise for rate) + - variables with _ml are guassian bin with the highest likelhood + - posterior is a mixture of guassian distributions + - the regular version computes weighted average of those guassian distributions + - N_c is the observed libsize + - n_c is the observed gene counts for a specific gene +*/ +void get_gene_expression_level(double *n_c, double *N_c, double n, double vmin, double vmax, double &mu, double &var_mu, double *delta, double *var_delta, int C, int numbin, double a, double b, double *lik, double &v_ml, double &mu_v_ml, double &var_mu_v_ml, double *delta_v_ml, double *var_delta_v_ml);