zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Requested by Geraldine: adding a utility to register deprecated walkers (and the major version of the first release since they were removed) so that the User Error printed out for e.g. CountCovariates now states: Walker CountCovariates is no longer available in the GATK; it has been deprecated since version 2.0.

This commit is contained in:
Eric Banks 2012-08-01 09:50:00 -04:00
parent 7cf4b63d76
commit 56f8afab97
2 changed files with 38 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

35
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -274,6 +274,38 @@ public class GenomeAnalysisEngine {
//return result;
}
// TODO -- Let's move this to a utility class in unstable - but which one?
// **************************************************************************************
// * Handle Deprecated Walkers *
// **************************************************************************************
// Mapping from walker name to major version number where the walker first disappeared
private static Map<String, String> deprecatedGATKWalkers = new HashMap<String, String>();
static {
deprecatedGATKWalkers.put("CountCovariates", "2.0");
deprecatedGATKWalkers.put("TableRecalibration", "2.0");
}
/**
* Utility method to check whether a given walker has been deprecated in a previous GATK release
*
* @param walkerName the walker class name (not the full package) to check
*/
public static boolean isDeprecatedWalker(final String walkerName) {
return deprecatedGATKWalkers.containsKey(walkerName);
}
/**
* Utility method to check whether a given walker has been deprecated in a previous GATK release
*
* @param walkerName the walker class name (not the full package) to check
*/
public static String getDeprecatedMajorVersionNumber(final String walkerName) {
return deprecatedGATKWalkers.get(walkerName);
}
// **************************************************************************************
/**
* Retrieves an instance of the walker based on the walker name.
*
@ -287,6 +319,9 @@ public class GenomeAnalysisEngine {
if ( isGATKLite() && GATKLiteUtils.isAvailableOnlyInFullGATK(walkerName) ) {
e = new UserException.NotSupportedInGATKLite("the " + walkerName + " walker is available only in the full version of the GATK");
}
else if ( isDeprecatedWalker(walkerName) ) {
e = new UserException.DeprecatedWalker(walkerName, getDeprecatedMajorVersionNumber(walkerName));
}
throw e;
}
}

6
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -316,9 +316,9 @@ public class UserException extends ReviewedStingException {
public static class MissingWalker extends UserException {
public MissingWalker(String walkerName, String message) {
super(String.format("Walker %s is not available: %s", walkerName, message));
public static class DeprecatedWalker extends UserException {
public DeprecatedWalker(String walkerName, String version) {
super(String.format("Walker %s is no longer available in the GATK; it has been deprecated since version %s", walkerName, version));
}
}