From 2e9fffdb1b0ee3c68c8afcd8a4610aae891b22bb Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Wed, 20 Jan 2016 15:00:57 +0100
Subject: [PATCH] PindelVCF wrapper
---
.../biopet/extensions/pindel/PindelVCF.scala | 90 +++++++++++++++++++
1 file changed, 90 insertions(+)
create mode 100644 public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
new file mode 100644
index 000000000..bcf16c8f1
--- /dev/null
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
@@ -0,0 +1,90 @@
+package nl.lumc.sasc.biopet.extensions.pindel
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ Version, Reference, BiopetCommandLineFunction }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by wyleung on 20-1-16.
+ */
+class PindelVCF(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
+ executable = config("exe", default = "pindel2vcf")
+
+ override def defaultCoreMemory = 2.0
+ override def defaultThreads = 1
+
+ def versionRegex = """Version:? (.*)""".r
+ override def versionExitcode = List(1)
+ def versionCommand = executable + " -h"
+
+ /**
+ * Required parameters
+ */
+ @Input
+ var reference: File = referenceFasta
+
+ @Output
+ var outputVCF: File = _
+
+ var referenceDate: String = config("reference_date")
+
+ override def beforeGraph: Unit = {
+ if (reference == null) reference = referenceFasta()
+ }
+
+ var pindelOutput: Option[File] = config("pindel_output")
+ var pindelOutputRoot: Option[File] = config("pindel_output_root")
+ var chromosome: Option[String] = config("chromosome")
+ var windowSize: Option[Int] = config("window_size")
+ var minCoverage: Option[Int] = config("min_coverage")
+ var hetCutoff: Option[Float] = config("het_cutoff")
+ var homCutoff: Option[Float] = config("hom_cutoff")
+ var minSize: Option[Int] = config("min_size")
+ var maxSize: Option[Int] = config("max_size")
+ var bothStrandSupported: Boolean = config("both_strand_supported", default = false)
+ var minSupportingSamples: Option[Int] = config("min_supporting_samples")
+ var minSupportingReads: Option[Int] = config("min_supporting_reads")
+ var maxSupportingReads: Option[Int] = config("max_supporting_reads")
+ var regionStart: Option[Int] = config("region_start")
+ var regionEnd: Option[Int] = config("region_end")
+ var maxInternalRepeats: Option[Int] = config("max_internal_repeats")
+ var compactOutLimit: Option[Int] = config("compact_output_limit")
+ var maxInternalRepeatLength: Option[Int] = config("max_internal_repeatlength")
+ var maxPostindelRepeats: Option[Int] = config("max_postindel_repeat")
+ var maxPostindelRepeatLength: Option[Int] = config("max_postindel_repeatlength")
+ var onlyBalancedSamples: Boolean = config("only_balanced_samples")
+ var somaticP: Boolean = config("somatic_p")
+ var minimumStrandSupport: Option[Int] = config("minimum_strand_support")
+ var gatkCompatible: Boolean = config("gatk_compatible")
+
+ def cmdLine = required(executable) +
+ required("--reference_name", referenceSpecies) +
+ required("--reference_date", referenceDate) +
+ optional("--pindel_output", pindelOutput) +
+ optional("--pindel_output_root", pindelOutputRoot) +
+ required("--vcf", outputVCF) +
+ optional("--chromosome", chromosome) +
+ optional("--window_size", windowSize) +
+ optional("--min_coverage", minCoverage) +
+ optional("--het_cutoff", hetCutoff) +
+ optional("--hom_cutoff", homCutoff) +
+ optional("--min_size", minSize) +
+ optional("--max_size", maxSize) +
+ conditional(bothStrandSupported, "--both_strands_supported") +
+ optional("--min_supporting_samples", minSupportingSamples) +
+ optional("--min_supporting_reads", minSupportingReads) +
+ optional("--max_supporting_reads", maxSupportingReads) +
+ optional("--region_start", regionStart) +
+ optional("--region_end", regionEnd) +
+ optional("--max_internal_repeats", maxInternalRepeats) +
+ optional("--compact_output_limit", compactOutLimit) +
+ optional("--max_internal_repeatlength", maxInternalRepeatLength) +
+ optional("--max_postindel_repeats", maxPostindelRepeats) +
+ optional("--max_postindel_repeatlength", maxPostindelRepeatLength) +
+ conditional(onlyBalancedSamples, "--only_balanced_samples") +
+ conditional(somaticP, "--somatic_p") +
+ optional("--minimum_strand_support", minimumStrandSupport) +
+ conditional(gatkCompatible, "--gatk_compatible")
+}
--
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