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Removed deprecated getDbsnpFile. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5221 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-02-08 21:12:15 +00:00
parent a8ab5a5fb9
commit 4d1cca95bb
6 changed files with 11 additions and 19 deletions
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12
java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java
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@ -64,18 +64,6 @@ public class PipelineProject {
this.referenceFile = referenceFile;
}
/** use genotype dbsnp file */
@Deprecated
public File getDbsnpFile() {
return getGenotypeDbsnp();
}
/** use genotype dbsnp file */
@Deprecated
public void setDbsnpFile(File dbsnpFile) {
this.setGenotypeDbsnp(dbsnpFile);
}
public File getGenotypeDbsnp() {
return genotypeDbsnp;
}

8
java/test/org/broadinstitute/sting/datasources/pipeline/PipelineUnitTest.java
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@ -39,7 +39,8 @@ public class PipelineUnitTest {
pipeline.getProject().setName("PRJ_NAME");
pipeline.getProject().setReferenceFile(new File("my.fasta"));
pipeline.getProject().setDbsnpFile(new File("my.dbsnp"));
pipeline.getProject().setGenotypeDbsnp(new File("my.vcf"));
pipeline.getProject().setEvalDbsnp(new File("my.dbsnp"));
pipeline.getProject().getTags().put("testProjectTag", "project value here");
PipelineSample sample = new PipelineSample();
@ -57,7 +58,10 @@ public class PipelineUnitTest {
Assert.assertEquals(pipelineLoad.getProject().getName(), pipeline.getProject().getName());
Assert.assertEquals(pipeline.getProject().getReferenceFile(), pipelineLoad.getProject().getReferenceFile());
Assert.assertEquals(pipeline.getProject().getIntervalList(), pipelineLoad.getProject().getIntervalList());
Assert.assertEquals(pipeline.getProject().getDbsnpFile(), pipelineLoad.getProject().getDbsnpFile());
Assert.assertEquals(pipeline.getProject().getGenotypeDbsnp(), pipelineLoad.getProject().getGenotypeDbsnp());
Assert.assertEquals(pipeline.getProject().getGenotypeDbsnpType(), pipelineLoad.getProject().getGenotypeDbsnpType());
Assert.assertEquals(pipeline.getProject().getEvalDbsnp(), pipelineLoad.getProject().getEvalDbsnp());
Assert.assertEquals(pipeline.getProject().getEvalDbsnpType(), pipelineLoad.getProject().getEvalDbsnpType());
Assert.assertEquals(pipelineLoad.getProject().getTags().size(), pipeline.getProject().getTags().size());
for (Map.Entry<String, String> entry : pipeline.getProject().getTags().entrySet())

2
scala/qscript/oneoffs/kshakir/UGMemoryTests.scala
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@ -40,7 +40,7 @@ class UGMemoryTests extends QScript {
snps.jarFile = qscript.gatkJar
snps.reference_sequence = pipeline.getProject.getReferenceFile
snps.intervals = List(pipeline.getProject.getIntervalList)
snps.DBSNP = pipeline.getProject.getDbsnpFile
snps.rodBind :+= new RodBind("dbsnp", pipeline.getProject.getGenotypeDbsnpType, pipeline.getProject.getGenotypeDbsnp)
snps.downsample_to_coverage = Some(qscript.downsampling_coverage)
snps.annotation ++= List("AlleleBalance")
snps.group :+= "Standard"

2
scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala
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@ -27,7 +27,7 @@ class BamProcessing(attribs: Pipeline, gatkJar: File, fixMatesJar: File) {
trait StandardCommandLineGATK extends CommandLineGATK {
this.reference_sequence = library.attributes.getProject.getReferenceFile
this.intervals = List(library.attributes.getProject.getIntervalList)
this.DBSNP = library.attributes.getProject.getDbsnpFile
this.rodBind :+= new RodBind("dbsnp", library.attributes.getProject.getGenotypeDbsnpType, library.attributes.getProject.getGenotypeDbsnp)
this.memoryLimit = Some(2)
this.jarFile = library.gatkJar
}

4
scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
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@ -22,7 +22,7 @@ class VariantCalling(attribs: Pipeline,gatkJar: File) {
trait StandardCommandLineGATK extends CommandLineGATK {
this.reference_sequence = vc.attributes.getProject.getReferenceFile
this.intervals = List(vc.attributes.getProject.getIntervalList)
this.DBSNP = vc.attributes.getProject.getDbsnpFile
this.rodBind :+= new RodBind("dbsnp", vc.attributes.getProject.getGenotypeDbsnpType, vc.attributes.getProject.getGenotypeDbsnp)
// set global memory limit on the low side. Additional input bams will affect it.
this.memoryLimit = Some(2)
this.jarFile = vc.gatkJar
@ -36,7 +36,7 @@ class VariantCalling(attribs: Pipeline,gatkJar: File) {
def addTrait[T <: CommandLineGATK](c : T) : T = {
c.reference_sequence = vc.attributes.getProject.getReferenceFile
c.intervals = List(vc.attributes.getProject.getIntervalList)
c.DBSNP = vc.attributes.getProject.getDbsnpFile
c.rodBind :+= new RodBind("dbsnp", vc.attributes.getProject.getGenotypeDbsnpType, vc.attributes.getProject.getGenotypeDbsnp)
// set global memory limit on the low side. Additional input bams will affect it.
c.memoryLimit = Some(2)
c.jarFile = vc.gatkJar

2
scala/src/org/broadinstitute/sting/queue/util/PipelineUtils.scala
View File

@ -73,7 +73,7 @@ object PipelineUtils{
pipeProject.setName(name)
pipeProject.setReferenceFile(ref)
pipeProject.setIntervalList(ivals)
pipeProject.setDbsnpFile(dbsnp)
pipeProject.setGenotypeDbsnp(dbsnp)
newPipeline.setProject(pipeProject)
newPipeline.setSamples(pipeSamples)