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Creating sample-bam list instead of joining 

This should save us at least one day in the trio decoy processing.
This commit is contained in:
Mauricio Carneiro 2011-08-22 18:00:44 -04:00
parent 04d8bcaf19
commit 136f0eb685
6 changed files with 14 additions and 17 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

19
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -218,7 +218,6 @@ class DataProcessingPipeline extends QScript {
return revertedBAM return revertedBAM
} }
/**************************************************************************** /****************************************************************************
* Main script * Main script
****************************************************************************/ ****************************************************************************/
@ -271,13 +270,12 @@ class DataProcessingPipeline extends QScript {
val postValidateLog = swapExt(bam, ".bam", ".post.validation") val postValidateLog = swapExt(bam, ".bam", ".post.validation")
//todo -- update the validation to work with .list files
// Validation is an optional step for the BAM file generated after // Validation is an optional step for the BAM file generated after
// alignment and the final bam file of the pipeline. // alignment and the final bam file of the pipeline.
// if (!noValidation) { if (!noValidation && sampleFile.endsWith(".bam")) { // todo -- implement validation for .list BAM files
// add(validate(bam, preValidateLog), add(validate(sampleFile, preValidateLog),
// validate(recalBam, postValidateLog)) validate(recalBam, postValidateLog))
// } }
if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY) if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
add(target(sampleFile, targetIntervals)) add(target(sampleFile, targetIntervals))
@ -390,7 +388,7 @@ class DataProcessingPipeline extends QScript {
} }
case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs { case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs {
this.input = List(inBam) this.input :+= inBam
this.output = outBam this.output = outBam
this.metrics = metricsFile this.metrics = metricsFile
this.memoryLimit = 16 this.memoryLimit = 16
@ -406,7 +404,7 @@ class DataProcessingPipeline extends QScript {
} }
case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam with ExternalCommonArgs { case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam with ExternalCommonArgs {
this.input = List(inSam) this.input :+= inSam
this.output = outBam this.output = outBam
this.sortOrder = sortOrderP this.sortOrder = sortOrderP
this.analysisName = queueLogDir + outBam + ".sortSam" this.analysisName = queueLogDir + outBam + ".sortSam"
@ -414,7 +412,7 @@ class DataProcessingPipeline extends QScript {
} }
case class validate (inBam: File, outLog: File) extends ValidateSamFile with ExternalCommonArgs { case class validate (inBam: File, outLog: File) extends ValidateSamFile with ExternalCommonArgs {
this.input = List(inBam) this.input :+= inBam
this.output = outLog this.output = outLog
this.REFERENCE_SEQUENCE = qscript.reference this.REFERENCE_SEQUENCE = qscript.reference
this.isIntermediate = false this.isIntermediate = false
@ -424,8 +422,7 @@ class DataProcessingPipeline extends QScript {
case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups with ExternalCommonArgs { case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups with ExternalCommonArgs {
@Output(doc="output bai file") var bai = swapExt(outBam, ".bam", ".bai") this.input :+= inBam
this.input = List(inBam)
this.output = outBam this.output = outBam
this.RGID = readGroup.id this.RGID = readGroup.id
this.RGCN = readGroup.cn this.RGCN = readGroup.cn

2
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala
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@ -15,7 +15,7 @@ class AddOrReplaceReadGroups extends org.broadinstitute.sting.queue.function.Jav
javaMainClass = "net.sf.picard.sam.AddOrReplaceReadGroups" javaMainClass = "net.sf.picard.sam.AddOrReplaceReadGroups"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true) @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
var input: List[File] = _ var input: List[File] = Nil
@Output(doc="The output BAM file with the modified/added read groups", shortName = "output", fullName = "output_bam_file", required = true) @Output(doc="The output BAM file with the modified/added read groups", shortName = "output", fullName = "output_bam_file", required = true)
var output: File = _ var output: File = _

2
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala
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@ -15,7 +15,7 @@ class MarkDuplicates extends org.broadinstitute.sting.queue.function.JavaCommand
javaMainClass = "net.sf.picard.sam.MarkDuplicates" javaMainClass = "net.sf.picard.sam.MarkDuplicates"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true) @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
var input: List[File] = _ var input: List[File] = Nil
@Output(doc="The output file to write marked records to", shortName = "output", fullName = "output_bam_file", required = true) @Output(doc="The output file to write marked records to", shortName = "output", fullName = "output_bam_file", required = true)
var output: File = _ var output: File = _

2
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala
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@ -16,7 +16,7 @@ class MergeSamFiles extends org.broadinstitute.sting.queue.function.JavaCommandL
javaMainClass = "net.sf.picard.sam.MergeSamFiles" javaMainClass = "net.sf.picard.sam.MergeSamFiles"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true) @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
var input: List[File] = _ var input: List[File] = Nil
@Output(doc="The output merged BAM file", shortName = "output", fullName = "output_bam_file", required = true) @Output(doc="The output merged BAM file", shortName = "output", fullName = "output_bam_file", required = true)
var output: File = _ var output: File = _

2
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala
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@ -16,7 +16,7 @@ class SortSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFun
javaMainClass = "net.sf.picard.sam.SortSam" javaMainClass = "net.sf.picard.sam.SortSam"
@Input(doc="The input SAM or BAM files to sort.", shortName = "input", fullName = "input_bam_files", required = true) @Input(doc="The input SAM or BAM files to sort.", shortName = "input", fullName = "input_bam_files", required = true)
var input: List[File] = _ var input: List[File] = Nil
@Output(doc="The sorted BAM or SAM output file.", shortName = "output", fullName = "output_bam_file", required = true) @Output(doc="The sorted BAM or SAM output file.", shortName = "output", fullName = "output_bam_file", required = true)
var output: File = _ var output: File = _

4
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala
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@ -17,7 +17,7 @@ class ValidateSamFile extends org.broadinstitute.sting.queue.function.JavaComman
javaMainClass = "net.sf.picard.sam.ValidateSamFile" javaMainClass = "net.sf.picard.sam.ValidateSamFile"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true) @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
var input: List[File] = _ var input: List[File] = Nil
@Output(doc="Send output to a file instead of stdout", shortName = "output", fullName = "output_file", required = false) @Output(doc="Send output to a file instead of stdout", shortName = "output", fullName = "output_file", required = false)
var output: File = _ var output: File = _
@ -26,7 +26,7 @@ class ValidateSamFile extends org.broadinstitute.sting.queue.function.JavaComman
var MODE: Mode = Mode.VERBOSE var MODE: Mode = Mode.VERBOSE
@Argument(doc="List of validation error types to ignore.", shortName = "ignore", fullName = "ignore_error_types", required = false) @Argument(doc="List of validation error types to ignore.", shortName = "ignore", fullName = "ignore_error_types", required = false)
var IGNORE: List[String] = _ var IGNORE: List[String] = Nil
@Argument(doc = "The maximum number of lines output in verbose mode.", shortName = "max", fullName = "max_output", required = false) @Argument(doc = "The maximum number of lines output in verbose mode.", shortName = "max", fullName = "max_output", required = false)
var MAX_OUTPUT: Int = 100 var MAX_OUTPUT: Int = 100