458 lines
20 KiB
Scala
Executable File
458 lines
20 KiB
Scala
Executable File
package oneoffs.carneiro
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.queue.function.ListWriterFunction
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import net.sf.samtools.{SAMFileReader,SAMReadGroupRecord}
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import scala.io.Source._
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import collection.JavaConversions._
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class dataProcessingV2 extends QScript {
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qscript =>
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/****************************************************************************
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* Required Parameters (if default values are not good for you)
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****************************************************************************/
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@Input(doc="input BAM file - or list of BAM files", fullName="input", shortName="i", required=true)
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var input: File = _
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@Input(doc="path to GenomeAnalysisTK.jar", fullName="path_to_gatk_jar", shortName="gatk", required=true)
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var GATKjar: File = _
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@Input(doc="path to AnalyzeCovariates.jar", fullName="path_to_ac_jar", shortName="ac", required=true)
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var ACJar: File = _
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@Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=true)
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var R: String = _
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@Input(doc="path to Picard's MarkDuplicates.jar", fullName="path_to_dedup_jar", shortName="dedup", required=false)
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var dedupJar: File = new File("/seq/software/picard/current/bin/MarkDuplicates.jar")
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@Input(doc="path to Picard's MergeSamFiles.jar", fullName="path_to_merge_jar", shortName="merge", required=false)
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var mergeBamJar: File = new File("/seq/software/picard/current/bin/MergeSamFiles.jar")
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@Input(doc="path to Picard's ValidateSam.jar", fullName="path_to_validate_jar", shortName="validate", required=false)
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var validateSamJar: File = new File("/seq/software/picard/current/bin/ValidateSamFile.jar")
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@Input(doc="Reference fasta file", fullName="reference", shortName="R", required=false)
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var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
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/****************************************************************************
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* Optional Parameters
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****************************************************************************/
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@Input(doc="path to Picard's RevertSam.jar", fullName="path_to_revert_jar", shortName="revert", required=false)
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var revertSamJar: File = _
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@Input(doc="path to Picard's SortSam.jar", fullName="path_to_sort_jar", shortName="sort", required=false)
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var sortSamJar: File = _
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@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)
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var bwaPath: File = _
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@Input(doc="dbsnp ROD to use (VCF)", fullName="dbsnp", shortName="D", required=false)
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var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
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@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
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var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
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@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)
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var projectName: String = "project"
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@Input(doc="Output path for the processed BAM files.", fullName="output_directory", shortName="outputDir", required=false)
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var outputDir: String = ""
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@Input(doc="the -L interval string to be used by GATK - output bams at interval only", fullName="gatk_interval_string", shortName="L", required=false)
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var intervalString: String = ""
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@Input(doc="an intervals file to be used by GATK - output bams at intervals only", fullName="gatk_interval_file", shortName="intervals", required=false)
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var intervals: File = _
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@Input(doc="Perform cleaning on knowns only", fullName="knowns_only", shortName="knowns", required=false)
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var knownsOnly: Boolean = false
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@Input(doc="Perform cleaning using Smith Waterman", fullName="use_smith_waterman", shortName="sw", required=false)
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var useSW: Boolean = false
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@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)
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var useBWAse: Boolean = false
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@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)
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var useBWApe: Boolean = false
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/****************************************************************************
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* Global Variables
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****************************************************************************/
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val queueLogDir: String = ".qlog/" // Gracefully hide Queue's output
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var nContigs: Int = 0 // Use the number of contigs for scatter gathering jobs
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/****************************************************************************
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* Helper functions
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****************************************************************************/
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// Utility function to check if there are multiple samples in a BAM file (currently we can't deal with that)
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def hasMultipleSamples(readGroups: java.util.List[SAMReadGroupRecord]): Boolean = {
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var sample: String = ""
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for (r <- readGroups) {
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if (sample.isEmpty)
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sample = r.getSample()
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else if (sample != r.getSample())
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return true;
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}
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return false
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}
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// Utility function to merge all bam files of similar samples. Generates on BAM file per sample.
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// It uses the sample information on the header of the input BAM files.
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def createSampleFiles(bamFiles: List[File]): Map[String, File] = {
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// Creating a table with SAMPLE information from each input BAM file
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val sampleTable = scala.collection.mutable.Map.empty[String, List[File]]
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for (bam <- bamFiles) {
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val samReader = new SAMFileReader(bam)
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val header = samReader.getFileHeader()
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val readGroups = header.getReadGroups()
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// only allow one sample per file. Bam files with multiple samples would require pre-processing of the file
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// with PrintReads to separate the samples. Tell user to do it himself!
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assert(!hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
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// Fill out the sample table with the readgroups in this file
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for (rg <- readGroups) {
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val sample = rg.getSample()
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if (!sampleTable.contains(sample))
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sampleTable(sample) = List(bam)
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else if ( !sampleTable(sample).contains(bam))
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sampleTable(sample) :+= bam
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}
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}
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// Creating one file for each sample in the dataset
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val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
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for ((sample, flist) <- sampleTable) {
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val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".bam")
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sampleBamFiles(sample) = sampleFileName
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add(joinBams(flist, sampleFileName))
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}
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return sampleBamFiles.toMap
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}
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// Checks how many contigs are in the dataset. Uses the BAM file header information.
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def getNumberOfContigs(): Int = {
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val bam = fromFile(input).getLines.next
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val samReader = new SAMFileReader(new File(bam))
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return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
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}
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// Takes a list of processed BAM files, revert them to unprocessed and realigns each lane, producing a list of
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// per-lane aligned bam files, ready to be processed.
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def performAlignment(bamList: File): List[File] = {
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return List()
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}
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def createListFromFile(in: File):List[File] = {
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if (in.toString.endsWith("bam"))
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return List(in)
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var l: List[File] = List()
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for (bam <- fromFile(in).getLines)
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l :+= new File(bam)
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return l
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}
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/****************************************************************************
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* Main script
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****************************************************************************/
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def script = {
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//todo -- (option - BWA) run BWA on each bam file (per lane bam file) before performing per sample processing
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val perLaneAlignedBamFiles: List[File] = if (useBWApe || useBWAse) { performAlignment(input) } else { createListFromFile(input) }
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// Generate a BAM file per sample joining all per lane files if necessary
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val sampleBamFiles = createSampleFiles(perLaneAlignedBamFiles)
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// keep a record of the number of contigs in this bam file (they should all be the same
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nContigs = getNumberOfContigs()
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// Final output list of processed bam files
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var cohortList: List[File] = List()
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// Simple progress report
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println("\nFound the following samples: ")
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for ((sample, file) <- sampleBamFiles)
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println("\t" + sample + " -> " + file)
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// If this is a 'knowns only' indel realignment run, do it only once for all samples.
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val globalIntervals = new File(outputDir + projectName + ".intervals")
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if (knownsOnly)
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add(target(null, globalIntervals))
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// Put each sample through the pipeline
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for ((sample, bam) <- sampleBamFiles) {
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// BAM files generated by the pipeline
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val cleanedBam = swapExt(bam, ".bam", ".clean.bam")
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val dedupedBam = swapExt(bam, ".bam", ".clean.dedup.bam")
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val recalBam = swapExt(bam, ".bam", ".clean.dedup.recal.bam")
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// Accessory files
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val targetIntervals = if (knownsOnly) {globalIntervals} else {swapExt(bam, ".bam", ".intervals")}
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val metricsFile = swapExt(bam, ".bam", ".metrics")
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val preRecalFile = swapExt(bam, ".bam", ".pre_recal.csv")
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val postRecalFile = swapExt(bam, ".bam", ".post_recal.csv")
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val preOutPath = swapExt(bam, ".bam", ".pre")
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val postOutPath = swapExt(bam, ".bam", ".post")
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val preValidateLog = swapExt(bam, ".bam", ".pre.validation")
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val postValidateLog = swapExt(bam, ".bam", ".post.validation")
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add(validate(bam, preValidateLog))
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if (!knownsOnly)
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add(target(bam, targetIntervals))
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add(clean(bam, targetIntervals, cleanedBam),
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dedup(cleanedBam, dedupedBam, metricsFile),
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cov(dedupedBam, preRecalFile),
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recal(dedupedBam, preRecalFile, recalBam),
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cov(recalBam, postRecalFile),
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analyzeCovariates(preRecalFile, preOutPath),
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analyzeCovariates(postRecalFile, postOutPath),
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validate(recalBam, postValidateLog))
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cohortList :+= recalBam
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}
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// output a BAM list with all the processed per sample files
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val cohortFile = new File(qscript.outputDir + qscript.projectName + ".cohort.list")
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add(writeList(cohortList, cohortFile))
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}
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/****************************************************************************
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* Classes (Walkers and non-GATK programs)
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****************************************************************************/
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// General arguments to GATK walkers
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trait CommandLineGATKArgs extends CommandLineGATK {
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this.jarFile = qscript.GATKjar
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this.reference_sequence = qscript.reference
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this.memoryLimit = 4
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this.isIntermediate = true
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}
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case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
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if (!knownsOnly)
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this.input_file :+= inBams
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this.out = outIntervals
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this.mismatchFraction = 0.0
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.rodBind :+= RodBind("indels", "VCF", indels)
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this.scatterCount = nContigs
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this.analysisName = queueLogDir + outIntervals + ".target"
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this.jobName = queueLogDir + outIntervals + ".target"
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}
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case class clean (inBams: File, tIntervals: File, outBam: File) extends IndelRealigner with CommandLineGATKArgs {
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this.input_file :+= inBams
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this.targetIntervals = tIntervals
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this.out = outBam
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
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this.useOnlyKnownIndels = knownsOnly
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this.doNotUseSW = useSW
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this.compress = 0
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this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
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this.scatterCount = nContigs
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this.analysisName = queueLogDir + outBam + ".clean"
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this.jobName = queueLogDir + outBam + ".clean"
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}
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//todo -- add scatter gather capability (waiting for khalid's modifications to the queue base
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case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
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this.input_file :+= inBam
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this.recal_file = outRecalFile
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this.jobQueue = "gsa" // should take this out once scatter gather is available.
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this.analysisName = queueLogDir + outRecalFile + ".covariates"
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this.jobName = queueLogDir + outRecalFile + ".covariates"
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}
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//todo -- add scatter gather capability (waiting for khalid's modifications to the queue base
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case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
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@Output(doc="recalibrated bam index") var recalIndex = new File(outBam + ".bai")
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this.input_file :+= inBam
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this.recal_file = inRecalFile
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this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
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this.out = outBam
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if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
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else if (qscript.intervals != null) this.intervals :+= qscript.intervals
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this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
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this.index_output_bam_on_the_fly = true
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this.isIntermediate = false
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this.jobQueue = "gsa" // should take this out once scatter gather is available.
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this.analysisName = queueLogDir + outBam + ".recalibration"
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this.jobName = queueLogDir + outBam + ".recalibration"
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}
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// Outside tools (not GATK walkers)
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case class analyzeCovariates (inRecalFile: File, outPath: File) extends AnalyzeCovariates {
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this.jarFile = qscript.ACJar
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this.resources = qscript.R
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this.recal_file = inRecalFile
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this.output_dir = outPath.toString
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this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
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this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
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}
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case class dedup (inBam: File, outBam: File, metricsFile: File) extends PicardBamFunction {
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@Input(doc="fixed bam") var clean = inBam
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@Output(doc="deduped bam") var deduped = outBam
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@Output(doc="metrics file") var metrics = metricsFile
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override def inputBams = List(clean)
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override def outputBam = deduped
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override def commandLine = super.commandLine + " M=" + metricsFile
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this.sortOrder = null
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this.createIndex = true
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this.memoryLimit = 6
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this.isIntermediate = true
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this.jarFile = qscript.dedupJar
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this.analysisName = queueLogDir + outBam + ".dedup"
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this.jobName = queueLogDir + outBam + ".dedup"
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}
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case class joinBams (inBams: List[File], outBam: File) extends PicardBamFunction {
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@Input(doc="input bam list") var join = inBams
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@Output(doc="joined bam") var joined = outBam
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@Output(doc="joined bam index") var joinedIndex = new File(outBam + "bai")
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override def inputBams = join
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override def outputBam = joined
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override def commandLine = super.commandLine + " CREATE_INDEX=true"
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this.jarFile = qscript.mergeBamJar
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this.isIntermediate = true
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this.analysisName = queueLogDir + outBam + ".joinBams"
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this.jobName = queueLogDir + outBam + ".joinBams"
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}
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case class sortSam (inSam: File, outBam: File) extends PicardBamFunction {
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@Input(doc="input unsorted sam file") var sam = inSam
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@Output(doc="sorted bam") var bam = outBam
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@Output(doc="sorted bam index") var bamIndex = new File(outBam + "bai")
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override def inputBams = List(sam)
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override def outputBam = bam
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override def commandLine = super.commandLine + " CREATE_INDEX=true"
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this.jarFile = qscript.sortSamJar
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this.isIntermediate = true
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this.analysisName = queueLogDir + outBam + ".sortSam"
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this.jobName = queueLogDir + outBam + ".sortSam"
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}
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case class validate (inBam: File, outLog: File) extends PicardBamFunction {
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@Input(doc="input bam list") var toValidate = inBam
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@Output(doc="validation log") var validate = outLog
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override def inputBams = List(inBam)
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override def outputBam = outLog
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override def commandLine = super.commandLine + " VALIDATE_INDEX=true MODE=SUMMARY REFERENCE_SEQUENCE=" + qscript.reference
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sortOrder = null
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this.jarFile = qscript.validateSamJar
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this.isIntermediate = false
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this.analysisName = queueLogDir + outLog + ".validate"
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this.jobName = queueLogDir + outLog + ".validate"
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}
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case class revert (inBam: File, outBam: File) extends PicardBamFunction {
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@Input(doc="old annotated bam") var oldBam = inBam
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@Output(doc="reverted bam") var revertedBam = outBam
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@Output(doc="reverted bam index") var revertedBamIndex = new File(outBam + ".bai")
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override def inputBams = List(oldBam)
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override def outputBam = revertedBam
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override def commandLine = super.commandLine + " CREATE_INDEX=true"
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this.isIntermediate = true
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this.jarFile = qscript.dedupJar
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this.analysisName = queueLogDir + outBam + ".dedup"
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this.jobName = queueLogDir + outBam + ".dedup"
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}
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case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction {
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@Input(doc="bam file to be aligned") var bam = inBam
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@Output(doc="output sai file") var sai = outSai
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def commandLine = bwaPath + " aln -q 5 " + reference + " -b " + bam + " > " + sai
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this.isIntermediate = true
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this.analysisName = queueLogDir + outSai + ".bwa_aln_se"
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this.jobName = queueLogDir + outSai + ".bwa_aln_se"
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}
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case class bwa_aln_pe1 (inBam: File, outSai1: File) extends CommandLineFunction {
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@Input(doc="bam file to be aligned") var bam = inBam
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@Output(doc="output sai file for 1st mating pair") var sai = outSai1
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def commandLine = bwaPath + " aln -q 5 " + reference + " -b1 " + bam + " > " + sai
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this.isIntermediate = true
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this.analysisName = queueLogDir + outSai1 + ".bwa_aln_pe1"
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this.jobName = queueLogDir + outSai1 + ".bwa_aln_pe1"
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}
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case class bwa_aln_pe2 (inBam: File, outSai2: File) extends CommandLineFunction {
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@Input(doc="bam file to be aligned") var bam = inBam
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@Output(doc="output sai file for 2nd mating pair") var sai = outSai2
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def commandLine = bwaPath + " aln -q 5 " + reference + " -b2 " + bam + " > " + sai
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this.isIntermediate = true
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this.analysisName = queueLogDir + outSai2 + ".bwa_aln_pe2"
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this.jobName = queueLogDir + outSai2 + ".bwa_aln_pe2"
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}
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case class bwa_sam_se (inBam: File, inSai: File, outBam: File, readGroup: String) extends CommandLineFunction {
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@Input(doc="bam file to be aligned") var bam = inBam
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@Input(doc="bwa alignment index file") var sai = inSai
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@Output(doc="output aligned bam file") var alignedBam = outBam
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def commandLine = bwaPath + " samse " + reference + " " + sai + " " + bam + " -r " + readGroup + " > " + alignedBam
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this.isIntermediate = true
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this.analysisName = queueLogDir + outBam + ".bwa_sam_se"
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this.jobName = queueLogDir + outBam + ".bwa_sam_se"
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}
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case class bwa_sam_pe (inBam: File, inSai1: File, inSai2:File, outBam: File, readGroup: String) extends CommandLineFunction {
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@Input(doc="bam file to be aligned") var bam = inBam
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@Input(doc="bwa alignment index file for 1st mating pair") var sai1 = inSai1
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@Input(doc="bwa alignment index file for 2nd mating pair") var sai2 = inSai2
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@Output(doc="output aligned bam file") var alignedBam = outBam
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def commandLine = bwaPath + " samse " + reference + " " + sai1 + " " + sai2 + " " + bam + " -r " + readGroup + " > " + alignedBam
|
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this.isIntermediate = true
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this.analysisName = queueLogDir + outBam + ".bwa_sam_pe"
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this.jobName = queueLogDir + outBam + ".bwa_sam_pe"
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}
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case class writeList(inBams: List[File], outBamList: File) extends ListWriterFunction {
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this.inputFiles = inBams
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this.listFile = outBamList
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this.analysisName = queueLogDir + outBamList + ".bamList"
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this.jobName = queueLogDir + outBamList + ".bamList"
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}
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}
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