Commit 273091b4 authored by akaljuvee's avatar akaljuvee

filling the samples table

parent 7d179c4e
...@@ -20,9 +20,14 @@ import nl.lumc.sasc.biopet.extensions.Pysvtools ...@@ -20,9 +20,14 @@ import nl.lumc.sasc.biopet.extensions.Pysvtools
import nl.lumc.sasc.biopet.extensions.tools.VcfStatsForSv import nl.lumc.sasc.biopet.extensions.tools.VcfStatsForSv
import nl.lumc.sasc.biopet.pipelines.shiva.svcallers._ import nl.lumc.sasc.biopet.pipelines.shiva.svcallers._
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging } import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.QScript
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scala.concurrent.ExecutionContext.Implicits.global
/** /**
* Common trait for ShivaVariantcalling * Common trait for ShivaVariantcalling
* *
...@@ -43,7 +48,16 @@ class ShivaSvCalling(val parent: Configurable) extends QScript with SummaryQScri ...@@ -43,7 +48,16 @@ class ShivaSvCalling(val parent: Configurable) extends QScript with SummaryQScri
/** Executed before script */ /** Executed before script */
def init(): Unit = { def init(): Unit = {
if (inputBamsArg.nonEmpty) inputBams = BamUtils.sampleBamMap(inputBamsArg) if (inputBamsArg.nonEmpty) {
inputBams = BamUtils.sampleBamMap(inputBamsArg)
val db = SummaryDb.openSqliteSummary(summaryDbFile)
for (sampleName <- inputBams.keys) {
if (Await.result(db.getSampleId(summaryRunId, sampleName), Duration.Inf).isEmpty) {
db.createSample(sampleName, summaryRunId)
}
}
}
outputMergedVCF = new File(outputDir, "allsamples.merged.vcf") outputMergedVCF = new File(outputDir, "allsamples.merged.vcf")
} }
......
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