Commit 998687b1 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'fix-bamutils-insertsize' into 'develop'

BamUtils Insertsize estimation is more acurate by sampling from all over the contig.

Updated BamUtils to fix the insertsize estimation used in the PindelConfig tool.

See merge request !371
parents d7177565 26d14d83
......@@ -18,8 +18,10 @@ package nl.lumc.sasc.biopet.utils
import java.io.File
import htsjdk.samtools.{ SamReader, SamReaderFactory }
import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
import scala.collection.JavaConversions._
import scala.collection.mutable
import scala.collection.parallel.immutable
/**
......@@ -57,39 +59,76 @@ object BamUtils {
* @param end postion to stop scanning
* @return Int with insertsize for this contig
*/
def contigInsertSize(inputBam: File, contig: String, start: Int, end: Int, samplingSize: Int = 100000): Option[Int] = {
val inputSam: SamReader = SamReaderFactory.makeDefault.open(inputBam)
val samIterator = inputSam.query(contig, start, end, true)
val insertsizes: List[Int] = (for {
read <- samIterator.toStream.takeWhile(rec => {
val paired = rec.getReadPairedFlag && rec.getProperPairFlag
val bothMapped = if (paired) ((rec.getReadUnmappedFlag == false) && (rec.getMateUnmappedFlag == false)) else false
paired && bothMapped
}).take(samplingSize)
} yield {
read.getInferredInsertSize.asInstanceOf[Int].abs
})(collection.breakOut)
val cti = insertsizes.foldLeft((0.0, 0))((t, r) => (t._1 + r, t._2 + 1))
samIterator.close()
inputSam.close()
val ret = if (cti._2 == 0) None else Some((cti._1 / cti._2).toInt)
ret
def contigInsertSize(inputBam: File, contig: String, start: Int, end: Int,
samplingSize: Int = 10000,
binSize: Int = 1000000): Option[Int] = {
// create a bedList to devide the contig into multiple pieces
val insertSizesOnAllFragments = BedRecordList.fromList(Seq(BedRecord(contig, start, end)))
.scatter(binSize)
.allRecords.par.flatMap({
bedRecord =>
// for each scatter, open the bamfile for this specific region-query
val inputSam: SamReader = SamReaderFactory.makeDefault.open(inputBam)
val samIterator = inputSam.query(bedRecord.chr, bedRecord.start, bedRecord.end, true)
val counts: mutable.Map[Int, Int] = mutable.Map()
for (i <- 0 until samplingSize if samIterator.hasNext) {
val rec = samIterator.next()
val isPaired = rec.getReadPairedFlag
val minQ10 = rec.getMappingQuality >= 10
val pairOnSameContig = rec.getContig == rec.getMateReferenceName
if (isPaired && minQ10 && pairOnSameContig) {
val insertSize = rec.getInferredInsertSize.abs
counts(insertSize) = counts.getOrElse(insertSize, 0) + 1
}
}
counts.keys.size match {
case 1 => Some(counts.keys.head)
case 0 => None
case _ => {
Some(counts.foldLeft(0)((old, observation) => {
observation match {
case (insertSize: Int, observations: Int) => {
(old + (insertSize * observations)) / (observations + 1)
}
case _ => 0
}
}))
}
}
})
insertSizesOnAllFragments.size match {
case 1 => Some(insertSizesOnAllFragments.head)
case 0 => None
case _ => {
Some(
insertSizesOnAllFragments.foldLeft(0)((old, observation) => {
(old + observation) / 2
}))
}
}
}
/**
* Estimate the insertsize for one single bamfile and return the insertsize
*
* @param bamFile bamfile to estimate avg insertsize from
* @param bamFile bamfile to estimate average insertsize from
* @return
*/
def sampleBamInsertSize(bamFile: File, samplingSize: Int = 100000): Int = {
def sampleBamInsertSize(bamFile: File, samplingSize: Int = 10000, binSize: Int = 1000000): 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, samplingSize)
val bamInsertSizes = inputSam.getFileHeader.getSequenceDictionary.getSequences.par.map({
contig => BamUtils.contigInsertSize(bamFile, contig.getSequenceName, 1, contig.getSequenceLength, samplingSize, binSize)
}).toList
val counts = baminsertsizes.flatMap(x => x)
val counts = bamInsertSizes.flatMap(x => x)
// avoid division by zero
if (counts.size != 0) {
counts.sum / counts.size
} else {
......@@ -103,8 +142,8 @@ object BamUtils {
* @param bamFiles input bam files
* @return
*/
def sampleBamsInsertSize(bamFiles: List[File], samplingSize: Int = 100000): immutable.ParMap[File, Int] = bamFiles.par.map { bamFile =>
bamFile -> sampleBamInsertSize(bamFile, samplingSize)
def sampleBamsInsertSize(bamFiles: List[File], samplingSize: Int = 10000, binSize: Int = 1000000): immutable.ParMap[File, Int] = bamFiles.par.map { bamFile =>
bamFile -> sampleBamInsertSize(bamFile, samplingSize, binSize)
}.toMap
}
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