1.2.0 (#84)

* Removing ./idea/ and ./vscode/ from the git

* Removing ./idea/ and ./vscode/ from the git

* --tune_fdr now lists the default value in the help

* the FDR threshold is now listed when using --tune

* Adjusting FDR threshold formatting

* Added in a flag to disable summary statistics

* Added in an annotation coverage summary statistic as a default behavior (disabled with --disable_summary)

Author: DanielOlson

.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/

.idea/.gitignore

@@ -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,