From f1599432771af45d80bbbbfbb99fd5b5890d043e Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Fri, 16 Oct 2015 11:23:24 +0200
Subject: [PATCH] added tabix to bcftools output
---
.../lumc/sasc/biopet/extensions/Tabix.scala | 26 +++++++++++++++----
.../shiva/ShivaVariantcallingTrait.scala | 3 ++-
2 files changed, 23 insertions(+), 6 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
index 4a80600c5..d8f36a194 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
@@ -35,10 +35,9 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
@Output(doc = "Output (for region query)", required = false)
var outputQuery: File = null
- @Output(doc = "Output (for indexing)", required = false) // NOTE: it's a def since we can't change the index name ~ it's always input_name + .tbi
- lazy val outputIndex: File = {
- require(input != null, "Input must be defined")
- new File(input.toString + ".tbi")
+ def outputIndex: File = {
+ require(input != null, "Input should be defined")
+ new File(input.getAbsolutePath + ".tbi")
}
@Argument(doc = "Regions to query", required = false)
@@ -70,7 +69,8 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
p match {
case Some(fmt) =>
require(validFormats.contains(fmt), "-p flag must be one of " + validFormats.mkString(", "))
- case None => ;
+ outputFiles :+= outputIndex
+ case None =>
}
}
@@ -96,3 +96,19 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
else baseCommand
}
}
+
+object Tabix {
+ def apply(root: Configurable, input: File) = {
+ val tabix = new Tabix(root)
+ tabix.input = input
+ tabix.p = tabix.input.getName match {
+ case s if s.endsWith(".vcf.gz") => Some("vcf")
+ case s if s.endsWith(".bed.gz") => Some("bed")
+ case s if s.endsWith(".sam.gz") => Some("sam")
+ case s if s.endsWith(".gff.gz") => Some("gff")
+ case s if s.endsWith(".psltbl.gz") => Some("psltbl")
+ case _ => throw new IllegalArgumentException("Unknown file type")
+ }
+ tabix
+ }
+}
\ No newline at end of file
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
index 985d75879..365d4e638 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
@@ -163,7 +163,6 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
val mp = new SamtoolsMpileup(qscript)
mp.input = inputBams
mp.u = true
- //TODO: proper piping should be implemented
mp.reference = referenceFasta()
val bt = new BcftoolsCall(qscript)
@@ -172,6 +171,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
bt.c = true
add(mp | bt > outputFile)
+ add(Tabix(qscript, outputFile))
}
}
@@ -197,6 +197,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
bt.output = new File(outputDir, inputBam.getName + ".vcf.gz")
add(mp | bt)
+ add(Tabix(qscript, bt.output))
bt.output
}
--
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