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Updated paths to new bams. 

Metrics of the new bams have changed slightly but should still fall within test toleraneces.
Will reset metrics in a later checkin after confirming changes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5125 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-01-29 10:55:26 +00:00
parent afeb0f63c3
commit b0a3c70f90
1 changed files with 20 additions and 9 deletions
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29
scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala
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@ -11,6 +11,18 @@ import org.broadinstitute.sting.queue.pipeline._
class FullCallingPipelineTest { class FullCallingPipelineTest {
def datasets = List(k1gChr20Dataset, k1gExomeDataset) def datasets = List(k1gChr20Dataset, k1gExomeDataset)
val k1gBams = List(
new K1gBam("C474", "NA19651", 1),
new K1gBam("C474", "NA19655", 1),
new K1gBam("C474", "NA19669", 1),
new K1gBam("C454", "NA19834", 1),
new K1gBam("C460", "HG01440", 1),
new K1gBam("C456", "NA12342", 1),
new K1gBam("C456", "NA12748", 1),
new K1gBam("C474", "NA19649", 1),
new K1gBam("C474", "NA19652", 1),
new K1gBam("C474", "NA19654", 1))
// In fullCallingPipeline.q VariantEval is always compared against 129. // In fullCallingPipeline.q VariantEval is always compared against 129.
// Until the newvarianteval is finalized which will allow java import of the prior results, // Until the newvarianteval is finalized which will allow java import of the prior results,
// we re-run VariantEval to validate the run, and replicate that behavior here. // we re-run VariantEval to validate the run, and replicate that behavior here.
@ -46,6 +58,8 @@ class FullCallingPipelineTest {
dataset dataset
} }
class K1gBam(val squidId: String, val sampleId: String, val version: Int)
def newK1gDataset(projectName: String) = { def newK1gDataset(projectName: String) = {
val project = new PipelineProject val project = new PipelineProject
project.setName(projectName) project.setName(projectName)
@ -53,16 +67,13 @@ class FullCallingPipelineTest {
project.setDbsnpFile(new File(BaseTest.b37dbSNP132)) project.setDbsnpFile(new File(BaseTest.b37dbSNP132))
project.setRefseqTable(new File(BaseTest.hg19Refseq)) project.setRefseqTable(new File(BaseTest.hg19Refseq))
val squid = "C426"
val ids = List(
"NA19651","NA19655","NA19669","NA19834","HG01440",
"NA12342","NA12748","NA19649","NA19652","NA19654")
var samples = List.empty[PipelineSample] var samples = List.empty[PipelineSample]
for (id <- ids) { for (k1gBam <- k1gBams) {
val sample = new PipelineSample val sample = new PipelineSample
sample.setId(projectName + "_" + id) sample.setId(projectName + "_" + k1gBam.sampleId)
sample.setBamFiles(Map("recalibrated" -> new File("/seq/picard_aggregation/%1$s/%2$s/v6/%2$s.bam".format(squid,id)))) sample.setBamFiles(Map("recalibrated" -> new File("/seq/picard_aggregation/%1$s/%2$s/v%3$s/%2$s.bam"
sample.setTags(Map("SQUIDProject" -> squid, "CollaboratorID" -> id)) .format(k1gBam.squidId, k1gBam.sampleId, k1gBam.version))))
sample.setTags(Map("SQUIDProject" -> k1gBam.squidId, "CollaboratorID" -> k1gBam.sampleId))
samples :+= sample samples :+= sample
} }
@ -80,7 +91,7 @@ class FullCallingPipelineTest {
final def convertDatasets: Array[Array[AnyRef]] = final def convertDatasets: Array[Array[AnyRef]] =
datasets.map(dataset => Array(dataset.asInstanceOf[AnyRef])).toArray datasets.map(dataset => Array(dataset.asInstanceOf[AnyRef])).toArray
@Test(dataProvider="datasets", enabled=false) @Test(dataProvider="datasets")
def testFullCallingPipeline(dataset: PipelineDataset) = { def testFullCallingPipeline(dataset: PipelineDataset) = {
val projectName = dataset.pipeline.getProject.getName val projectName = dataset.pipeline.getProject.getName
val testName = "fullCallingPipeline-" + projectName val testName = "fullCallingPipeline-" + projectName