From 89544c209c0344fbf9aca9f283daa0fa428f9398 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 28 Sep 2011 11:19:17 -0400
Subject: [PATCH 2/4] Fixing contracts

changed return type to Pair, changing contracts accordingly.
---
 .../java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 5fa410922..14ebbaa6f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -825,7 +825,7 @@ public class ReadUtils {
      * @return the read coordinate corresponding to the requested reference coordinate. (see warning!)
      */
     @Requires({"refCoord >= read.getUnclippedStart()", "refCoord <= read.getUnclippedEnd()"})
-    @Ensures({"result >= 0", "result < read.getReadLength()"})
+    @Ensures({"result.getFirst() >= 0", "result.getFirst() < read.getReadLength()"})
     public static Pair<Integer, Boolean> getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) {
         int readBases = 0;
         int refBases = 0;

From 1e32281a15dc773ec41aaf5a17342d37f181fb43 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 28 Sep 2011 11:31:20 -0400
Subject: [PATCH 3/4] Fix to not show -null when missing short name argument

---
 .../utils/help/GenericDocumentationHandler.java    | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
index 7ea77a939..b100b3e1b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -432,11 +432,17 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
      * Returns a Pair of (main, synonym) names for argument with fullName s1 and
      * shortName s2.  The main is selected to be the longest of the two, provided
      * it doesn't exceed MAX_DISPLAY_NAME, in which case the shorter is taken.
-     * @param s1
-     * @param s2
-     * @return
+     *
+     * @param s1 the short argument name without -, or null if not provided
+     * @param s2 the long argument name without --, or null if not provided
+     * @return A pair of fully qualified names (with - or --) for the argument.  The first
+     *  element is the primary display name while the second (potentially null) is a
+     *  synonymous name.
      */
     Pair<String, String> displayNames(String s1, String s2) {
+        s1 = s1 == null ? null : "-" + s1;
+        s2 = s2 == null ? null : "--" + s2;
+
         if ( s1 == null ) return new Pair<String, String>(s2, null);
         if ( s2 == null ) return new Pair<String, String>(s1, null);
 
@@ -510,7 +516,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
      */
     protected Map<String, Object> docForArgument(FieldDoc fieldDoc, ArgumentSource source, ArgumentDefinition def) {
         Map<String, Object> root = new HashMap<String, Object>();
-        Pair<String, String> names = displayNames("-" + def.shortName, "--" + def.fullName);
+        Pair<String, String> names = displayNames(def.shortName, def.fullName);
 
         root.put("name", names.getFirst() );
 

From a5006831d7b52748a77aa86512979d220c9540a7 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 28 Sep 2011 11:35:52 -0400
Subject: [PATCH 4/4] Shows "" not empty space when default string value is ""

---
 .../sting/utils/help/GenericDocumentationHandler.java    | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
index b100b3e1b..20f9eccd3 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -325,11 +325,14 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
                 return Arrays.toString((Object[])value);
             else
                 throw new RuntimeException("Unexpected array type in prettyPrintValue.  Value was " + value + " type is " + type);
-        } else if ( RodBinding.class.isAssignableFrom(value.getClass() ) )
+        } else if ( RodBinding.class.isAssignableFrom(value.getClass() ) ) {
             // annoying special case to handle the UnBound() constructor
             return "none";
-
-        return value.toString();
+        } else if ( value instanceof String ) {
+            return value.equals("") ? "\"\"" : value;
+        } else {
+            return value.toString();
+        }
     }
 
     /**