From 58c7b27ccc1469202f3a6642308eed370dbcdf9e Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 26 Apr 2011 00:12:41 +0000
Subject: [PATCH] Missing file from last checkin.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5688 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../queue/extensions/gatk/GATKIntervals.scala | 61 +++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100755 scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala

diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
new file mode 100755
index 000000000..577781de9
--- /dev/null
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
@@ -0,0 +1,61 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.queue.extensions.gatk
+
+import java.io.File
+import collection.JavaConversions._
+import org.broadinstitute.sting.utils.interval.IntervalUtils
+import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource
+import net.sf.samtools.SAMFileHeader
+import java.util.Collections
+import org.broadinstitute.sting.utils.GenomeLocParser
+
+case class GATKIntervals(reference: File, intervals: List[String]) {
+  private lazy val referenceDataSource = new ReferenceDataSource(reference)
+  private var splitsBySize = Map.empty[Int, java.util.List[java.lang.Integer]]
+
+  lazy val samFileHeader = {
+    val header = new SAMFileHeader
+    header.setSequenceDictionary(referenceDataSource.getReference.getSequenceDictionary)
+    header
+  }
+
+  lazy val locs = {
+    val parser = new GenomeLocParser(referenceDataSource.getReference)
+    val parsedLocs = IntervalUtils.parseIntervalArguments(parser, intervals, false)
+    Collections.sort(parsedLocs)
+    parsedLocs
+  }
+
+  lazy val contigs = locs.map(_.getContig).distinct
+
+  def getSplits(size: Int) = {
+    splitsBySize.getOrElse(size, {
+      val splits: java.util.List[java.lang.Integer] = IntervalUtils.splitFixedIntervals(locs, size)
+      splitsBySize += size -> splits
+      splits
+    })
+  }
+}