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Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable

This commit is contained in:
Guillermo del Angel 2012-08-01 10:55:37 -04:00
parent 01265f78e6 05bf6e3726
commit 84cd23f891
6 changed files with 43 additions and 8 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"

4
public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
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@ -41,7 +41,7 @@ class DataProcessingPipelineTest {
" -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf",
" -test ",
" -p " + projectName).mkString
spec.fileMD5s += testOut -> "0f0b32e94640a8d548b4c1134ad4c075"
spec.fileMD5s += testOut -> "021db3a52ee40d9193895213aaa05dd5"
PipelineTest.executeTest(spec)
}
@ -60,7 +60,7 @@ class DataProcessingPipelineTest {
" -bwa /home/unix/carneiro/bin/bwa",
" -bwape ",
" -p " + projectName).mkString
spec.fileMD5s += testOut -> "6b4f13d22b45d7d617ee959fdc278ed2"
spec.fileMD5s += testOut -> "94e32ee974aa15d05ee7d3e99f2f8c8f"
PipelineTest.executeTest(spec)
}

2
public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
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@ -40,7 +40,7 @@ class PacbioProcessingPipelineTest {
" -blasr ",
" -test ",
" -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf").mkString
spec.fileMD5s += testOut -> "2f2026882a2850bb14a858524158d5a8"
spec.fileMD5s += testOut -> "8b5f9e8e1ba5bd686e3084eaeea23889"
PipelineTest.executeTest(spec)
}
}