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Disabled the help system's printout of cmdline options when GATK errors out. Now the user has to explicitly ask for it using -h.

This commit is contained in:
Geraldine Van der Auwera 2013-08-16 12:09:09 -04:00
parent a21d5252c8
commit 9bb0aac7bf
1 changed files with 19 additions and 11 deletions
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30
public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
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@ -246,7 +246,7 @@ public abstract class CommandLineProgram {
}
}
catch (ArgumentException e) {
clp.parser.printHelp(clp.getApplicationDetails());
//clp.parser.printHelp(clp.getApplicationDetails());
// Rethrow the exception to exit with an error.
throw e;
}
@ -370,8 +370,8 @@ public abstract class CommandLineProgram {
errorPrintf("------------------------------------------------------------------------------------------%n");
errorPrintf("A GATK RUNTIME ERROR has occurred (version %s):%n", CommandLineGATK.getVersionNumber());
errorPrintf("%n");
errorPrintf("Please check the documentation guide to see if this is a known problem%n");
errorPrintf("If not, please post the error, with stack trace, to the GATK forum%n");
errorPrintf("This might be a bug. Please check the documentation guide to see if this is a known problem.%n");
errorPrintf("If not, please post the error message, with stack trace, to the GATK forum.%n");
printDocumentationReference();
if ( msg == null ) // some exceptions don't have detailed messages
msg = "Code exception (see stack trace for error itself)";
@ -387,12 +387,17 @@ public abstract class CommandLineProgram {
errorPrintf("------------------------------------------------------------------------------------------%n");
errorPrintf("A USER ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber());
errorPrintf("The invalid arguments or inputs must be corrected before the GATK can proceed%n");
errorPrintf("Please do not post this error to the GATK forum%n");
errorPrintf("%n");
errorPrintf("See the documentation (rerun with -h) for this tool to view allowable command-line arguments.%n");
errorPrintf("This means that one or more arguments or inputs in your command are incorrect.%n");
errorPrintf("The error message below tells you what is the problem.%n");
errorPrintf("%n");
errorPrintf("If the problem is an invalid argument, please check the online documentation guide%n");
errorPrintf("(or rerun your command with --help) to view allowable command-line arguments for this tool.%n");
errorPrintf("%n");
printDocumentationReference();
errorPrintf("%n");
errorPrintf("Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.%n");
errorPrintf("%n");
errorPrintf("MESSAGE: %s%n", e.getMessage().trim());
errorPrintf("------------------------------------------------------------------------------------------%n");
System.exit(1);
@ -404,14 +409,17 @@ public abstract class CommandLineProgram {
errorPrintf("------------------------------------------------------------------------------------------%n");
errorPrintf("A BAM ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber());
errorPrintf("The invalid inputs must be corrected before the GATK can proceed%n");
errorPrintf("Please do not post this error to the GATK forum until you have followed the instructions below%n");
errorPrintf("%n");
errorPrintf("Please make sure that your BAM file is well-formed by running Picard's validator on it%n");
errorPrintf("(see http://picard.sourceforge.net/command-line-overview.shtml#ValidateSamFile for details)%n");
errorPrintf("Also, please ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'%n");
errorPrintf("This means that there is something wrong with the BAM file(s) you provided.%n");
errorPrintf("The error message below tells you what is the problem.%n");
errorPrintf("%n");
printDocumentationReference();
errorPrintf("%n");
errorPrintf("Please do NOT post this error to the GATK forum until you have followed these instructions:%n");
errorPrintf("- Make sure that your BAM file is well-formed by running Picard's validator on it%n");
errorPrintf("(see http://picard.sourceforge.net/command-line-overview.shtml#ValidateSamFile for details)%n");
errorPrintf("- Ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'%n");
errorPrintf("%n");
errorPrintf("MESSAGE: %s%n", t.getMessage().trim());
errorPrintf("------------------------------------------------------------------------------------------%n");
System.exit(1);