1.2.0

.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/

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,

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;

src/main.cpp

@@ -105,15 +105,15 @@ 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;
       double false_coverage =
           (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) {