Implemented and tested BWA alignment in the data processing pipeline.
caveat: Right now bwa only supports one read group, so if the original file had multiple @RG lines, only the first one will be kept. (working on a solution to this) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5931 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro
parent
c85a1d9210
commit
36db9bdcd5
|
|
@ -0,0 +1,497 @@
|
|||
package oneoffs.carneiro
|
||||
|
||||
import org.broadinstitute.sting.queue.extensions.gatk._
|
||||
import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction
|
||||
import org.broadinstitute.sting.queue.QScript
|
||||
import org.broadinstitute.sting.queue.function.ListWriterFunction
|
||||
|
||||
import net.sf.samtools.{SAMFileReader,SAMReadGroupRecord}
|
||||
|
||||
import scala.io.Source._
|
||||
import collection.JavaConversions._
|
||||
|
||||
|
||||
class dataProcessingV2 extends QScript {
|
||||
qscript =>
|
||||
|
||||
/****************************************************************************
|
||||
* Required Parameters (if default values are not good for you)
|
||||
****************************************************************************/
|
||||
|
||||
|
||||
@Input(doc="input BAM file - or list of BAM files", fullName="input", shortName="i", required=true)
|
||||
var input: File = _
|
||||
|
||||
@Input(doc="path to GenomeAnalysisTK.jar", fullName="path_to_gatk_jar", shortName="gatk", required=true)
|
||||
var GATKjar: File = _
|
||||
|
||||
@Input(doc="path to AnalyzeCovariates.jar", fullName="path_to_ac_jar", shortName="ac", required=true)
|
||||
var ACJar: File = _
|
||||
|
||||
@Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=true)
|
||||
var R: String = _
|
||||
|
||||
@Input(doc="path to Picard's MarkDuplicates.jar", fullName="path_to_dedup_jar", shortName="dedup", required=false)
|
||||
var dedupJar: File = new File("/seq/software/picard/current/bin/MarkDuplicates.jar")
|
||||
|
||||
@Input(doc="path to Picard's MergeSamFiles.jar", fullName="path_to_merge_jar", shortName="merge", required=false)
|
||||
var mergeBamJar: File = new File("/seq/software/picard/current/bin/MergeSamFiles.jar")
|
||||
|
||||
@Input(doc="path to Picard's ValidateSamFile.jar", fullName="path_to_validate_jar", shortName="validate", required=false)
|
||||
var validateSamJar: File = new File("/seq/software/picard/current/bin/ValidateSamFile.jar")
|
||||
|
||||
@Input(doc="Reference fasta file", fullName="reference", shortName="R", required=false)
|
||||
var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
|
||||
|
||||
|
||||
|
||||
/****************************************************************************
|
||||
* Optional Parameters
|
||||
****************************************************************************/
|
||||
|
||||
|
||||
@Input(doc="path to Picard's RevertSam.jar (if re-aligning a previously processed BAM file)", fullName="path_to_revert_jar", shortName="revert", required=false)
|
||||
var revertSamJar: File = _
|
||||
|
||||
@Input(doc="path to Picard's SortSam.jar (if re-aligning a previously processed BAM file)", fullName="path_to_sort_jar", shortName="sort", required=false)
|
||||
var sortSamJar: File = _
|
||||
|
||||
@Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
|
||||
var bwaPath: File = _
|
||||
|
||||
@Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=false)
|
||||
var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
|
||||
|
||||
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
|
||||
var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
|
||||
|
||||
@Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", fullName="project", shortName="p", required=false)
|
||||
var projectName: String = "project"
|
||||
|
||||
@Input(doc="Output path for the processed BAM files.", fullName="output_directory", shortName="outputDir", required=false)
|
||||
var outputDir: String = ""
|
||||
|
||||
@Input(doc="the -L interval string to be used by GATK - output bams at interval only", fullName="gatk_interval_string", shortName="L", required=false)
|
||||
var intervalString: String = ""
|
||||
|
||||
@Input(doc="an intervals file to be used by GATK - output bams at intervals only", fullName="gatk_interval_file", shortName="intervals", required=false)
|
||||
var intervals: File = _
|
||||
|
||||
@Input(doc="Perform cleaning on knowns only", fullName="knowns_only", shortName="knowns", required=false)
|
||||
var knownsOnly: Boolean = false
|
||||
|
||||
@Input(doc="Perform cleaning using Smith Waterman", fullName="use_smith_waterman", shortName="sw", required=false)
|
||||
var useSW: Boolean = false
|
||||
|
||||
@Input(doc="Decompose input BAM file and fully realign it using BWA and assume Single Ended reads", fullName="use_bwa_single_ended", shortName="bwase", required=false)
|
||||
var useBWAse: Boolean = false
|
||||
|
||||
@Input(doc="Decompose input BAM file and fully realign it using BWA and assume Pair Ended reads", fullName="use_bwa_pair_ended", shortName="bwape", required=false)
|
||||
var useBWApe: Boolean = false
|
||||
|
||||
|
||||
|
||||
/****************************************************************************
|
||||
* Global Variables
|
||||
****************************************************************************/
|
||||
|
||||
val queueLogDir: String = ".qlog/" // Gracefully hide Queue's output
|
||||
var nContigs: Int = 0 // Use the number of contigs for scatter gathering jobs
|
||||
|
||||
|
||||
|
||||
/****************************************************************************
|
||||
* Helper classes and methods
|
||||
****************************************************************************/
|
||||
|
||||
|
||||
// Utility function to check if there are multiple samples in a BAM file (currently we can't deal with that)
|
||||
def hasMultipleSamples(readGroups: java.util.List[SAMReadGroupRecord]): Boolean = {
|
||||
var sample: String = ""
|
||||
for (r <- readGroups) {
|
||||
if (sample.isEmpty)
|
||||
sample = r.getSample
|
||||
else if (sample != r.getSample)
|
||||
return true;
|
||||
}
|
||||
return false
|
||||
}
|
||||
|
||||
// Utility function to merge all bam files of similar samples. Generates on BAM file per sample.
|
||||
// It uses the sample information on the header of the input BAM files.
|
||||
//
|
||||
// Because the realignment only happens after these scripts are executed, in case you are using
|
||||
// bwa realignment, this function will operate over the original bam files and output over the
|
||||
// (to be realigned) bam files.
|
||||
def createSampleFiles(bamFiles: List[File], realignedBamFiles: List[File] = null): Map[String, File] = {
|
||||
assert(bamFiles.length == realignedBamFiles.length, "List of orignal files must have the same number of files than the list of realigned bam files: " + bamFiles.length + " / " + realignedBamFiles.length)
|
||||
|
||||
// Creating a table with SAMPLE information from each input BAM file
|
||||
val sampleTable = scala.collection.mutable.Map.empty[String, List[File]]
|
||||
val realignedIterator = realignedBamFiles.iterator
|
||||
for (bam <- bamFiles) {
|
||||
val rBam = realignedIterator.next // advance to next element in the realignedBam list so they're in sync.
|
||||
|
||||
val samReader = new SAMFileReader(bam)
|
||||
val header = samReader.getFileHeader
|
||||
val readGroups = header.getReadGroups
|
||||
|
||||
// only allow one sample per file. Bam files with multiple samples would require pre-processing of the file
|
||||
// with PrintReads to separate the samples. Tell user to do it himself!
|
||||
assert(!hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
|
||||
|
||||
// Fill out the sample table with the readgroups in this file
|
||||
for (rg <- readGroups) {
|
||||
val sample = rg.getSample
|
||||
if (!sampleTable.contains(sample))
|
||||
sampleTable(sample) = List(rBam)
|
||||
else if ( !sampleTable(sample).contains(rBam))
|
||||
sampleTable(sample) :+= rBam
|
||||
}
|
||||
}
|
||||
|
||||
// Creating one file for each sample in the dataset
|
||||
val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
|
||||
for ((sample, flist) <- sampleTable) {
|
||||
val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".bam")
|
||||
sampleBamFiles(sample) = sampleFileName
|
||||
add(joinBams(flist, sampleFileName))
|
||||
}
|
||||
return sampleBamFiles.toMap
|
||||
}
|
||||
|
||||
// Checks how many contigs are in the dataset. Uses the BAM file header information.
|
||||
def getNumberOfContigs(bamFile: File): Int = {
|
||||
val samReader = new SAMFileReader(new File(bamFile))
|
||||
return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
|
||||
}
|
||||
|
||||
// Rebuilds the Read Group string to give BWA
|
||||
def buildReadGroupString(samReader: SAMFileReader): List[String] = {
|
||||
val readGroups = samReader.getFileHeader.getReadGroups
|
||||
var l: List[String] = List()
|
||||
for (rg <- readGroups) {
|
||||
l :+= "@RG\t" +
|
||||
SAMReadGroupRecord.READ_GROUP_ID_TAG + ":" + rg.getReadGroupId + "\t" +
|
||||
SAMReadGroupRecord.PLATFORM_TAG + ":" + rg.getPlatformUnit + "\t" +
|
||||
SAMReadGroupRecord.LIBRARY_TAG + ":" + rg.getLibrary + "\t" +
|
||||
SAMReadGroupRecord.READ_GROUP_SAMPLE_TAG + ":" + rg.getSample + "\t" +
|
||||
SAMReadGroupRecord.SEQUENCING_CENTER_TAG + ":" + rg.getSequencingCenter
|
||||
}
|
||||
return l
|
||||
}
|
||||
|
||||
// Takes a list of processed BAM files and realign them using the BWA option requested (bwase or bwape).
|
||||
// Returns a list of realigned BAM files.
|
||||
def performAlignment(bams: List[File]): List[File] = {
|
||||
var realignedBams: List[File] = List()
|
||||
for (bam <- bams) {
|
||||
val saiFile1 = swapExt(bam, ".bam", "1.sai")
|
||||
val saiFile2 = swapExt(bam, ".bam", "2.sai")
|
||||
val realignedSamFile = swapExt(bam, ".bam", ".realigned.sam")
|
||||
val realignedBamFile = swapExt(bam, ".bam", ".realigned.bam")
|
||||
val readGroupString = buildReadGroupString(new SAMFileReader(bam))
|
||||
if (useBWAse) {
|
||||
add(bwa_aln_se(bam, saiFile1),
|
||||
bwa_sam_se(bam, saiFile1, realignedSamFile, readGroupString))
|
||||
}
|
||||
else {
|
||||
add(bwa_aln_pe(bam, saiFile1, 1),
|
||||
bwa_aln_pe(bam, saiFile2, 2),
|
||||
bwa_sam_pe(bam, saiFile1, saiFile2, realignedSamFile, readGroupString))
|
||||
}
|
||||
add(sortSam(realignedSamFile, realignedBamFile))
|
||||
realignedBams :+= realignedBamFile
|
||||
}
|
||||
return realignedBams
|
||||
}
|
||||
|
||||
// Reads a BAM LIST file and creates a scala list with all the files
|
||||
def createListFromFile(in: File):List[File] = {
|
||||
if (in.toString.endsWith("bam"))
|
||||
return List(in)
|
||||
var l: List[File] = List()
|
||||
for (bam <- fromFile(in).getLines)
|
||||
l :+= new File(bam)
|
||||
return l
|
||||
}
|
||||
|
||||
|
||||
|
||||
/****************************************************************************
|
||||
* Main script
|
||||
****************************************************************************/
|
||||
|
||||
|
||||
def script = {
|
||||
|
||||
// keep a record of the number of contigs in the first bam file in the list
|
||||
val bams = createListFromFile(input)
|
||||
nContigs = getNumberOfContigs(bams(0))
|
||||
|
||||
val realignedBams = if (useBWApe || useBWAse) {performAlignment(bams)} else {bams}
|
||||
|
||||
// Generate a BAM file per sample joining all per lane files if necessary
|
||||
val sampleBamFiles: Map[String, File] = createSampleFiles(bams, realignedBams)
|
||||
|
||||
|
||||
println("nContigs: " + nContigs)
|
||||
|
||||
// Final output list of processed bam files
|
||||
var cohortList: List[File] = List()
|
||||
|
||||
// Simple progress report
|
||||
println("\nFound the following samples: ")
|
||||
for ((sample, file) <- sampleBamFiles)
|
||||
println("\t" + sample + " -> " + file)
|
||||
|
||||
// If this is a 'knowns only' indel realignment run, do it only once for all samples.
|
||||
val globalIntervals = new File(outputDir + projectName + ".intervals")
|
||||
if (knownsOnly)
|
||||
add(target(null, globalIntervals))
|
||||
|
||||
// Put each sample through the pipeline
|
||||
for ((sample, bam) <- sampleBamFiles) {
|
||||
|
||||
// BAM files generated by the pipeline
|
||||
val cleanedBam = swapExt(bam, ".bam", ".clean.bam")
|
||||
val dedupedBam = swapExt(bam, ".bam", ".clean.dedup.bam")
|
||||
val recalBam = swapExt(bam, ".bam", ".clean.dedup.recal.bam")
|
||||
|
||||
// Accessory files
|
||||
val targetIntervals = if (knownsOnly) {globalIntervals} else {swapExt(bam, ".bam", ".intervals")}
|
||||
val metricsFile = swapExt(bam, ".bam", ".metrics")
|
||||
val preRecalFile = swapExt(bam, ".bam", ".pre_recal.csv")
|
||||
val postRecalFile = swapExt(bam, ".bam", ".post_recal.csv")
|
||||
val preOutPath = swapExt(bam, ".bam", ".pre")
|
||||
val postOutPath = swapExt(bam, ".bam", ".post")
|
||||
val preValidateLog = swapExt(bam, ".bam", ".pre.validation")
|
||||
val postValidateLog = swapExt(bam, ".bam", ".post.validation")
|
||||
|
||||
add(validate(bam, preValidateLog))
|
||||
|
||||
if (!knownsOnly)
|
||||
add(target(bam, targetIntervals))
|
||||
|
||||
add(clean(bam, targetIntervals, cleanedBam),
|
||||
dedup(cleanedBam, dedupedBam, metricsFile),
|
||||
cov(dedupedBam, preRecalFile),
|
||||
recal(dedupedBam, preRecalFile, recalBam),
|
||||
cov(recalBam, postRecalFile),
|
||||
analyzeCovariates(preRecalFile, preOutPath),
|
||||
analyzeCovariates(postRecalFile, postOutPath),
|
||||
validate(recalBam, postValidateLog))
|
||||
|
||||
cohortList :+= recalBam
|
||||
}
|
||||
|
||||
// output a BAM list with all the processed per sample files
|
||||
val cohortFile = new File(qscript.outputDir + qscript.projectName + ".cohort.list")
|
||||
add(writeList(cohortList, cohortFile))
|
||||
}
|
||||
|
||||
|
||||
|
||||
/****************************************************************************
|
||||
* Classes (Walkers and non-GATK programs)
|
||||
****************************************************************************/
|
||||
|
||||
|
||||
// General arguments to GATK walkers
|
||||
trait CommandLineGATKArgs extends CommandLineGATK {
|
||||
this.jarFile = qscript.GATKjar
|
||||
this.reference_sequence = qscript.reference
|
||||
this.memoryLimit = 4
|
||||
this.isIntermediate = true
|
||||
}
|
||||
|
||||
case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
|
||||
if (!knownsOnly)
|
||||
this.input_file :+= inBams
|
||||
this.out = outIntervals
|
||||
this.mismatchFraction = 0.0
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
|
||||
this.rodBind :+= RodBind("indels", "VCF", indels)
|
||||
this.scatterCount = nContigs
|
||||
this.analysisName = queueLogDir + outIntervals + ".target"
|
||||
this.jobName = queueLogDir + outIntervals + ".target"
|
||||
}
|
||||
|
||||
case class clean (inBams: File, tIntervals: File, outBam: File) extends IndelRealigner with CommandLineGATKArgs {
|
||||
this.input_file :+= inBams
|
||||
this.targetIntervals = tIntervals
|
||||
this.out = outBam
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
|
||||
this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
|
||||
this.useOnlyKnownIndels = knownsOnly
|
||||
this.doNotUseSW = !useSW
|
||||
this.compress = 0
|
||||
this.scatterCount = nContigs
|
||||
this.analysisName = queueLogDir + outBam + ".clean"
|
||||
this.jobName = queueLogDir + outBam + ".clean"
|
||||
}
|
||||
|
||||
case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
|
||||
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
|
||||
this.input_file :+= inBam
|
||||
this.recal_file = outRecalFile
|
||||
if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
|
||||
else if (qscript.intervals != null) this.intervals :+= qscript.intervals
|
||||
this.scatterCount = nContigs
|
||||
this.analysisName = queueLogDir + outRecalFile + ".covariates"
|
||||
this.jobName = queueLogDir + outRecalFile + ".covariates"
|
||||
}
|
||||
|
||||
case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
|
||||
this.input_file :+= inBam
|
||||
this.recal_file = inRecalFile
|
||||
this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
|
||||
this.out = outBam
|
||||
if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
|
||||
else if (qscript.intervals != null) this.intervals :+= qscript.intervals
|
||||
this.scatterCount = nContigs
|
||||
this.isIntermediate = false
|
||||
this.analysisName = queueLogDir + outBam + ".recalibration"
|
||||
this.jobName = queueLogDir + outBam + ".recalibration"
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
// Outside tools (not GATK walkers)
|
||||
|
||||
case class analyzeCovariates (inRecalFile: File, outPath: File) extends AnalyzeCovariates {
|
||||
this.jarFile = qscript.ACJar
|
||||
this.resources = qscript.R
|
||||
this.recal_file = inRecalFile
|
||||
this.output_dir = outPath.toString
|
||||
this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
|
||||
this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
|
||||
}
|
||||
|
||||
case class dedup (inBam: File, outBam: File, metricsFile: File) extends PicardBamFunction {
|
||||
@Input(doc="fixed bam") var clean = inBam
|
||||
@Output(doc="deduped bam") var deduped = outBam
|
||||
@Output(doc="deduped bam index") var dedupedIndex = new File(outBam + "bai")
|
||||
@Output(doc="metrics file") var metrics = metricsFile
|
||||
override def inputBams = List(clean)
|
||||
override def outputBam = deduped
|
||||
override def commandLine = super.commandLine + " M=" + metricsFile
|
||||
this.sortOrder = null
|
||||
this.createIndex = true
|
||||
this.memoryLimit = 6
|
||||
this.isIntermediate = true
|
||||
this.jarFile = qscript.dedupJar
|
||||
this.analysisName = queueLogDir + outBam + ".dedup"
|
||||
this.jobName = queueLogDir + outBam + ".dedup"
|
||||
}
|
||||
|
||||
case class joinBams (inBams: List[File], outBam: File) extends PicardBamFunction {
|
||||
@Input(doc="input bam list") var join = inBams
|
||||
@Output(doc="joined bam") var joined = outBam
|
||||
@Output(doc="joined bam index") var joinedIndex = new File(outBam + "bai")
|
||||
override def inputBams = join
|
||||
override def outputBam = joined
|
||||
override def commandLine = super.commandLine + " CREATE_INDEX=true"
|
||||
this.jarFile = qscript.mergeBamJar
|
||||
this.isIntermediate = true
|
||||
this.analysisName = queueLogDir + outBam + ".joinBams"
|
||||
this.jobName = queueLogDir + outBam + ".joinBams"
|
||||
}
|
||||
|
||||
case class sortSam (inSam: File, outBam: File) extends PicardBamFunction {
|
||||
@Input(doc="input unsorted sam file") var sam = inSam
|
||||
@Output(doc="sorted bam") var bam = outBam
|
||||
@Output(doc="sorted bam index") var bamIndex = new File(outBam + "bai")
|
||||
override def inputBams = List(sam)
|
||||
override def outputBam = bam
|
||||
override def commandLine = super.commandLine + " CREATE_INDEX=true"
|
||||
this.jarFile = qscript.sortSamJar
|
||||
this.isIntermediate = true
|
||||
this.analysisName = queueLogDir + outBam + ".sortSam"
|
||||
this.jobName = queueLogDir + outBam + ".sortSam"
|
||||
}
|
||||
|
||||
case class validate (inBam: File, outLog: File) extends PicardBamFunction {
|
||||
@Input(doc="input bam list") var toValidate = inBam
|
||||
@Output(doc="validation log") var validate = outLog
|
||||
override def inputBams = List(inBam)
|
||||
override def outputBam = outLog
|
||||
override def commandLine = super.commandLine + " VALIDATE_INDEX=true MODE=SUMMARY REFERENCE_SEQUENCE=" + qscript.reference
|
||||
sortOrder = null
|
||||
this.jarFile = qscript.validateSamJar
|
||||
this.isIntermediate = false
|
||||
this.analysisName = queueLogDir + outLog + ".validate"
|
||||
this.jobName = queueLogDir + outLog + ".validate"
|
||||
}
|
||||
|
||||
case class revert (inBam: File, outBam: File) extends PicardBamFunction {
|
||||
@Input(doc="old annotated bam") var oldBam = inBam
|
||||
@Output(doc="reverted bam") var revertedBam = outBam
|
||||
@Output(doc="reverted bam index") var revertedBamIndex = new File(outBam + ".bai")
|
||||
override def inputBams = List(oldBam)
|
||||
override def outputBam = revertedBam
|
||||
override def commandLine = super.commandLine + " CREATE_INDEX=true"
|
||||
this.isIntermediate = true
|
||||
this.jarFile = qscript.dedupJar
|
||||
this.analysisName = queueLogDir + outBam + ".dedup"
|
||||
this.jobName = queueLogDir + outBam + ".dedup"
|
||||
}
|
||||
|
||||
case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction {
|
||||
@Input(doc="bam file to be aligned") var bam = inBam
|
||||
@Output(doc="output sai file") var sai = outSai
|
||||
def commandLine = bwaPath + " aln -q 5 " + reference + " -b " + bam + " > " + sai
|
||||
this.isIntermediate = true
|
||||
this.analysisName = queueLogDir + outSai + ".bwa_aln_se"
|
||||
this.jobName = queueLogDir + outSai + ".bwa_aln_se"
|
||||
}
|
||||
|
||||
case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction {
|
||||
@Input(doc="bam file to be aligned") var bam = inBam
|
||||
@Output(doc="output sai file for 1st mating pair") var sai = outSai1
|
||||
def commandLine = bwaPath + " aln -q 5 " + reference + " -b" + index + " " + bam + " > " + sai
|
||||
this.isIntermediate = true
|
||||
this.analysisName = queueLogDir + outSai1 + ".bwa_aln_pe1"
|
||||
this.jobName = queueLogDir + outSai1 + ".bwa_aln_pe1"
|
||||
}
|
||||
|
||||
case class bwa_sam_se (inBam: File, inSai: File, outBam: File, readGroup: List[String]) extends CommandLineFunction {
|
||||
@Input(doc="bam file to be aligned") var bam = inBam
|
||||
@Input(doc="bwa alignment index file") var sai = inSai
|
||||
@Output(doc="output aligned bam file") var alignedBam = outBam
|
||||
var readGroupParameters = ""
|
||||
for (rg <- readGroup) {
|
||||
readGroupParameters += " -r \'" + rg + "\'"
|
||||
}
|
||||
def commandLine = bwaPath + " samse " + readGroupParameters + " " + reference + " " + sai + " " + bam + " > " + alignedBam
|
||||
this.isIntermediate = true
|
||||
this.analysisName = queueLogDir + outBam + ".bwa_sam_se"
|
||||
this.jobName = queueLogDir + outBam + ".bwa_sam_se"
|
||||
}
|
||||
|
||||
case class bwa_sam_pe (inBam: File, inSai1: File, inSai2:File, outBam: File, readGroup: List[String]) extends CommandLineFunction {
|
||||
@Input(doc="bam file to be aligned") var bam = inBam
|
||||
@Input(doc="bwa alignment index file for 1st mating pair") var sai1 = inSai1
|
||||
@Input(doc="bwa alignment index file for 2nd mating pair") var sai2 = inSai2
|
||||
@Output(doc="output aligned bam file") var alignedBam = outBam
|
||||
var readGroupParameters = ""
|
||||
for (rg <- readGroup) {
|
||||
readGroupParameters += " -r \'" + rg + "\'"
|
||||
}
|
||||
def commandLine = bwaPath + " sampe " + readGroupParameters + " " + reference + " " + sai1 + " " + sai2 + " " + bam + " " + bam + " > " + alignedBam
|
||||
this.isIntermediate = true
|
||||
this.analysisName = queueLogDir + outBam + ".bwa_sam_pe"
|
||||
this.jobName = queueLogDir + outBam + ".bwa_sam_pe"
|
||||
}
|
||||
|
||||
case class writeList(inBams: List[File], outBamList: File) extends ListWriterFunction {
|
||||
this.inputFiles = inBams
|
||||
this.listFile = outBamList
|
||||
this.analysisName = queueLogDir + outBamList + ".bamList"
|
||||
this.jobName = queueLogDir + outBamList + ".bamList"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue