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gatk-3.8/scala/qscript/oneoffs/chartl/BootstrapCalls.q

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Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.{GenotypeMergeType, VariantMergeType}
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript
class BootstrapCalls extends QScript {
@Argument(doc="Bam file list",shortName="I",required=true)
var bamList: File = _
@Argument(doc="Intervals file",shortName="L",required=true)
var intervalFile: File = _
@Argument(doc="Output file",shortName="o",required=true)
var bootstrapMergedOut: File = _
@Argument(doc="Reference file",shortName="R",required=true)
var reference: File = _
@Argument(doc="Downsampling Level",shortName="D",required=false)
var downsamplingLevel: Int = 4
@Argument(doc="Num Bootstrap Callsets",shortName="B",required=false)
var numberOfBootstraps: Int = 25
@Argument(doc="call confidence",shortName="conf",required=false)
var standCallConf: Double = 4.0
@Argument(doc="dbsnp file (vcf version)",shortName="dbsnp",required=false)
var dbsnp: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.leftAligned.vcf")
@Argument(doc="sting jar",shortName="s",required=true)
var sting: File = _
/**********************
* URGENT NOTE:
* for this to do any good you need to take out the random seeds in
* ReservoirDownsampler: 20
* MathUtils: 649
*
* You will also need to hack the recalibrator to always trust AC (which are no longer integer-valued)
* and to deal with double-valued AC fields
*/
def script = {
val bams: List[File] = extractFileEntries(bamList)
trait UGArgs extends UnifiedGenotyper {
this.input_file = bams
this.reference_sequence = reference
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.dcov = downsamplingLevel
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
this.intervals :+= intervalFile
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.stand_call_conf = standCallConf
this.stand_emit_conf = standCallConf
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
this.rodBind :+= new RodBind("dbsnp","vcf",dbsnp)
this.scatterCount = 20
this.jarFile = sting
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.memoryLimit = 4
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
}
val bootstrapBase = swapExt(bootstrapMergedOut,".vcf",".boot%d.vcf").getAbsolutePath
var calls : List[UnifiedGenotyper] = Nil
for ( i <- 0 until (numberOfBootstraps+1) ) {
var ug : UnifiedGenotyper = new UnifiedGenotyper with UGArgs
ug.out = new File(bootstrapBase.format(i))
ug.analysisName = "Boostrap%d".format(i)
calls :+= ug
}
addAll(calls)
trait MergeArgs extends BootstrapCallsMerger {
this.reference_sequence = reference
this.intervals :+= intervalFile
this.scatterCount = 40
this.jarFile = sting
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.memoryLimit = 4
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
this.rodBind ++= calls.map(u => u.out).zipWithIndex.map(u => new RodBind("bootstrap_%d".format(u._2),"vcf",u._1))
this.out = bootstrapMergedOut
}
var merge : BootstrapCallsMerger = new BootstrapCallsMerger with MergeArgs
add(merge)
trait ClusterArgs extends GenerateVariantClusters {
this.reference_sequence = reference
this.intervals :+= intervalFile
this.rodBind :+= new RodBind("input","vcf",merge.out)
this.rodBind :+= new RodBind("hapmap","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf"))
this.rodBind :+= new RodBind("truthHapMap","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf"))
this.rodBind :+= new RodBind("1kg","vcf", new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/1212samples.b37.sites.vcf"))
this.rodBind :+= new RodBind("truth1kg","vcf", new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/1212samples.b37.sites.vcf"))
this.cluster_file = swapExt(bootstrapMergedOut,"vcf","cluster")
this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.qual = 100
this.std = 3.5
this.mG = 8
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
this.trustAllPolymorphic = true
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.memoryLimit = 8
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
this.jarFile = sting
}
var clust : GenerateVariantClusters = new GenerateVariantClusters with ClusterArgs
add(clust)
trait VQSRArgs extends VariantRecalibrator {
this.reference_sequence = reference
this.intervals :+= intervalFile
this.out = swapExt(bootstrapMergedOut,"vcf","recal.vcf")
this.rodBind :+= new RodBind("input","vcf",merge.out)
this.rodBind :+= new RodBind("hapmap","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf"))
this.rodBind :+= new RodBind("1kg","vcf", new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/1212samples.b37.sites.vcf"))
this.rodBind :+= new RodBind("truthHapMap","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf"))
this.rodBind :+= new RodBind("truth1kg","vcf", new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/1212samples.b37.sites.vcf"))
this.cluster_file = swapExt(bootstrapMergedOut,"vcf","cluster")
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.sm = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
this.tranche ++= List("0.1", "0.5", "0.7", "1.0", "3.0", "5.0", "10.0", "100.0")
this.trustAllPolymorphic = true
this.tranchesFile = swapExt(bootstrapMergedOut,"vcf","tranche")
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.memoryLimit=8
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
this.jarFile = sting
this.rodBind :+= new RodBind("dbsnp","vcf",dbsnp)
}
var recal : VariantRecalibrator = new VariantRecalibrator with VQSRArgs
add(recal)
trait CutArgs extends ApplyVariantCuts {
this.reference_sequence = reference
this.intervals :+= intervalFile
this.rodBind :+= new RodBind("input","vcf",recal.out)
this.tranchesFile = recal.tranchesFile
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.fdr_filter_level = 1.0
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
this.out = swapExt(bootstrapMergedOut,".vcf",".recal.cut.vcf")
this.jarFile = sting
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.memoryLimit = 4
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
this.scatterCount = 5
}
var cut : ApplyVariantCuts = new ApplyVariantCuts with CutArgs
add(cut)
class RmHeader extends CommandLineFunction {
@Input(doc="vcf") var vcf : File = _
@Output(doc="headerless vcf") var noheadvcf : File = _
def commandLine : String = {
"head -n 1 %s > %s ; grep -v \\#\\# %s >> %s".format(vcf.getAbsolutePath,noheadvcf.getAbsolutePath,
vcf.getAbsolutePath,noheadvcf.getAbsolutePath)
}
}
var rm : RmHeader = new RmHeader
rm.vcf = cut.out
rm.noheadvcf = swapExt(cut.out,".vcf",".nohead.vcf")
add(rm)
trait CombineArgs extends CombineVariants {
this.reference_sequence = reference
this.intervals :+= intervalFile
Added in unit tests for the statistics calculated by the test runner; and bug-fixes to the calculations; so we have some assurance that the statistics coming out the back-end are correct. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5380 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 00:54:02 +08:00
this.rodBind :+= new RodBind("loCov","vcf",rm.noheadvcf)
this.rodBind :+= new RodBind("hiCov","vcf",new File("/humgen/gsa-pipeline/PVQF4/all_batches_v001/batch_001/SnpCalls/ESPGO_Gabriel_NHLBI_EOMI_setone_EOMI_Project.cleaned.annotated.handfiltered.vcf"))
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.variantMergeOptions = VariantMergeType.UNION
this.genotypeMergeOptions = GenotypeMergeType.PRIORITIZE
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
this.priority = "hiCov,loCov"
this.out = swapExt(bootstrapMergedOut,".vcf",".merged.combined.vcf")
this.jarFile = sting
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.memoryLimit = 6
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
}
var combine : CombineVariants = new CombineVariants with CombineArgs
add(combine)
trait EvalArgs extends VariantEval {
this.reference_sequence = reference
this.intervals :+= intervalFile
Added in unit tests for the statistics calculated by the test runner; and bug-fixes to the calculations; so we have some assurance that the statistics coming out the back-end are correct. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5380 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 00:54:02 +08:00
this.rodBind :+= new RodBind("evalCombined","vcf",combine.out)
//this.rodBind :+= new RodBind("evalCut","vcf",rm.noheadvcf)
//this.rodBind :+= new RodBind("evalFCP","vcf",new File("/humgen/gsa-pipeline/PVQF4/all_batches_v001/batch_001/SnpCalls/ESPGO_Gabriel_NHLBI_EOMI_setone_EOMI_Project.cleaned.annotated.handfiltered.vcf"))
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
this.rodBind :+= new RodBind("dbsnp","vcf",dbsnp)
this.jarFile = sting
this.ST = List("Filter","Novelty","JexlExpression")
this.select_names = List("lowOnly","filteredInLow","Intersection","filteredInHi","hiOnly","filteredInAll")
this.select_exps = List("\"set == 'loCov'\"","\"set == 'hiCov-filterInloCov'\"",
"\"set == 'Intersection'\"", "\"set == 'filterInhiCov-loCov'\"",
"\"set == 'hiCov'\"","\"set == 'FilteredInAll'\"")
this.EV = List("TiTvVariantEvaluator","CountVariants","CompOverlap")
this.out = swapExt(bootstrapMergedOut,".vcf",".merged.combined.eval")
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 22:03:51 +08:00
this.nt = 8
this.memoryLimit = 12
Miscellaneous changes: - RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it) - VCFUtils: grabbing VCF headers given a prefix - MathUtils: Useful functions for calculating statistics on collections of Numbers - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure. - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored in the window optionally different from those returned by whatever statistic is run across the window Added: - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation for when one of the sample sets is small, and the other large. Unit tests to follow. - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-04 06:43:36 +08:00
}
var eval : VariantEval = new VariantEval with EvalArgs
add(eval)
}
}