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Commit 99f13260 authored by Peter van 't Hof's avatar Peter van 't Hof
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Added flagstats to bamstats

parent 498358c5
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Showing with 307 additions and 253 deletions
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
View file @ 99f13260
......@@ -18,12 +18,13 @@ import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommandFunction
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.tools.flagstat
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BiopetFlagstat(val root: Configurable) extends ToolCommandFunction with Summarizable {
def toolObject = nl.lumc.sasc.biopet.tools.BiopetFlagstat
def toolObject = flagstat.BiopetFlagstat
@Input(doc = "Input bam", shortName = "input", required = true)
var input: File = _
......
biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
View file @ 99f13260
......@@ -14,6 +14,7 @@
*/
package nl.lumc.sasc.biopet
import nl.lumc.sasc.biopet.tools.flagstat.BiopetFlagstat
import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
object BiopetToolsExecutable extends BiopetExecutable {
......@@ -25,7 +26,7 @@ object BiopetToolsExecutable extends BiopetExecutable {
nl.lumc.sasc.biopet.tools.BaseCounter,
nl.lumc.sasc.biopet.tools.BastyGenerateFasta,
nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
nl.lumc.sasc.biopet.tools.BiopetFlagstat,
BiopetFlagstat,
nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam,
nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
nl.lumc.sasc.biopet.tools.FastqSplitter,
......
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala deleted 100644 → 0
View file @ 498358c5
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
import nl.lumc.sasc.biopet.utils.{ ToolCommand, ConfigUtils }
import scala.collection.JavaConversions._
import scala.collection.mutable
object BiopetFlagstat extends ToolCommand {
case class Args(inputFile: File = null,
outputFile: Option[File] = None,
summaryFile: Option[File] = None,
region: Option[String] = None) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
c.copy(inputFile = x)
} text "input bam file"
opt[File]('o', "outputFile") valueName "<file>" action { (x, c) =>
c.copy(outputFile = Some(x))
} text "output file"
opt[File]('s', "summaryFile") valueName "<file>" action { (x, c) =>
c.copy(summaryFile = Some(x))
} text "summary output file"
opt[String]('r', "region") valueName "<chr:start-stop>" action { (x, c) =>
c.copy(region = Some(x))
}
}
/**
* @param args the command line arguments
*/
def main(args: Array[String]): Unit = {
val argsParser = new OptParser
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
val inputSam = SamReaderFactory.makeDefault.open(commandArgs.inputFile)
val iterSam = if (commandArgs.region.isEmpty) inputSam.iterator else {
val regionRegex = """(.*):(.*)-(.*)""".r
commandArgs.region.get match {
case regionRegex(chr, start, stop) => inputSam.query(chr, start.toInt, stop.toInt, false)
case _ => sys.error("Region wrong format")
}
}
val flagstatCollector = new FlagstatCollector
flagstatCollector.loadDefaultFunctions()
val m = 10
val max = 60
for (t <- 0 to (max / m))
flagstatCollector.addFunction("MAPQ>" + (t * m), record => record.getMappingQuality > (t * m))
flagstatCollector.addFunction("First normal, second read inverted (paired end orientation)", record => {
if (record.getReadPairedFlag &&
record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag != record.getMateNegativeStrandFlag &&
((record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
else false
})
flagstatCollector.addFunction("First normal, second read normal", record => {
if (record.getReadPairedFlag &&
record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag == record.getMateNegativeStrandFlag &&
((record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
else false
})
flagstatCollector.addFunction("First inverted, second read inverted", record => {
if (record.getReadPairedFlag &&
record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag == record.getMateNegativeStrandFlag &&
((record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
else false
})
flagstatCollector.addFunction("First inverted, second read normal", record => {
if (record.getReadPairedFlag &&
record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag != record.getMateNegativeStrandFlag &&
((record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
else false
})
flagstatCollector.addFunction("Mate in same strand", record => record.getReadPairedFlag && record.getReadNegativeStrandFlag && record.getMateNegativeStrandFlag &&
record.getReferenceIndex == record.getMateReferenceIndex)
flagstatCollector.addFunction("Mate on other chr", record => record.getReadPairedFlag && record.getReferenceIndex != record.getMateReferenceIndex)
logger.info("Start reading file: " + commandArgs.inputFile)
for (record <- iterSam) {
if (flagstatCollector.readsCount % 1e6 == 0 && flagstatCollector.readsCount > 0)
logger.info("Reads prosessed: " + flagstatCollector.readsCount)
flagstatCollector.loadRecord(record)
}
commandArgs.summaryFile.foreach {
case file =>
val writer = new PrintWriter(file)
writer.println(flagstatCollector.summary)
writer.close()
}
commandArgs.outputFile match {
case Some(file) => {
val writer = new PrintWriter(file)
writer.println(flagstatCollector.report)
writer.close()
}
case _ => println(flagstatCollector.report)
}
}
class FlagstatCollector {
private var functionCount = 0
var readsCount = 0
private val names: mutable.Map[Int, String] = mutable.Map()
private var functions: Array[SAMRecord => Boolean] = Array()
private var totalCounts: Array[Long] = Array()
private var crossCounts = Array.ofDim[Long](1, 1)
def loadDefaultFunctions() {
addFunction("All", record => true)
addFunction("Mapped", record => !record.getReadUnmappedFlag)
addFunction("Duplicates", record => record.getDuplicateReadFlag)
addFunction("FirstOfPair", record => if (record.getReadPairedFlag) record.getFirstOfPairFlag else false)
addFunction("SecondOfPair", record => if (record.getReadPairedFlag) record.getSecondOfPairFlag else false)
addFunction("ReadNegativeStrand", record => record.getReadNegativeStrandFlag)
addFunction("NotPrimaryAlignment", record => record.getNotPrimaryAlignmentFlag)
addFunction("ReadPaired", record => record.getReadPairedFlag)
addFunction("ProperPair", record => if (record.getReadPairedFlag) record.getProperPairFlag else false)
addFunction("MateNegativeStrand", record => if (record.getReadPairedFlag) record.getMateNegativeStrandFlag else false)
addFunction("MateUnmapped", record => if (record.getReadPairedFlag) record.getMateUnmappedFlag else false)
addFunction("ReadFailsVendorQualityCheck", record => record.getReadFailsVendorQualityCheckFlag)
addFunction("SupplementaryAlignment", record => record.getSupplementaryAlignmentFlag)
addFunction("SecondaryOrSupplementary", record => record.isSecondaryOrSupplementary)
}
def loadRecord(record: SAMRecord) {
readsCount += 1
val values: Array[Boolean] = new Array(names.size)
for (t <- 0 until names.size) {
values(t) = functions(t)(record)
if (values(t)) {
totalCounts(t) += 1
}
}
for (t <- 0 until names.size) {
for (t2 <- 0 until names.size) {
if (values(t) && values(t2)) {
crossCounts(t)(t2) += 1
}
}
}
}
def addFunction(name: String, function: SAMRecord => Boolean) {
functionCount += 1
crossCounts = Array.ofDim[Long](functionCount, functionCount)
totalCounts = new Array[Long](functionCount)
val temp = new Array[SAMRecord => Boolean](functionCount)
for (t <- 0 until (temp.length - 1)) temp(t) = functions(t)
functions = temp
val index = functionCount - 1
names += (index -> name)
functions(index) = function
totalCounts(index) = 0
}
def report: String = {
val buffer = new StringBuilder
buffer.append("Number\tTotal Flags\tFraction\tName\n")
for (t <- 0 until names.size) {
val precentage = (totalCounts(t).toFloat / readsCount) * 100
buffer.append("#" + (t + 1) + "\t" + totalCounts(t) + "\t" + f"$precentage%.4f" + "%\t" + names(t) + "\n")
}
buffer.append("\n")
buffer.append(crossReport() + "\n")
buffer.append(crossReport(fraction = true) + "\n")
buffer.toString()
}
def summary: String = {
val map = (for (t <- 0 until names.size) yield {
names(t) -> totalCounts(t)
}).toMap ++ Map("Singletons" -> crossCounts(names.find(_._2 == "Mapped").map(_._1).getOrElse(-1))(names.find(_._2 == "MateUnmapped").map(_._1).getOrElse(-1))
)
ConfigUtils.mapToJson(map).spaces4
}
def crossReport(fraction: Boolean = false): String = {
val buffer = new StringBuilder
for (t <- 0 until names.size) // Header for table
buffer.append("\t#" + (t + 1))
buffer.append("\n")
for (t <- 0 until names.size) {
buffer.append("#" + (t + 1) + "\t")
for (t2 <- 0 until names.size) {
val reads = crossCounts(t)(t2)
if (fraction) {
val precentage = (reads.toFloat / totalCounts(t).toFloat) * 100
buffer.append(f"$precentage%.4f" + "%")
} else buffer.append(reads)
if (t2 == names.size - 1) buffer.append("\n")
else buffer.append("\t")
}
}
buffer.toString()
}
} // End of class
}
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
View file @ 99f13260
......@@ -114,7 +114,7 @@ object BamStats extends ToolCommand {
.grouped((region.length.toDouble / threadBinSize).ceil.toInt)
.map(scatters => Future { processThread(scatters, bamFile) })
val stats = waitOnFutures(scattersFutures.toList, Some(region.chr))
val contigDir = new File(outputDir, "contigs" + File.separator + region.chr)
val contigDir = new File(outputDir, "contigs" + File.separator + region.chr)
contigDir.mkdirs()
stats.writeStatsToFiles(contigDir)
stats
......@@ -166,6 +166,7 @@ object BamStats extends ToolCommand {
// Read based stats
if (samRecord.getAlignmentStart > threadStart && samRecord.getAlignmentStart <= threadEnd) {
totalStats.flagstat.loadRecord(samRecord)
totalStats.totalReads += 1
if (samRecord.isSecondaryOrSupplementary) totalStats.secondary += 1
if (samRecord.getReadUnmappedFlag) totalStats.unmapped += 1
......@@ -202,16 +203,18 @@ object BamStats extends ToolCommand {
/**
* This method will only count the unmapped fragments
*
* @param bamFile Input bamfile
*
* @param bamFile Input bamfile
* @return Output stats
*/
def processUnmappedReads(bamFile: File): Stats = {
val stats = Stats()
val samReader = SamReaderFactory.makeDefault().open(bamFile)
var size = samReader.queryUnmapped().size
stats.totalReads += size
stats.unmapped += size
for (samRecord <- samReader.queryUnmapped()) {
stats.flagstat.loadRecord(samRecord)
stats.totalReads += 1
stats.unmapped += 1
}
samReader.close()
stats
}
......
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
View file @ 99f13260
......@@ -2,12 +2,15 @@ package nl.lumc.sasc.biopet.tools.bamstats
import java.io.File
import nl.lumc.sasc.biopet.tools.flagstat.FlagstatCollector
/**
* Created by pjvanthof on 05/07/16.
*/
case class Stats(var totalReads: Long = 0L,
var unmapped: Long = 0L,
var secondary: Long = 0L,
flagstat: FlagstatCollector = new FlagstatCollector(),
mappingQualityHistogram: Histogram[Int] = new Histogram[Int](),
insertSizeHistogram: Histogram[Int] = new Histogram[Int](),
clippingHistogram: Histogram[Int] = new Histogram[Int](),
......@@ -16,10 +19,14 @@ case class Stats(var totalReads: Long = 0L,
_5_ClippingHistogram: Histogram[Int] = new Histogram[Int](),
_3_ClippingHistogram: Histogram[Int] = new Histogram[Int]()) {
flagstat.loadDefaultFunctions()
flagstat.loadAditionalFunctions(1, 0)
/** This will add an other [[Stats]] inside `this` */
def +=(other: Stats): Stats = {
this.totalReads += other.totalReads
this.unmapped += other.unmapped
this.flagstat += other.flagstat
this.mappingQualityHistogram += other.mappingQualityHistogram
this.insertSizeHistogram += other.insertSizeHistogram
this.clippingHistogram += other.clippingHistogram
......@@ -31,6 +38,8 @@ case class Stats(var totalReads: Long = 0L,
}
def writeStatsToFiles(outputDir: File): Unit = {
this.flagstat.writeReportToFile(new File(outputDir, "flagstats"))
this.flagstat.writeSummaryTofile(new File(outputDir, "flagstats.summary.json"))
this.mappingQualityHistogram.writeToTsv(new File(outputDir, "mapping_quality.tsv"))
this.insertSizeHistogram.writeToTsv(new File(outputDir, "insert_size.tsv"))
this.clippingHistogram.writeToTsv(new File(outputDir, "clipping.tsv"))
......
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala 0 → 100644
View file @ 99f13260
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.tools.flagstat
import java.io.{ File, PrintWriter }
import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, ToolCommand }
import scala.collection.JavaConversions._
import scala.collection.mutable
object BiopetFlagstat extends ToolCommand {
case class Args(inputFile: File = null,
outputFile: Option[File] = None,
summaryFile: Option[File] = None,
region: Option[String] = None) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
c.copy(inputFile = x)
} text "input bam file"
opt[File]('o', "outputFile") valueName "<file>" action { (x, c) =>
c.copy(outputFile = Some(x))
} text "output file"
opt[File]('s', "summaryFile") valueName "<file>" action { (x, c) =>
c.copy(summaryFile = Some(x))
} text "summary output file"
opt[String]('r', "region") valueName "<chr:start-stop>" action { (x, c) =>
c.copy(region = Some(x))
}
}
/**
* @param args the command line arguments
*/
def main(args: Array[String]): Unit = {
val argsParser = new OptParser
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
val inputSam = SamReaderFactory.makeDefault.open(commandArgs.inputFile)
val iterSam = if (commandArgs.region.isEmpty) inputSam.iterator else {
val regionRegex = """(.*):(.*)-(.*)""".r
commandArgs.region.get match {
case regionRegex(chr, start, stop) => inputSam.query(chr, start.toInt, stop.toInt, false)
case _ => sys.error("Region wrong format")
}
}
val flagstatCollector = new FlagstatCollector
flagstatCollector.loadDefaultFunctions()
flagstatCollector.loadAditionalFunctions()
logger.info("Start reading file: " + commandArgs.inputFile)
for (record <- iterSam) {
if (flagstatCollector.readsCount % 1e6 == 0 && flagstatCollector.readsCount > 0)
logger.info("Reads prosessed: " + flagstatCollector.readsCount)
flagstatCollector.loadRecord(record)
}
commandArgs.summaryFile.foreach(file => flagstatCollector.writeSummaryTofile(file))
commandArgs.outputFile match {
case Some(file) => flagstatCollector.writeReportToFile(file)
case _ => println(flagstatCollector.report)
}
}
}
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala 0 → 100644
View file @ 99f13260
package nl.lumc.sasc.biopet.tools.flagstat
import java.io.{ File, PrintWriter }
import htsjdk.samtools.SAMRecord
import nl.lumc.sasc.biopet.utils.ConfigUtils
import scala.collection.mutable
/**
* Created by pjvan_thof on 21-7-16.
*/
class FlagstatCollector {
protected[FlagstatCollector] var functionCount = 0
var readsCount = 0
protected[FlagstatCollector] val names: mutable.Map[Int, String] = mutable.Map()
protected[FlagstatCollector] var functions: Array[SAMRecord => Boolean] = Array()
protected[FlagstatCollector] var totalCounts: Array[Long] = Array()
protected[FlagstatCollector] var crossCounts = Array.ofDim[Long](1, 1)
def loadDefaultFunctions() {
addFunction("All", record => true)
addFunction("Mapped", record => !record.getReadUnmappedFlag)
addFunction("Duplicates", record => record.getDuplicateReadFlag)
addFunction("FirstOfPair", record => if (record.getReadPairedFlag) record.getFirstOfPairFlag else false)
addFunction("SecondOfPair", record => if (record.getReadPairedFlag) record.getSecondOfPairFlag else false)
addFunction("ReadNegativeStrand", record => record.getReadNegativeStrandFlag)
addFunction("NotPrimaryAlignment", record => record.getNotPrimaryAlignmentFlag)
addFunction("ReadPaired", record => record.getReadPairedFlag)
addFunction("ProperPair", record => if (record.getReadPairedFlag) record.getProperPairFlag else false)
addFunction("MateNegativeStrand", record => if (record.getReadPairedFlag) record.getMateNegativeStrandFlag else false)
addFunction("MateUnmapped", record => if (record.getReadPairedFlag) record.getMateUnmappedFlag else false)
addFunction("ReadFailsVendorQualityCheck", record => record.getReadFailsVendorQualityCheckFlag)
addFunction("SupplementaryAlignment", record => record.getSupplementaryAlignmentFlag)
addFunction("SecondaryOrSupplementary", record => record.isSecondaryOrSupplementary)
}
def loadAditionalFunctions(m: Int = 10, max: Int = 60): Unit = {
for (t <- 0 to (max / m))
this.addFunction("MAPQ>" + (t * m), record => record.getMappingQuality > (t * m))
this.addFunction("First normal, second read inverted (paired end orientation)", record => {
if (record.getReadPairedFlag &&
record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag != record.getMateNegativeStrandFlag &&
((record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
else false
})
this.addFunction("First normal, second read normal", record => {
if (record.getReadPairedFlag &&
record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag == record.getMateNegativeStrandFlag &&
((record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
else false
})
this.addFunction("First inverted, second read inverted", record => {
if (record.getReadPairedFlag &&
record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag == record.getMateNegativeStrandFlag &&
((record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
else false
})
this.addFunction("First inverted, second read normal", record => {
if (record.getReadPairedFlag &&
record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag != record.getMateNegativeStrandFlag &&
((record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
(record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
else false
})
this.addFunction("Mate in same strand", record => record.getReadPairedFlag && record.getReadNegativeStrandFlag && record.getMateNegativeStrandFlag &&
record.getReferenceIndex == record.getMateReferenceIndex)
this.addFunction("Mate on other chr", record => record.getReadPairedFlag && record.getReferenceIndex != record.getMateReferenceIndex)
}
def loadRecord(record: SAMRecord) {
readsCount += 1
val values: Array[Boolean] = new Array(names.size)
for (t <- 0 until names.size) {
values(t) = functions(t)(record)
if (values(t)) {
totalCounts(t) += 1
}
}
for (t <- 0 until names.size) {
for (t2 <- 0 until names.size) {
if (values(t) && values(t2)) {
crossCounts(t)(t2) += 1
}
}
}
}
def addFunction(name: String, function: SAMRecord => Boolean) {
functionCount += 1
crossCounts = Array.ofDim[Long](functionCount, functionCount)
totalCounts = new Array[Long](functionCount)