From 5164aa32b8dff52bd545cd5e35bdc9bdfa2b6c78 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 29 Jan 2016 14:45:54 +0100
Subject: [PATCH] Adding samplingSize to BamUtils - estimateInsertSize
---
.../nl/lumc/sasc/biopet/utils/BamUtils.scala | 8 +++----
.../pipelines/shiva/svcallers/Pindel.scala | 21 ++++---------------
2 files changed, 8 insertions(+), 21 deletions(-)
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
index 7b7e2ee02..56e42f1ce 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
@@ -67,10 +67,10 @@ object BamUtils {
* @param bamFile bamfile to estimate avg insertsize from
* @return
*/
- def sampleBamInsertSize(bamFile: File): Int = {
+ def sampleBamInsertSize(bamFile: File, samplingSize: Int = 100000): Int = {
val inputSam: SamReader = SamReaderFactory.makeDefault.open(bamFile)
val baminsertsizes = inputSam.getFileHeader.getSequenceDictionary.getSequences.par.map({
- contig => BamUtils.contigInsertSize(bamFile, contig.getSequenceName, 1, contig.getSequenceLength)
+ contig => BamUtils.contigInsertSize(bamFile, contig.getSequenceName, 1, contig.getSequenceLength, samplingSize)
}).toList
val counts = baminsertsizes.flatMap(x => x)
val sum = counts.reduceLeft(_ + _)
@@ -84,8 +84,8 @@ object BamUtils {
* @param bamFiles input bam files
* @return
*/
- def sampleBamInsertSize(bamFiles: List[File]): immutable.ParMap[File, Int] = bamFiles.par.map { bamFile =>
- bamFile -> sampleBamInsertSize(bamFile)
+ def sampleBamsInsertSize(bamFiles: List[File], samplingSize: Int = 100000): immutable.ParMap[File, Int] = bamFiles.par.map { bamFile =>
+ bamFile -> sampleBamInsertSize(bamFile, samplingSize)
}.toMap
}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
index a452c0fee..44393b3fb 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
@@ -15,11 +15,9 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
-import java.io.File
import java.text.SimpleDateFormat
import java.util.Calendar
-import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.extensions.pindel._
import nl.lumc.sasc.biopet.utils.BamUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -31,9 +29,10 @@ class Pindel(val root: Configurable) extends SvCaller {
def this() = this(null)
/** Default pipeline config */
- override def defaults = Map("pindelvcf" -> Map(
- "rdate" -> new SimpleDateFormat("yyyyMMdd").format(Calendar.getInstance().getTime())
- ))
+ override def defaults = Map(
+ "pindelvcf" -> Map(
+ "rdate" -> new SimpleDateFormat("yyyyMMdd").format(Calendar.getInstance().getTime())
+ ))
def biopetScript() {
for ((sample, bamFile) <- inputBams) {
@@ -44,8 +43,6 @@ class Pindel(val root: Configurable) extends SvCaller {
cfg.input = bamFile
val insertSize: Int = BamUtils.sampleBamInsertSize(bamFile)
-
- // FIXME: get the real insert size of the bam (from bammetrics?)
cfg.insertsize = insertSize
cfg.sampleName = sample
cfg.output = config_file
@@ -67,14 +64,4 @@ class Pindel(val root: Configurable) extends SvCaller {
}
}
-}
-
-object Pindel extends PipelineCommand {
- def apply(root: Configurable, input: File, reference: File, runDir: String): Pindel = {
- val pindel = new Pindel(root)
- // run the following for activating the pipeline steps
- pindel.init()
- pindel.biopetScript()
- pindel
- }
}
\ No newline at end of file
--
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