From 99b31701a60b5fec77c1f88e170f068149c57250 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 21 Jul 2016 15:46:07 +0200
Subject: [PATCH] Fixed number of bins
---
.../scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala | 5 +++--
.../shiva/variantcallers/HaploTypeCallerGvcfTest.scala | 4 ++--
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
index e40f3614a..530614d2f 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
@@ -109,9 +109,10 @@ object BamStats extends ToolCommand {
def processContig(region: BedRecord, bamFile: File, binSize: Int, threadBinSize: Int, outputDir: File): Stats = {
val scattersFutures = region
.scatter(binSize)
- .grouped((region.length.toDouble / threadBinSize).ceil.toInt)
+ .grouped((region.length.toDouble / binSize).ceil.toInt / (region.length.toDouble / threadBinSize).ceil.toInt)
.map(scatters => Future { processThread(scatters, bamFile) })
- val stats = waitOnFutures(scattersFutures.toList, Some(region.chr))
+ .toList
+ val stats = waitOnFutures(scattersFutures, Some(region.chr))
val contigDir = new File(outputDir, "contigs" + File.separator + region.chr)
contigDir.mkdirs()
stats.writeStatsToFiles(contigDir)
diff --git a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
index f07376157..f028be3ce 100644
--- a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
+++ b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
@@ -7,8 +7,8 @@ import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
/**
- * Created by Sander Bollen on 13-7-16.
- */
+ * Created by Sander Bollen on 13-7-16.
+ */
class HaploTypeCallerGvcfTest extends TestNGSuite with Matchers {
@Test
--
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