Removed deprecated getDbsnpFile.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5221 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java

@@ -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;
     }

java/test/org/broadinstitute/sting/datasources/pipeline/PipelineUnitTest.java

@@ -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())

scala/qscript/oneoffs/kshakir/UGMemoryTests.scala

@@ -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"

scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala

@@ -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
   }

scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala

@@ -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

scala/src/org/broadinstitute/sting/queue/util/PipelineUtils.scala

@@ -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)