From def3530d24e6bf63607b5bcef40ae7120a9f11fb Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 18 Aug 2015 16:25:01 +0200
Subject: [PATCH] Template for new tool
---
.../sasc/biopet/tools/RegionAfCount.scala | 62 +++++++++++++++++++
1 file changed, 62 insertions(+)
create mode 100644 public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
new file mode 100644
index 000000000..1fe29f166
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
@@ -0,0 +1,62 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.tools
+
+import java.io.{InputStream, File}
+
+import htsjdk.samtools.util.Interval
+import htsjdk.samtools.{QueryInterval, SAMRecord, SamReader, SamReaderFactory}
+import htsjdk.tribble.AbstractFeatureReader._
+import htsjdk.tribble.TabixFeatureReader
+import htsjdk.tribble.bed.{SimpleBEDFeature, BEDCodec, FullBEDFeature}
+import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
+import htsjdk.variant.variantcontext.{VariantContext, VariantContextBuilder}
+import htsjdk.variant.vcf.{VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine}
+import nl.lumc.sasc.biopet.core.ToolCommand
+
+import scala.collection.JavaConversions._
+import scala.collection.JavaConverters._
+import scala.collection.mutable
+
+object RegionAfCount extends ToolCommand {
+ case class Args(bedFile: File = null,
+ outputFile: File = null,
+ vcfFiles: List[File] = Nil) extends AbstractArgs
+
+ class OptParser extends AbstractOptParser {
+ opt[File]('b', "bedFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+ c.copy(bedFile = x)
+ }
+ opt[File]('o', "outputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+ c.copy(outputFile = x)
+ }
+ opt[File]('v', "vcfFile") unbounded () minOccurs 1 action { (x, c) =>
+ c.copy(vcfFiles = x :: c.vcfFiles)
+ }
+ }
+
+ def main(args: Array[String]): Unit = {
+ val argsParser = new OptParser
+ val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+ //val bedReader = new TabixFeatureReader[BEDCodec, File](cmdArgs.bedFile.getAbsolutePath, new BEDCodec)
+
+ val bedIt = asScalaIteratorConverter(getFeatureReader(cmdArgs.bedFile.toPath.toString, new BEDCodec(), false).iterator).asScala
+ for ( bedRecord <- bedIt) {
+ bedRecord.getName()
+ }
+ }
+}
\ No newline at end of file
--
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