From 1df0bfa416f2e4ac397b6cbf7ed9c20601c2f93c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 21 Jul 2014 11:22:43 +0200
Subject: [PATCH] Added Alignment Metrics
---
.../CollectAlignmentSummaryMetrics.scala | 55 +++++++++++++++++++
1 file changed, 55 insertions(+)
create mode 100644 biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectAlignmentSummaryMetrics.scala
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectAlignmentSummaryMetrics.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectAlignmentSummaryMetrics.scala
new file mode 100644
index 000000000..beb427f35
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectAlignmentSummaryMetrics.scala
@@ -0,0 +1,55 @@
+package nl.lumc.sasc.biopet.function.picard
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
+
+class CollectAlignmentSummaryMetrics(val root:Configurable) extends Picard {
+ javaMainClass = "picard.analysis.CollectAlignmentSummaryMetrics"
+
+ @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
+ var input: File = _
+
+ @Argument(doc="MAX_INSERT_SIZE", required = false)
+ var maxInstertSize: Int = config("maxInstertSize", 100000)
+
+ @Argument(doc="ADAPTER_SEQUENCE", required = false)
+ var adapterSequence: List[String] = config("adapterSequence", Nil)
+
+ @Argument(doc="IS_BISULFITE_SEQUENCED", required = false)
+ var isBisulfiteSequenced: Boolean = config("isBisulfiteSequenced", false)
+
+ @Output(doc="The output file to write statistics to", required = true)
+ var output: File = _
+
+ @Argument(doc="Reference file", required = false)
+ var reference: File = config("reference", "")
+
+ @Argument(doc="ASSUME_SORTED", required = false)
+ var assumeSorted: Boolean = config("assumeSorted", false)
+
+ @Argument(doc="METRIC_ACCUMULATION_LEVEL", required=false)
+ var metricAccumulationLevel: List[String] = config("metricaccumulationlevel", List())
+
+ @Argument(doc="STOP_AFTER", required = false)
+ var stopAfter: Long = config("stopAfter", 0)
+
+ override def commandLine = super.commandLine +
+ required("INPUT=", input, spaceSeparated=false) +
+ required("OUTPUT=", output, spaceSeparated=false) +
+ optional("REFERENCE_SEQUENCE=", reference, spaceSeparated=false) +
+ repeat("METRIC_ACCUMULATION_LEVEL=", metricAccumulationLevel, spaceSeparated=false) +
+ required("MAX_INSERT_SIZE=", maxInstertSize, spaceSeparated=false) +
+ required("IS_BISULFITE_SEQUENCED=", isBisulfiteSequenced, spaceSeparated=false) +
+ optional("ASSUME_SORTED=", assumeSorted, spaceSeparated=false) +
+ optional("STOP_AFTER=", stopAfter, spaceSeparated=false)
+}
+
+object CollectAlignmentSummaryMetrics {
+ def apply(root:Configurable, input:File, outputDir:String) : CollectAlignmentSummaryMetrics = {
+ val collectAlignmentSummaryMetrics = new CollectAlignmentSummaryMetrics(root)
+ collectAlignmentSummaryMetrics.input = input
+ collectAlignmentSummaryMetrics.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".alignmentMetrics")
+ return collectAlignmentSummaryMetrics
+ }
+}
\ No newline at end of file
--
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