From 53d2233faf790bf953e53ab67a616f3985551073 Mon Sep 17 00:00:00 2001
From: magicDGS <daniel.gomez.sanchez@hotmail.es>
Date: Thu, 28 Sep 2017 09:26:47 +0200
Subject: [PATCH 1/3] Add CommandLineProgram interface

---
 .../barclay/argparser/CommandLineProgram.java | 68 +++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java

diff --git a/src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java b/src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java
new file mode 100644
index 00000000..45f51848
--- /dev/null
+++ b/src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java
@@ -0,0 +1,68 @@
+package org.broadinstitute.barclay.argparser;
+
+/**
+ * Interface class to facilitate implementing command-line programs.
+ *
+ * <p>It should be considered as a marker interface to identify runnable Command Line Program
+ * classes in different toolkits, to aggregate them when looking for them. In addition, it includes
+ * the method {@link #instanceMain(String[])} to be call to parse the arguments and run the
+ * actual work.
+ *
+ * <p>Tool classes may want to extend this interface and {@link CommandLinePluginProvider} to
+ * include plugins in their command line.
+ *
+ * <p>Usage example:
+ *
+ * <ul>
+ *     <li>
+ *         Extend the class. Users may want to extend also {@link CommandLinePluginProvider} to
+ *         include plugins in the command line.
+ *     </li>
+ *     <li>
+ *         Mark the class with {@link CommandLineProgramProperties} to include information for the
+ *         tool. Users may consider to annotate with {@link BetaFeature} tools tat are in experimental
+ *         phase.
+ *     </li>
+ *     <li>
+ *         Include data members marked with {@link Argument}, {@link ArgumentCollection},
+ *         {@link PositionalArguments} or {@link TaggedArgument} to include in the command line.
+ *         This members could be also annotated with {@link Hidden} or {@link Advanced} to tweak
+ *         how they are display.
+ *     </li>
+ *     <li>
+ *         Implement {@link #instanceMain(String[])} to use {@link CommandLineArgumentParser} to
+ *         parse the arguments and use the data members to perform the work.
+ *     </li>
+ *     <<li>
+ *         In a Main class, look for all the classes implementing {@link CommandLineProgram} (e.g.,
+ *         using {@link ClassFinder}). Matching the class name with a provided String, the user can
+ *         select the tool to be run, and the Main class can call {@link #instanceMain(String[])}
+ *         with the provided arguments.
+ *     </li>
+ * </ul>
+ *
+ * <p>Note: Barclay does not use or enforce this class for any purpose.
+ *
+ * @author Daniel Gomez-Sanchez (magicDGS)
+ */
+public interface CommandLineProgram {
+
+    /**
+     * Implements the work to be done with the tool.
+     *
+     * <p>This method should implement:
+     *
+     * <ul>
+     *     <li>Command line parsing using {@link CommandLineParser}</li>
+     *     <li>Run the actual work of the tool using data members populated by the parser.</li>
+     *     <li>Return the result of the tool.</li>
+     * </ul>
+     *
+     * <p>Note: Most exceptions should be cached by the caller.
+     *
+     * @param argv arguments to pass to the {@link CommandLineParser}.
+     *
+     * @return result object after performing the work. May be {@code null}.
+     */
+    public Object instanceMain(final String[] argv);
+}

From 17849c54a306ba67c99b2b5ada52c8d1e59966a8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20G=C3=B3mez-S=C3=A1nchez?=
 <daniel.gomez.sanchez@hotmail.es>
Date: Fri, 29 Sep 2017 18:40:48 +0200
Subject: [PATCH 2/3] Fix typo

---
 .../broadinstitute/barclay/argparser/CommandLineProgram.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java b/src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java
index 45f51848..a126199d 100644
--- a/src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java
+++ b/src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java
@@ -58,7 +58,7 @@ public interface CommandLineProgram {
      *     <li>Return the result of the tool.</li>
      * </ul>
      *
-     * <p>Note: Most exceptions should be cached by the caller.
+     * <p>Note: Most exceptions should be caught by the caller.
      *
      * @param argv arguments to pass to the {@link CommandLineParser}.
      *

From 39716f25c1c08e86f53a0634eea5f4bae43fb472 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20G=C3=B3mez-S=C3=A1nchez?=
 <daniel.gomez.sanchez@hotmail.es>
Date: Mon, 2 Oct 2017 15:04:44 +0200
Subject: [PATCH 3/3] Fix typo

---
 .../broadinstitute/barclay/argparser/CommandLineProgram.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java b/src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java
index a126199d..b62017e6 100644
--- a/src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java
+++ b/src/main/java/org/broadinstitute/barclay/argparser/CommandLineProgram.java
@@ -20,7 +20,7 @@
  *     </li>
  *     <li>
  *         Mark the class with {@link CommandLineProgramProperties} to include information for the
- *         tool. Users may consider to annotate with {@link BetaFeature} tools tat are in experimental
+ *         tool. Users may consider to annotate with {@link BetaFeature} tools that are in experimental
  *         phase.
  *     </li>
  *     <li>