From 03df7987ee3b15018f0e939de56b536e647b633c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 20 Oct 2015 19:58:43 +0200
Subject: [PATCH] Added piping support to coverage script
---
.../lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index f6a6dc090..3e38aa9aa 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, PipelineCommand, SampleLibraryTag}
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
@@ -173,11 +173,12 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
//FIXME:should use piping
- add(BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, depth = true), isIntermediate = true)
+ val bedCov = BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, depth = true)
val covStats = CoverageStats(this, coverageFile, targetDir)
covStats.title = Some("Coverage for " + targetName)
covStats.subTitle = Some(".")
- add(covStats)
+ val pipe = new BiopetFifoPipe(this, bedCov :: covStats :: Nil)
+ add(pipe)
addSummarizable(covStats, targetName + "_cov_stats")
}
--
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