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-rw-r--r--src/io.cpp54
-rw-r--r--src/io.h4
-rw-r--r--src/lm.cpp6
-rw-r--r--src/mvlmm.cpp8
-rw-r--r--src/param.cpp4
-rw-r--r--src/param.h3
-rwxr-xr-xtest/test_suite.sh6
7 files changed, 30 insertions, 55 deletions
diff --git a/src/io.cpp b/src/io.cpp
index 8d77b0f..71d55c3 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -49,43 +49,17 @@
using namespace std;
// Print progress bar.
-void ProgressBar(string str, double p, double total) {
- double progress = (100.0 * p / total);
- int barsize = (int)(progress / 2.0);
- char bar[51];
-
- cout << str;
- for (int i = 0; i < 50; i++) {
- if (i < barsize) {
- bar[i] = '=';
- } else {
- bar[i] = ' ';
- }
- cout << bar[i];
- }
- cout << setprecision(2) << fixed << progress << "%\r" << flush;
-
- return;
-}
-
-// Print progress bar with acceptance ratio.
void ProgressBar(string str, double p, double total, double ratio) {
- double progress = (100.0 * p / total);
- int barsize = (int)(progress / 2.0);
- char bar[51];
-
- cout << str;
- for (int i = 0; i < 50; i++) {
- if (i < barsize) {
- bar[i] = '=';
- } else {
- bar[i] = ' ';
- }
- cout << bar[i];
- }
- cout << setprecision(2) << fixed << progress << "% " << ratio << "\r"
- << flush;
- return;
+ assert(p<=total);
+ const double progress = (100.0 * p / total);
+ const uint barsize = (int)(progress / 2.0); // characters
+ cout << str << " ";
+ cout << std::string(barsize,'=');
+ cout << std::string(50-barsize,' ');
+ cout << setprecision(0) << fixed << progress << "%";
+ if (ratio != -1.0)
+ cout << setprecision(2) << " " << ratio;
+ cout << "\r" << flush;
}
bool isBlankLine(char const *line) {
@@ -1407,7 +1381,7 @@ bool BimbamKin(const string file_geno, const set<string> ksnps,
string line;
!safeGetline(infile, line).eof();
if (t % display_pace == 0 || t == (indicator_snp.size() - 1)) {
- ProgressBar("Reading SNPs ", t, indicator_snp.size() - 1);
+ ProgressBar("Reading SNPs", t, indicator_snp.size() - 1);
}
if (indicator_snp[t] == 0)
continue;
@@ -1556,7 +1530,7 @@ bool PlinkKin(const string &file_bed, vector<int> &indicator_snp,
for (size_t t = 0; t < indicator_snp.size(); ++t) {
if (t % display_pace == 0 || t == (indicator_snp.size() - 1)) {
- ProgressBar("Reading SNPs ", t, indicator_snp.size() - 1);
+ ProgressBar("Reading SNPs", t, indicator_snp.size() - 1);
}
if (indicator_snp[t] == 0) {
continue;
@@ -2713,7 +2687,7 @@ bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps,
for (size_t t = 0; t < indicator_snp.size(); ++t) {
!safeGetline(infile, line).eof();
if (t % display_pace == 0 || t == (indicator_snp.size() - 1)) {
- ProgressBar("Reading SNPs ", t, indicator_snp.size() - 1);
+ ProgressBar("Reading SNPs", t, indicator_snp.size() - 1);
}
if (indicator_snp[t] == 0)
continue;
@@ -2918,7 +2892,7 @@ bool PlinkKin(const string &file_bed, const int display_pace,
for (size_t t = 0; t < indicator_snp.size(); ++t) {
if (t % display_pace == 0 || t == (indicator_snp.size() - 1)) {
- ProgressBar("Reading SNPs ", t, indicator_snp.size() - 1);
+ ProgressBar("Reading SNPs", t, indicator_snp.size() - 1);
}
if (indicator_snp[t] == 0) {
continue;
diff --git a/src/io.h b/src/io.h
index 1c187b8..c65a2b0 100644
--- a/src/io.h
+++ b/src/io.h
@@ -32,8 +32,8 @@
using namespace std;
-void ProgressBar(string str, double p, double total);
-void ProgressBar(string str, double p, double total, double ratio);
+void ProgressBar(string str, double p, double total, double ratio = -1.0);
+
std::istream &safeGetline(std::istream &is, std::string &t);
bool ReadFile_snps(const string file_snps, set<string> &setSnps);
diff --git a/src/lm.cpp b/src/lm.cpp
index a44bceb..ea628cf 100644
--- a/src/lm.cpp
+++ b/src/lm.cpp
@@ -331,7 +331,7 @@ void LM::AnalyzeGene(const gsl_matrix *W, const gsl_vector *x) {
for (size_t t = 0; t < ng_total; t++) {
getline(infile, line);
if (t % d_pace == 0 || t == ng_total - 1) {
- ProgressBar("Performing Analysis ", t, ng_total - 1);
+ ProgressBar("Performing Analysis", t, ng_total - 1);
}
ch_ptr = strtok((char *)line.c_str(), " , \t");
rs = ch_ptr;
@@ -421,7 +421,7 @@ void LM::AnalyzeBimbam(const gsl_matrix *W, const gsl_vector *y) {
for (size_t t = 0; t < indicator_snp.size(); ++t) {
getline(infile, line);
if (t % d_pace == 0 || t == (ns_total - 1)) {
- ProgressBar("Reading SNPs ", t, ns_total - 1);
+ ProgressBar("Reading SNPs", t, ns_total - 1);
}
if (indicator_snp[t] == 0) {
continue;
@@ -547,7 +547,7 @@ void LM::AnalyzePlink(const gsl_matrix *W, const gsl_vector *y) {
for (vector<SNPINFO>::size_type t = 0; t < snpInfo.size(); ++t) {
if (t % d_pace == 0 || t == snpInfo.size() - 1) {
- ProgressBar("Reading SNPs ", t, snpInfo.size() - 1);
+ ProgressBar("Reading SNPs", t, snpInfo.size() - 1);
}
if (indicator_snp[t] == 0) {
continue;
diff --git a/src/mvlmm.cpp b/src/mvlmm.cpp
index 88df111..c0dc143 100644
--- a/src/mvlmm.cpp
+++ b/src/mvlmm.cpp
@@ -3190,7 +3190,7 @@ void MVLMM::AnalyzeBimbam(const gsl_matrix *U, const gsl_vector *eval,
for (size_t t = 0; t < indicator_snp.size(); ++t) {
!safeGetline(infile, line).eof();
if (t % d_pace == 0 || t == (ns_total - 1)) {
- ProgressBar("Reading SNPs ", t, ns_total - 1);
+ ProgressBar("Reading SNPs", t, ns_total - 1);
}
if (indicator_snp[t] == 0) {
continue;
@@ -3639,7 +3639,7 @@ void MVLMM::AnalyzePlink(const gsl_matrix *U, const gsl_vector *eval,
}
for (vector<SNPINFO>::size_type t = 0; t < snpInfo.size(); ++t) {
if (t % d_pace == 0 || t == snpInfo.size() - 1) {
- ProgressBar("Reading SNPs ", t, snpInfo.size() - 1);
+ ProgressBar("Reading SNPs", t, snpInfo.size() - 1);
}
if (indicator_snp[t] == 0) {
continue;
@@ -4167,7 +4167,7 @@ void MVLMM::AnalyzeBimbamGXE(const gsl_matrix *U, const gsl_vector *eval,
for (size_t t = 0; t < indicator_snp.size(); ++t) {
!safeGetline(infile, line).eof();
if (t % d_pace == 0 || t == (ns_total - 1)) {
- ProgressBar("Reading SNPs ", t, ns_total - 1);
+ ProgressBar("Reading SNPs", t, ns_total - 1);
}
if (indicator_snp[t] == 0) {
continue;
@@ -4624,7 +4624,7 @@ void MVLMM::AnalyzePlinkGXE(const gsl_matrix *U, const gsl_vector *eval,
for (vector<SNPINFO>::size_type t = 0; t < snpInfo.size(); ++t) {
if (t % d_pace == 0 || t == snpInfo.size() - 1) {
- ProgressBar("Reading SNPs ", t, snpInfo.size() - 1);
+ ProgressBar("Reading SNPs", t, snpInfo.size() - 1);
}
if (indicator_snp[t] == 0) {
continue;
diff --git a/src/param.cpp b/src/param.cpp
index 8452fb8..d637481 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -87,7 +87,7 @@ void trim_individuals(vector<int> &idvs, size_t ni_max, bool debug) {
// ---- PARAM class implementation
PARAM::PARAM(void)
- : mode_silence(false), a_mode(0), k_mode(1), d_pace(100000),
+ : mode_silence(false), a_mode(0), k_mode(1), d_pace(DEFAULT_PACE),
file_out("result"), path_out("./output/"), miss_level(0.05),
maf_level(0.01), hwe_level(0), r2_level(0.9999), l_min(1e-5), l_max(1e5),
n_region(10), p_nr(0.001), em_prec(0.0001), nr_prec(0.0001),
@@ -1150,7 +1150,7 @@ void PARAM::CheckData(void) {
}
// Set d_pace to 1000 for gene expression.
- if (!file_gene.empty() && d_pace == 100000) {
+ if (!file_gene.empty() && d_pace == DEFAULT_PACE) {
d_pace = 1000;
}
diff --git a/src/param.h b/src/param.h
index 3976440..4b473c0 100644
--- a/src/param.h
+++ b/src/param.h
@@ -27,6 +27,7 @@
#include <vector>
#define K_BATCH_SIZE 10000 // #snps used for batched K
+#define DEFAULT_PACE 1000
using namespace std;
@@ -124,7 +125,7 @@ public:
uint a_mode; // Analysis mode, 1/2/3/4 for Frequentist tests
int k_mode; // Kinship read mode: 1: n by n matrix, 2: id/id/k_value;
vector<size_t> p_column; // Which phenotype column needs analysis.
- size_t d_pace; // Display pace
+ size_t d_pace = DEFAULT_PACE; // Display pace (-pace switch)
string file_bfile, file_mbfile;
string file_geno, file_mgeno;
diff --git a/test/test_suite.sh b/test/test_suite.sh
index 350fc27..dc6053a 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -62,7 +62,7 @@ testUnivariateLinearMixedModel() {
assertEquals "4038540440.86" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
-testMultivariateLinearMixedModel() {
+testLinearMixedModelPhenotypes() {
$gemma -g ../example/mouse_hs1940.geno.txt.gz \
-p ../example/mouse_hs1940.pheno.txt \
-n 1 6 \
@@ -92,8 +92,8 @@ testPlinkStandardRelatednessMatrixK() {
# Test for https://github.com/genetics-statistics/GEMMA/issues/58
# fixed GSLv2 NaN's that appeared with covariates.
-testPlinkMultivariateLinearMixedModel() {
- testname=testPlinkMultivariateLinearMixedModel
+testPlinkLinearMixedModelCovariates() {
+ testname=testPlinkLinearMixedModelCovariates
datadir=../example
$gemma -bfile $datadir/HLC \
-k output/testPlinkStandardRelatednessMatrixK.sXX.txt \
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-19 03:09:04 +0000