From 5933b5a10649ac252fbb638fc456eaea3b5ad668 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 16 Apr 2015 10:12:48 +0200
Subject: [PATCH] Refactor bed to interval
---
.../pipelines/bammetrics/BamMetrics.scala | 98 +++++++++++--------
.../bedtools/BedtoolsIntersect.scala | 4 +-
.../extensions/picard/BedToIntervalList.scala | 4 +-
3 files changed, 60 insertions(+), 46 deletions(-)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index 09f5a937b..574adb382 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -23,7 +23,7 @@ import java.io.File
import nl.lumc.sasc.biopet.tools.{ BedToInterval, BiopetFlagstat }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
-import nl.lumc.sasc.biopet.extensions.picard.{ CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics }
+import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
class BamMetrics(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
@@ -32,14 +32,11 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
@Input(doc = "Bam File", shortName = "BAM", required = true)
var inputBam: File = _
- @Input(doc = "Bed tracks targets", shortName = "target", required = false)
- var bedFiles: List[File] = Nil
+ /** Bed files for region of interests */
+ var roiBedFiles: List[File] = config("regions_of_interest", Nil)
- @Input(doc = "Bed tracks bait", shortName = "bait", required = false)
- var baitBedFile: File = _
-
- @Argument(doc = "", required = false)
- var wholeGenome = false
+ /** Bed of amplicon that is used */
+ var ampliconBedFile: Option[File] = config("amplicon_bed")
/** return location of summary file */
def summaryFile = (sampleId, libId) match {
@@ -56,12 +53,6 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
/** executed before script */
def init() {
- if (config.contains("target_bed")) {
- for (file <- config("target_bed").asList) {
- bedFiles +:= new File(file.toString)
- }
- }
- if (baitBedFile == null && config.contains("target_bait")) baitBedFile = config("target_bait")
}
/** Script to add jobs */
@@ -82,31 +73,60 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
add(collectAlignmentSummaryMetrics)
addSummarizable(collectAlignmentSummaryMetrics, "alignment_metrics")
- val baitIntervalFile = if (baitBedFile != null) new File(outputDir, baitBedFile.getName.stripSuffix(".bed") + ".interval") else null
- if (baitIntervalFile != null)
- add(BedToInterval(this, baitBedFile, inputBam, outputDir), true)
+ case class Intervals(bed: File, intervals: File)
+
+ // Create temp jobs to convert bed files to intervals lists
+ val roiIntervals = roiBedFiles.map(roiBedFile => {
+ val roiIntervals = swapExt(outputDir, roiBedFile, ".bed", ".intervals")
+ val ampBedToInterval = BedToIntervalList(this, roiBedFile, roiIntervals)
+ ampBedToInterval.isIntermediate = true
+ add(ampBedToInterval)
+ Intervals(roiBedFile, roiIntervals)
+ })
+
+ // Metrics that require a amplicon bed file
+ val ampIntervals = ampliconBedFile.collect {
+ case ampliconBedFile => {
+ val ampIntervals = swapExt(outputDir, ampliconBedFile, ".bed", ".intervals")
+ val ampBedToInterval = BedToIntervalList(this, ampliconBedFile, ampIntervals)
+ ampBedToInterval.isIntermediate = true
+ add(ampBedToInterval)
+
+ val chsMetrics = CalculateHsMetrics(this, inputBam,
+ List(ampIntervals), ampIntervals :: roiIntervals.map(_.intervals), outputDir)
+ add(chsMetrics)
- for (bedFile <- bedFiles) {
+ //TODO: target pcr metrics
+
+ Intervals(ampliconBedFile, ampIntervals)
+ }
+ }
+
+ // Create stats and coverage plot for each bed/interval file
+ for (intervals <- roiIntervals ++ ampIntervals) {
//TODO: Add target jobs to summary
- val targetDir = new File(outputDir, bedFile.getName.stripSuffix(".bed"))
- val targetFile = new File(targetDir, bedFile.getName.stripSuffix(".bed") + ".interval")
- val targetInterval = BedToInterval(this, bedFile, inputBam, targetFile)
- add(targetInterval, true)
- add(CalculateHsMetrics(this, inputBam, if (baitIntervalFile != null) baitIntervalFile
- else targetInterval.output, targetInterval.output, targetDir))
-
- val strictOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam")
- add(BedtoolsIntersect(this, inputBam, bedFile, strictOutputBam, minOverlap = config("strictintersectoverlap", default = 1.0)), true)
- add(SamtoolsFlagstat(this, strictOutputBam, targetDir))
- add(BiopetFlagstat(this, strictOutputBam, targetDir))
-
- val looseOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam")
- add(BedtoolsIntersect(this, inputBam, bedFile, looseOutputBam, minOverlap = config("looseintersectoverlap", default = 0.01)), true)
- add(SamtoolsFlagstat(this, looseOutputBam, targetDir))
- add(BiopetFlagstat(this, looseOutputBam, targetDir))
+ val targetDir = new File(outputDir, intervals.bed.getName.stripSuffix(".bed"))
+
+ val biStrict = BedtoolsIntersect(this, inputBam, intervals.bed,
+ output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam"),
+ minOverlap = config("strictintersectoverlap", default = 1.0))
+ biStrict.isIntermediate = true
+ add(biStrict)
+ add(SamtoolsFlagstat(this, biStrict.output, targetDir))
+ add(BiopetFlagstat(this, biStrict.output, targetDir))
+
+ val biLoose = BedtoolsIntersect(this, inputBam, intervals.bed,
+ output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam"),
+ minOverlap = config("looseintersectoverlap", default = 0.01))
+ biLoose.isIntermediate = true
+ add(biLoose)
+ add(SamtoolsFlagstat(this, biLoose.output, targetDir))
+ add(BiopetFlagstat(this, biLoose.output, targetDir))
val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
- add(BedtoolsCoverage(this, inputBam, bedFile, coverageFile, true), true)
+
+ //FIXME:should use piping
+ add(BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, true), true)
add(CoverageStats(this, coverageFile, targetDir))
}
@@ -115,13 +135,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
}
object BamMetrics extends PipelineCommand {
- /**
- * Make default implementation of BamMetrics
- * @param root
- * @param bamFile
- * @param outputDir
- * @return
- */
+ /** Make default implementation of BamMetrics */
def apply(root: Configurable, bamFile: File, outputDir: File): BamMetrics = {
val bamMetrics = new BamMetrics(root)
bamMetrics.inputBam = bamFile
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
index 2381f6f1d..0d18eb240 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
@@ -55,12 +55,12 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
object BedtoolsIntersect {
/** Returns default bedtools intersect */
def apply(root: Configurable, input: File, intersect: File, output: File,
- minOverlap: Double = 0, count: Boolean = false): BedtoolsIntersect = {
+ minOverlap: Option[Double] = None, count: Boolean = false): BedtoolsIntersect = {
val bedtoolsIntersect = new BedtoolsIntersect(root)
bedtoolsIntersect.input = input
bedtoolsIntersect.intersectFile = intersect
bedtoolsIntersect.output = output
- if (minOverlap > 0) bedtoolsIntersect.minOverlap = Option(minOverlap)
+ bedtoolsIntersect.minOverlap = minOverlap
bedtoolsIntersect.count = count
return bedtoolsIntersect
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
index 2faef859c..68954ec4f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvan_thof on 4/15/15.
@@ -27,7 +27,7 @@ class BedToIntervalList(val root: Configurable) extends Picard {
}
object BedToIntervalList {
- def apply(root:Configurable, input:File, output:File): BedToIntervalList = {
+ def apply(root: Configurable, input: File, output: File): BedToIntervalList = {
val bi = new BedToIntervalList(root)
bi.input = input
bi.output = output
--
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