From c1da8cd5e7376b70d3d2d8b8735f2140b999727c Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 2 Nov 2011 11:26:34 -0400
Subject: [PATCH] Final version of bp-resolved locus scatter/gather

-- Minor refactoring to allow LocusScatterFunction to have maxIntervals be the original scatter count, rather than capping this by the interval count as Contig and Interval do
---
 .../gatk/ContigScatterFunction.scala          |  2 ++
 .../gatk/IntervalScatterFunction.scala        |  2 ++
 .../gatk/LocusScatterFunction.scala           | 23 ++++++++++---------
 3 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala
index d2b3006a9..2609c3607 100755
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala
@@ -35,6 +35,8 @@ class ContigScatterFunction extends GATKScatterFunction with InProcessFunction {
   // Include unmapped reads by default.
   this.includeUnmapped = true
 
+  override def scatterCount = if (intervalFilesExist) super.scatterCount min this.maxIntervals else super.scatterCount
+
   protected override def maxIntervals = {
     GATKScatterFunction.getGATKIntervals(this.referenceSequence, this.intervals).contigs.size
   }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
index f65d5ab29..40a6fc4b4 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
@@ -35,6 +35,8 @@ class IntervalScatterFunction extends GATKScatterFunction with InProcessFunction
   protected override def maxIntervals =
     GATKScatterFunction.getGATKIntervals(this.referenceSequence, this.intervals).locs.size
 
+  override def scatterCount = if (intervalFilesExist) super.scatterCount min this.maxIntervals else super.scatterCount
+
   def run() {
     val gi = GATKScatterFunction.getGATKIntervals(this.referenceSequence, this.intervals)
     val splits = IntervalUtils.splitFixedIntervals(gi.locs, this.scatterOutputFiles.size)
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala
index 366d23488..8f52b9b82 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala
@@ -24,20 +24,21 @@
 
 package org.broadinstitute.sting.queue.extensions.gatk
 
+import collection.JavaConversions._
 import org.broadinstitute.sting.utils.interval.IntervalUtils
 import org.broadinstitute.sting.queue.function.InProcessFunction
 
 /**
  * A scatter function that divides down to the locus level.
  */
-class LocusScatterFunction extends IntervalScatterFunction {
-}
-//
-//class LocusScatterFunction extends GATKScatterFunction with InProcessFunction {
-//  // todo -- max intervals is actually the original scatter count, not capped by interval size
-//  def run() {
-//    val gi = GATKScatterFunction.getGATKIntervals(this.referenceSequence, this.intervals)
-//    val splits = IntervalUtils.splitLocusIntervals(gi.locs, this.scatterOutputFiles.size)
-//    IntervalUtils.scatterFixedIntervals(gi.samFileHeader, splits, this.scatterOutputFiles)
-//  }
-//}
\ No newline at end of file
+//class LocusScatterFunction extends IntervalScatterFunction { }
+
+class LocusScatterFunction extends GATKScatterFunction with InProcessFunction {
+  protected override def maxIntervals = scatterCount
+
+  def run() {
+    val gi = GATKScatterFunction.getGATKIntervals(this.referenceSequence, this.intervals)
+    val splits = IntervalUtils.splitLocusIntervals(gi.locs, this.scatterOutputFiles.size)
+    IntervalUtils.scatterFixedIntervals(gi.samFileHeader, splits, this.scatterOutputFiles)
+  }
+}
\ No newline at end of file