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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2012-08-01 09:50:31 -04:00
parent 0528337467 56f8afab97
commit 38e5419b11
4 changed files with 40 additions and 5 deletions
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35
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -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
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@ -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));
}
}

2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -347,6 +347,7 @@ class DataProcessingPipeline extends QScript {
this.knownSites ++= qscript.dbSNP
this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
this.input_file :+= inBam
this.disable_indel_quals = true
this.out = outRecalFile
if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform
if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString)
@ -359,7 +360,6 @@ class DataProcessingPipeline extends QScript {
case class recal (inBam: File, inRecalFile: File, outBam: File) extends PrintReads with CommandLineGATKArgs {
this.input_file :+= inBam
this.BQSR = inRecalFile
this.disable_indel_quals = true
this.baq = CalculationMode.CALCULATE_AS_NECESSARY
this.out = outBam
if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString)

2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
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@ -166,6 +166,7 @@ class PacbioProcessingPipeline extends QScript {
this.knownSites :+= dbSNP
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
this.input_file :+= inBam
this.disable_indel_quals = true
this.out = outRecalFile
this.analysisName = queueLogDir + outRecalFile + ".covariates"
this.jobName = queueLogDir + outRecalFile + ".covariates"
@ -178,7 +179,6 @@ class PacbioProcessingPipeline extends QScript {
this.input_file :+= inBam
this.BQSR = inRecalFile
this.out = outBam
this.disable_indel_quals = true
this.isIntermediate = false
this.analysisName = queueLogDir + outBam + ".recalibration"
this.jobName = queueLogDir + outBam + ".recalibration"