diff --git a/.gitignore b/.gitignore
index a16ba6e..f53ba36 100644
--- a/.gitignore
+++ b/.gitignore
@@ -95,50 +95,6 @@ Network Trash Folder
Temporary Items
.apdisk
-# -----------------------------------------------------------------------------
-# JetBrains
-# -----------------------------------------------------------------------------
-
-# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
-# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
-
-# User-specific stuff
-.idea/**/workspace.xml
-.idea/**/tasks.xml
-.idea/**/usage.statistics.xml
-.idea/**/dictionaries
-.idea/**/shelf
-
-# Generated files
-.idea/**/contentModel.xml
-
-# Sensitive or high-churn files
-.idea/**/dataSources/
-.idea/**/dataSources.ids
-.idea/**/dataSources.local.xml
-.idea/**/sqlDataSources.xml
-.idea/**/dynamic.xml
-.idea/**/uiDesigner.xml
-.idea/**/dbnavigator.xml
-
-# Gradle
-.idea/**/gradle.xml
-.idea/**/libraries
-
-# Gradle and Maven with auto-import
-# When using Gradle or Maven with auto-import, you should exclude module files,
-# since they will be recreated, and may cause churn. Uncomment if using
-# auto-import.
-# .idea/artifacts
-# .idea/compiler.xml
-# .idea/jarRepositories.xml
-# .idea/modules.xml
-# .idea/*.iml
-# .idea/modules
-# *.iml
-# *.ipr
-
-# CMake
cmake-build-*/
# Mongo Explorer plugin
@@ -156,31 +112,18 @@ out/
# JIRA plugin
atlassian-ide-plugin.xml
-# Cursive Clojure plugin
-.idea/replstate.xml
-
# Crashlytics plugin (for Android Studio and IntelliJ)
com_crashlytics_export_strings.xml
crashlytics.properties
crashlytics-build.properties
fabric.properties
-# Editor-based Rest Client
-.idea/httpRequests
-# Android studio 3.1+ serialized cache file
-.idea/caches/build_file_checksums.ser
-
-# -----------------------------------------------------------------------------
-# VSCode
-# -----------------------------------------------------------------------------
-
-.vscode/*
-!.vscode/settings.json
-!.vscode/tasks.json
-!.vscode/launch.json
-!.vscode/extensions.json
*.code-workspace
# Local History for Visual Studio Code
.history/
+
+
+/.vscode/
+/.idea/
diff --git a/.idea/.gitignore b/.idea/.gitignore
deleted file mode 100644
index 73f69e0..0000000
--- a/.idea/.gitignore
+++ /dev/null
@@ -1,8 +0,0 @@
-# Default ignored files
-/shelf/
-/workspace.xml
-# Datasource local storage ignored files
-/dataSources/
-/dataSources.local.xml
-# Editor-based HTTP Client requests
-/httpRequests/
diff --git a/.idea/ULTRA.iml b/.idea/ULTRA.iml
deleted file mode 100644
index f08604b..0000000
--- a/.idea/ULTRA.iml
+++ /dev/null
@@ -1,2 +0,0 @@
-
-
\ No newline at end of file
diff --git a/.idea/codeStyles/Project.xml b/.idea/codeStyles/Project.xml
deleted file mode 100644
index cb12a05..0000000
--- a/.idea/codeStyles/Project.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/.idea/codeStyles/codeStyleConfig.xml b/.idea/codeStyles/codeStyleConfig.xml
deleted file mode 100644
index 79ee123..0000000
--- a/.idea/codeStyles/codeStyleConfig.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
-
-
-
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index 79b3c94..0000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-
-
-
-
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index 300b38e..0000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
deleted file mode 100644
index 94a25f7..0000000
--- a/.idea/vcs.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-
-
-
-
-
-
\ No newline at end of file
diff --git a/.vscode/settings.json b/.vscode/settings.json
deleted file mode 100644
index 65c053b..0000000
--- a/.vscode/settings.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
- "files.associations": {
- "Dockerfile_*": "dockerfile",
- "cmath": "cpp"
- }
-}
\ No newline at end of file
diff --git a/src/cli.cpp b/src/cli.cpp
index 0ac98a9..c65770f 100644
--- a/src/cli.cpp
+++ b/src/cli.cpp
@@ -111,6 +111,10 @@ void Settings::prepare_settings() {
"Do not output BED or JSON annotation")
->group("Output");
+ app.add_flag("--disable_summary", this->disable_summary,
+ "Disable summary statistics")
+ ->group("Output");
+
app.add_flag(
"--fdr", this->estimate_fdr,
"Estimate the False Discovery rate (runtime will be twice as long)")
@@ -207,6 +211,7 @@ void Settings::prepare_settings() {
app.add_option("--tune_fdr", this->tune_fdr,
"FDR to be tuned against (see README)")
+ ->default_val(this->tune_fdr)
->group("Parameter Tuning");
app.add_flag("--tune_only", this->tune_only,
diff --git a/src/cli.hpp b/src/cli.hpp
index e924cda..44ebbec 100644
--- a/src/cli.hpp
+++ b/src/cli.hpp
@@ -5,7 +5,7 @@
#ifndef ULTRA_CLI_HPP
#define ULTRA_CLI_HPP
-#define ULTRA_VERSION_STRING "1.1.0"
+#define ULTRA_VERSION_STRING "1.2.0"
#define DEBUG_STRING ""
#ifdef DEBUG_PRAGMA
#undef DEBUG_STRING
@@ -30,6 +30,7 @@ struct Settings {
// Output settings
std::string out_file = "";
bool pval = false;
+ bool disable_summary = false;
bool disable_streaming_out = false;
float p_value_loc = 4.27294921875;
float p_value_scale = 1.8913602828979492;
diff --git a/src/main.cpp b/src/main.cpp
index a2c7a61..4f869fa 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -105,7 +105,7 @@ int main_wrapper(int argc, const char *argv[]) {
param_strings.size(), real_coverage, fdr, arg_string.c_str());
}
- printf("-----------\n");
+ printf("----------------------------\n");
if (best_coverage_index >= 0) {
double real_coverage =
(double)coverage[best_coverage_index] / (double)seq_length;
@@ -113,7 +113,7 @@ int main_wrapper(int argc, const char *argv[]) {
(double)shuffled_coverage[best_coverage_index] / (double)seq_length;
double fdr = false_coverage / real_coverage;
- printf("Best coverage within FDR limit: %.5f, %.5f, %s\n", real_coverage,
+ printf("Best coverage within FDR limit (%.3f): %.5f, %.5f, %s\n", settings->tune_fdr, real_coverage,
fdr, param_strings[best_coverage_index].c_str());
delete settings;
@@ -126,7 +126,7 @@ int main_wrapper(int argc, const char *argv[]) {
}
settings->assign_settings();
} else {
- printf("No parameters found within FDR limit.\n");
+ printf("No parameters found within FDR limit (%.3f).\n", settings->tune_fdr);
exit(0);
}
@@ -148,6 +148,12 @@ int main_wrapper(int argc, const char *argv[]) {
settings->mask_with_n);
fclose(f);
}
+ if (!settings->disable_summary) {
+ seq_length = ultra->reader->fastaReader->total_seq_length;
+ double coverage_ratio = (double)true_coverage / (double)seq_length;
+ printf("----------------------------\n");
+ printf("Annotation Coverage: %.4f (%llu / %llu)\n", coverage_ratio, true_coverage, seq_length);
+ }
delete ultra;
if (settings->estimate_fdr) {