From b1c4e0314fd08f54236ca574a2a916ade87a59e9 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Mon, 4 Apr 2016 11:56:59 +0200
Subject: [PATCH] A bit refactoring on the variable names
---
.../scala/nl/lumc/sasc/biopet/utils/BamUtils.scala | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 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 26be068c0..0a3939c88 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
@@ -73,7 +73,9 @@ object BamUtils {
val insertsizes: List[Int] = (for {
read <- samIterator.toStream.takeWhile(rec => {
+ // TODO: This value is now hard-coded. I'm not sure whether this is the best practice on selecting reads with a minimum required quality.
val minQ10 = rec.getMappingQuality >= 10
+ // with properPairFlag we exclude readpairs that span multiple contigs.
val paired = rec.getReadPairedFlag && rec.getProperPairFlag
val bothMapped = if (paired) ((rec.getReadUnmappedFlag == false) && (rec.getMateUnmappedFlag == false)) else false
paired && bothMapped && minQ10
@@ -81,11 +83,11 @@ object BamUtils {
} yield {
read.getInferredInsertSize.asInstanceOf[Int].abs
})(collection.breakOut)
- val cti = insertsizes.foldLeft((0.0, 0))((t, r) => (t._1 + r, t._2 + 1))
+ val lociInsertSize = insertsizes.foldLeft((0.0, 0))((t, r) => (t._1 + r, t._2 + 1))
samIterator.close()
inputSam.close()
- if (cti._2 == 0) None else Some((cti._1 / cti._2).toInt)
+ if (lociInsertSize._2 == 0) None else Some((lociInsertSize._1 / lociInsertSize._2).toInt)
}).toList.flatten
val contigInsertSize = insertSizesOnAllFragments.foldLeft((0.0, 0))((t, r) => (t._1 + r, t._2 + 1))
@@ -95,16 +97,17 @@ object BamUtils {
/**
* 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 = 10000, binSize: Int = 1000000): Int = {
val inputSam: SamReader = SamReaderFactory.makeDefault.open(bamFile)
- val baminsertsizes = inputSam.getFileHeader.getSequenceDictionary.getSequences.par.map({
+ 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 {
--
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