diff --git a/build.xml b/build.xml
index 9f162ec7b..6da364e26 100644
--- a/build.xml
+++ b/build.xml
@@ -1,97 +1,144 @@
- Compile and distribute the Sting toolkit
+ Compile and distribute the Sting toolkit
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diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
index 18ddde3b2..d171379bd 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
@@ -59,13 +59,14 @@ public class ArgumentParser {
// automatically generate the help statement
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp(100,
- "java -Xmx4096m -jar dist/GenomeAnalysisTK.jar",
- "",
- m_options,
- "",
- true);
+ "java -Xmx4096m -jar dist/GenomeAnalysisTK.jar",
+ "",
+ m_options,
+ "",
+ true);
}
+
/**
* addOptionalArg
*
@@ -77,6 +78,7 @@ public class ArgumentParser {
* @param fieldname the field to set when we've parsed this option
*/
public void addOptionalArg(String name, String letterform, String description, String fieldname) {
+
// we always want the help option to be available
Option opt = OptionBuilder.withLongOpt(name).withArgName(name)
.hasArg()
@@ -98,9 +100,15 @@ public class ArgumentParser {
* @param opt the option
*/
private void AddToOptionStorage(String name, String letterform, String fieldname, Option opt) {
+
// add to the option list
m_options.addOption(opt);
+ // first check to see if we've already added an option with the same name
+ if (m_option_names.contains(letterform)) {
+ throw new IllegalArgumentException(letterform + " was already added as an option");
+ }
+
// add the object with it's name to the storage location
try {
m_storageLocations.put(name, prog.getClass().getField(fieldname));
@@ -159,6 +167,7 @@ public class ArgumentParser {
}
+
/**
* addRequiredlArg
*
@@ -170,6 +179,7 @@ public class ArgumentParser {
* @param fieldname what field it should be stuck into on the calling class
*/
public void addRequiredlArgList(String name, String letterform, String description, String fieldname) {
+
// we always want the help option to be available
Option opt = OptionBuilder.isRequired()
.withLongOpt(name)
@@ -193,11 +203,22 @@ public class ArgumentParser {
* @param fieldname what field it should be stuck into on the calling class
*/
public void addOptionalFlag(String name, String letterform, String description, String fieldname) {
+
+ // if they've passed a non-Boolean as a object, beat them
+ try {
+ if (!(prog.getClass().getField(fieldname).getType() == Boolean.class)) {
+ throw new IllegalArgumentException("Fields to addOptionalFlag must be of type Boolean");
+ }
+ } catch (NoSuchFieldException e) {
+ throw new IllegalArgumentException("Fields to addOptionalFlag must exist!");
+ }
+
// we always want the help option to be available
Option opt = OptionBuilder.withLongOpt(name)
.withDescription(description)
.create(letterform);
+
// add it to the option
AddToOptionStorage(name, letterform, fieldname, opt);
@@ -215,6 +236,16 @@ public class ArgumentParser {
* @param fieldname what field it should be stuck into on the calling class
*/
public void addRequiredlFlag(String name, String letterform, String description, String fieldname) {
+
+ // if they've passed a non-Boolean as a object, beat them
+ try {
+ if (!(prog.getClass().getField(fieldname).getType() == Boolean.class)) {
+ throw new IllegalArgumentException("Fields to addRequiredlFlag must be of type Boolean");
+ }
+ } catch (NoSuchFieldException e) {
+ throw new IllegalArgumentException("Fields to addRequiredlFlag must exist!");
+ }
+
// we always want the help option to be available
Option opt = OptionBuilder.isRequired()
.withLongOpt(name)
@@ -231,15 +262,15 @@ public class ArgumentParser {
* This function is called to validate all the arguments to the program.
* If a required Arg isn't found, we generate the help message, and
* exit the program
- *
+ *
* @param args the command line arguments we recieved
*/
- public void processArgs(String[] args) {
+ public void processArgs(String[] args) throws ParseException {
CommandLineParser parser = new PosixParser();
try {
Collection