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Commit 967dd7ee authored by Peter van 't Hof's avatar Peter van 't Hof
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Remove short name methods

parent 9f3e8d4d
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
View file @ 967dd7ee
......@@ -22,132 +22,36 @@ class AnalyzeCovariates(val root: Configurable) extends CommandLineGATK with Sca
@Input(fullName = "beforeReportFile", shortName = "before", doc = "file containing the BQSR first-pass report file", required = false, exclusiveOf = "", validation = "")
var beforeReportFile: File = _
/**
* Short name of beforeReportFile
* @return Short name of beforeReportFile
*/
def before = this.beforeReportFile
/**
* Short name of beforeReportFile
* @param value Short name of beforeReportFile
*/
def before_=(value: File) { this.beforeReportFile = value }
/** file containing the BQSR second-pass report file */
@Input(fullName = "afterReportFile", shortName = "after", doc = "file containing the BQSR second-pass report file", required = false, exclusiveOf = "", validation = "")
var afterReportFile: File = _
/**
* Short name of afterReportFile
* @return Short name of afterReportFile
*/
def after = this.afterReportFile
/**
* Short name of afterReportFile
* @param value Short name of afterReportFile
*/
def after_=(value: File) { this.afterReportFile = value }
/** do not emit warning messages related to suspicious last modification time order of inputs */
@Argument(fullName = "ignoreLastModificationTimes", shortName = "ignoreLMT", doc = "do not emit warning messages related to suspicious last modification time order of inputs", required = false, exclusiveOf = "", validation = "")
var ignoreLastModificationTimes: Boolean = _
/**
* Short name of ignoreLastModificationTimes
* @return Short name of ignoreLastModificationTimes
*/
def ignoreLMT = this.ignoreLastModificationTimes
/**
* Short name of ignoreLastModificationTimes
* @param value Short name of ignoreLastModificationTimes
*/
def ignoreLMT_=(value: Boolean) { this.ignoreLastModificationTimes = value }
/** location of the output report */
@Output(fullName = "plotsReportFile", shortName = "plots", doc = "location of the output report", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction])
var plotsReportFile: File = _
/**
* Short name of plotsReportFile
* @return Short name of plotsReportFile
*/
def plots = this.plotsReportFile
/**
* Short name of plotsReportFile
* @param value Short name of plotsReportFile
*/
def plots_=(value: File) { this.plotsReportFile = value }
/** location of the csv intermediate file */
@Output(fullName = "intermediateCsvFile", shortName = "csv", doc = "location of the csv intermediate file", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction])
var intermediateCsvFile: File = _
/**
* Short name of intermediateCsvFile
* @return Short name of intermediateCsvFile
*/
def csv = this.intermediateCsvFile
/**
* Short name of intermediateCsvFile
* @param value Short name of intermediateCsvFile
*/
def csv_=(value: File) { this.intermediateCsvFile = value }
/** Filter out reads with CIGAR containing the N operator, instead of failing with an error */
@Argument(fullName = "filter_reads_with_N_cigar", shortName = "filterRNC", doc = "Filter out reads with CIGAR containing the N operator, instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_reads_with_N_cigar: Boolean = _
/**
* Short name of filter_reads_with_N_cigar
* @return Short name of filter_reads_with_N_cigar
*/
def filterRNC = this.filter_reads_with_N_cigar
/**
* Short name of filter_reads_with_N_cigar
* @param value Short name of filter_reads_with_N_cigar
*/
def filterRNC_=(value: Boolean) { this.filter_reads_with_N_cigar = value }
/** Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error */
@Argument(fullName = "filter_mismatching_base_and_quals", shortName = "filterMBQ", doc = "Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_mismatching_base_and_quals: Boolean = _
/**
* Short name of filter_mismatching_base_and_quals
* @return Short name of filter_mismatching_base_and_quals
*/
def filterMBQ = this.filter_mismatching_base_and_quals
/**
* Short name of filter_mismatching_base_and_quals
* @param value Short name of filter_mismatching_base_and_quals
*/
def filterMBQ_=(value: Boolean) { this.filter_mismatching_base_and_quals = value }
/** Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error */
@Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_bases_not_stored: Boolean = _
/**
* Short name of filter_bases_not_stored
* @return Short name of filter_bases_not_stored
*/
def filterNoBases = this.filter_bases_not_stored
/**
* Short name of filter_bases_not_stored
* @param value Short name of filter_bases_not_stored
*/
def filterNoBases_=(value: Boolean) { this.filter_bases_not_stored = value }
override def cmdLine = super.cmdLine +
optional("-before", beforeReportFile, spaceSeparated = true, escape = true, format = "%s") +
optional("-after", afterReportFile, spaceSeparated = true, escape = true, format = "%s") +
......@@ -162,9 +66,9 @@ class AnalyzeCovariates(val root: Configurable) extends CommandLineGATK with Sca
object AnalyzeCovariates {
def apply(root: Configurable, before: File, after: File, plots: File): AnalyzeCovariates = {
val ac = new AnalyzeCovariates(root)
ac.before = before
ac.after = after
ac.plots = plots
ac.beforeReportFile = before
ac.afterReportFile = after
ac.plotsReportFile = plots
ac
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
View file @ 967dd7ee
......@@ -74,18 +74,6 @@ class ApplyRecalibration(val root: Configurable) extends CommandLineGATK with Sc
@Input(fullName = "recal_file", shortName = "recalFile", doc = "The input recal file used by ApplyRecalibration", required = true, exclusiveOf = "", validation = "")
var recal_file: File = _
/**
* Short name of recal_file
* @return Short name of recal_file
*/
def recalFile = this.recal_file
/**
* Short name of recal_file
* @param value Short name of recal_file
*/
def recalFile_=(value: File) { this.recal_file = value }
/** Dependencies on the index of recal_file */
@Input(fullName = "recal_fileIndex", shortName = "", doc = "Dependencies on the index of recal_file", required = false, exclusiveOf = "", validation = "")
private var recal_fileIndex: Seq[File] = Nil
......@@ -94,35 +82,11 @@ class ApplyRecalibration(val root: Configurable) extends CommandLineGATK with Sc
@Input(fullName = "tranches_file", shortName = "tranchesFile", doc = "The input tranches file describing where to cut the data", required = false, exclusiveOf = "", validation = "")
var tranches_file: File = _
/**
* Short name of tranches_file
* @return Short name of tranches_file
*/
def tranchesFile = this.tranches_file
/**
* Short name of tranches_file
* @param value Short name of tranches_file
*/
def tranchesFile_=(value: File) { this.tranches_file = value }
/** The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value */
@Output(fullName = "out", shortName = "o", doc = "The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer])
var out: File = _
/**
* Short name of out
* @return Short name of out
*/
def o = this.out
/**
* Short name of out
* @param value Short name of out
*/
def o_=(value: File) { this.out = value }
/** Automatically generated index for out */
@Output(fullName = "outIndex", shortName = "", doc = "Automatically generated index for out", required = false, exclusiveOf = "", validation = "")
@Gather(enabled = false)
......@@ -148,50 +112,14 @@ class ApplyRecalibration(val root: Configurable) extends CommandLineGATK with Sc
@Argument(fullName = "ignore_filter", shortName = "ignoreFilter", doc = "If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file", required = false, exclusiveOf = "", validation = "")
var ignore_filter: Seq[String] = Nil
/**
* Short name of ignore_filter
* @return Short name of ignore_filter
*/
def ignoreFilter = this.ignore_filter
/**
* Short name of ignore_filter
* @param value Short name of ignore_filter
*/
def ignoreFilter_=(value: Seq[String]) { this.ignore_filter = value }
/** If specified, the variant recalibrator will ignore all input filters. Useful to rerun the VQSR from a filtered output file. */
@Argument(fullName = "ignore_all_filters", shortName = "ignoreAllFilters", doc = "If specified, the variant recalibrator will ignore all input filters. Useful to rerun the VQSR from a filtered output file.", required = false, exclusiveOf = "", validation = "")
var ignore_all_filters: Boolean = _
/**
* Short name of ignore_all_filters
* @return Short name of ignore_all_filters
*/
def ignoreAllFilters = this.ignore_all_filters
/**
* Short name of ignore_all_filters
* @param value Short name of ignore_all_filters
*/
def ignoreAllFilters_=(value: Boolean) { this.ignore_all_filters = value }
/** Don't output filtered loci after applying the recalibration */
@Argument(fullName = "excludeFiltered", shortName = "ef", doc = "Don't output filtered loci after applying the recalibration", required = false, exclusiveOf = "", validation = "")
var excludeFiltered: Boolean = _
/**
* Short name of excludeFiltered
* @return Short name of excludeFiltered
*/
def ef = this.excludeFiltered
/**
* Short name of excludeFiltered
* @param value Short name of excludeFiltered
*/
def ef_=(value: Boolean) { this.excludeFiltered = value }
/** Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously. */
@Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously.", required = false, exclusiveOf = "", validation = "")
var mode: String = _
......@@ -200,50 +128,14 @@ class ApplyRecalibration(val root: Configurable) extends CommandLineGATK with Sc
@Argument(fullName = "filter_reads_with_N_cigar", shortName = "filterRNC", doc = "Filter out reads with CIGAR containing the N operator, instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_reads_with_N_cigar: Boolean = _
/**
* Short name of filter_reads_with_N_cigar
* @return Short name of filter_reads_with_N_cigar
*/
def filterRNC = this.filter_reads_with_N_cigar
/**
* Short name of filter_reads_with_N_cigar
* @param value Short name of filter_reads_with_N_cigar
*/
def filterRNC_=(value: Boolean) { this.filter_reads_with_N_cigar = value }
/** Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error */
@Argument(fullName = "filter_mismatching_base_and_quals", shortName = "filterMBQ", doc = "Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_mismatching_base_and_quals: Boolean = _
/**
* Short name of filter_mismatching_base_and_quals
* @return Short name of filter_mismatching_base_and_quals
*/
def filterMBQ = this.filter_mismatching_base_and_quals
/**
* Short name of filter_mismatching_base_and_quals
* @param value Short name of filter_mismatching_base_and_quals
*/
def filterMBQ_=(value: Boolean) { this.filter_mismatching_base_and_quals = value }
/** Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error */
@Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_bases_not_stored: Boolean = _
/**
* Short name of filter_bases_not_stored
* @return Short name of filter_bases_not_stored
*/
def filterNoBases = this.filter_bases_not_stored
/**
* Short name of filter_bases_not_stored
* @param value Short name of filter_bases_not_stored
*/
def filterNoBases_=(value: Boolean) { this.filter_bases_not_stored = value }
override def freezeFieldValues() {
super.freezeFieldValues()
inputIndexes ++= input.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => new File(orig.getPath + ".idx"))
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
View file @ 967dd7ee
......@@ -44,66 +44,18 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
//@Gather(classOf[org.broadinstitute.gatk.engine.recalibration.BQSRGatherer])
var out: File = _
/**
* Short name of out
* @return Short name of out
*/
def o = this.out
/**
* Short name of out
* @param value Short name of out
*/
def o_=(value: File) { this.out = value }
/** List the available covariates and exit */
@Argument(fullName = "list", shortName = "ls", doc = "List the available covariates and exit", required = false, exclusiveOf = "", validation = "")
var list: Boolean = _
/**
* Short name of list
* @return Short name of list
*/
def ls = this.list
/**
* Short name of list
* @param value Short name of list
*/
def ls_=(value: Boolean) { this.list = value }
/** One or more covariates to be used in the recalibration. Can be specified multiple times */
@Argument(fullName = "covariate", shortName = "cov", doc = "One or more covariates to be used in the recalibration. Can be specified multiple times", required = false, exclusiveOf = "", validation = "")
var covariate: Seq[String] = Nil
/**
* Short name of covariate
* @return Short name of covariate
*/
def cov = this.covariate
/**
* Short name of covariate
* @param value Short name of covariate
*/
def cov_=(value: Seq[String]) { this.covariate = value }
/** Do not use the standard set of covariates, but rather just the ones listed using the -cov argument */
@Argument(fullName = "no_standard_covs", shortName = "noStandard", doc = "Do not use the standard set of covariates, but rather just the ones listed using the -cov argument", required = false, exclusiveOf = "", validation = "")
var no_standard_covs: Boolean = _
/**
* Short name of no_standard_covs
* @return Short name of no_standard_covs
*/
def noStandard = this.no_standard_covs
/**
* Short name of no_standard_covs
* @param value Short name of no_standard_covs
*/
def noStandard_=(value: Boolean) { this.no_standard_covs = value }
/** If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only. */
@Argument(fullName = "run_without_dbsnp_potentially_ruining_quality", shortName = "run_without_dbsnp_potentially_ruining_quality", doc = "If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only.", required = false, exclusiveOf = "", validation = "")
var run_without_dbsnp_potentially_ruining_quality: Boolean = _
......@@ -112,18 +64,6 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
@Argument(fullName = "solid_recal_mode", shortName = "sMode", doc = "How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS", required = false, exclusiveOf = "", validation = "")
var solid_recal_mode: String = _
/**
* Short name of solid_recal_mode
* @return Short name of solid_recal_mode
*/
def sMode = this.solid_recal_mode
/**
* Short name of solid_recal_mode
* @param value Short name of solid_recal_mode
*/
def sMode_=(value: String) { this.solid_recal_mode = value }
/** Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ */
@Argument(fullName = "solid_nocall_strategy", shortName = "solid_nocall_strategy", doc = "Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ", required = false, exclusiveOf = "", validation = "")
var solid_nocall_strategy: String = _
......@@ -132,210 +72,54 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
@Argument(fullName = "mismatches_context_size", shortName = "mcs", doc = "Size of the k-mer context to be used for base mismatches", required = false, exclusiveOf = "", validation = "")
var mismatches_context_size: Option[Int] = None
/**
* Short name of mismatches_context_size
* @return Short name of mismatches_context_size
*/
def mcs = this.mismatches_context_size
/**
* Short name of mismatches_context_size
* @param value Short name of mismatches_context_size
*/
def mcs_=(value: Option[Int]) { this.mismatches_context_size = value }
/** Size of the k-mer context to be used for base insertions and deletions */
@Argument(fullName = "indels_context_size", shortName = "ics", doc = "Size of the k-mer context to be used for base insertions and deletions", required = false, exclusiveOf = "", validation = "")
var indels_context_size: Option[Int] = None
/**
* Short name of indels_context_size
* @return Short name of indels_context_size
*/
def ics = this.indels_context_size
/**
* Short name of indels_context_size
* @param value Short name of indels_context_size
*/
def ics_=(value: Option[Int]) { this.indels_context_size = value }
/** The maximum cycle value permitted for the Cycle covariate */
@Argument(fullName = "maximum_cycle_value", shortName = "maxCycle", doc = "The maximum cycle value permitted for the Cycle covariate", required = false, exclusiveOf = "", validation = "")
var maximum_cycle_value: Option[Int] = None
/**
* Short name of maximum_cycle_value
* @return Short name of maximum_cycle_value
*/
def maxCycle = this.maximum_cycle_value
/**
* Short name of maximum_cycle_value
* @param value Short name of maximum_cycle_value
*/
def maxCycle_=(value: Option[Int]) { this.maximum_cycle_value = value }
/** default quality for the base mismatches covariate */
@Argument(fullName = "mismatches_default_quality", shortName = "mdq", doc = "default quality for the base mismatches covariate", required = false, exclusiveOf = "", validation = "")
var mismatches_default_quality: Option[Byte] = None
/**
* Short name of mismatches_default_quality
* @return Short name of mismatches_default_quality
*/
def mdq = this.mismatches_default_quality
/**
* Short name of mismatches_default_quality
* @param value Short name of mismatches_default_quality
*/
def mdq_=(value: Option[Byte]) { this.mismatches_default_quality = value }
/** default quality for the base insertions covariate */
@Argument(fullName = "insertions_default_quality", shortName = "idq", doc = "default quality for the base insertions covariate", required = false, exclusiveOf = "", validation = "")
var insertions_default_quality: Option[Byte] = None
/**
* Short name of insertions_default_quality
* @return Short name of insertions_default_quality
*/
def idq = this.insertions_default_quality
/**
* Short name of insertions_default_quality
* @param value Short name of insertions_default_quality
*/
def idq_=(value: Option[Byte]) { this.insertions_default_quality = value }
/** default quality for the base deletions covariate */
@Argument(fullName = "deletions_default_quality", shortName = "ddq", doc = "default quality for the base deletions covariate", required = false, exclusiveOf = "", validation = "")
var deletions_default_quality: Option[Byte] = None
/**
* Short name of deletions_default_quality
* @return Short name of deletions_default_quality
*/
def ddq = this.deletions_default_quality
/**
* Short name of deletions_default_quality
* @param value Short name of deletions_default_quality
*/
def ddq_=(value: Option[Byte]) { this.deletions_default_quality = value }
/** minimum quality for the bases in the tail of the reads to be considered */
@Argument(fullName = "low_quality_tail", shortName = "lqt", doc = "minimum quality for the bases in the tail of the reads to be considered", required = false, exclusiveOf = "", validation = "")
var low_quality_tail: Option[Byte] = None
/**
* Short name of low_quality_tail
* @return Short name of low_quality_tail
*/
def lqt = this.low_quality_tail
/**
* Short name of low_quality_tail
* @param value Short name of low_quality_tail
*/
def lqt_=(value: Option[Byte]) { this.low_quality_tail = value }
/** number of distinct quality scores in the quantized output */
@Argument(fullName = "quantizing_levels", shortName = "ql", doc = "number of distinct quality scores in the quantized output", required = false, exclusiveOf = "", validation = "")
var quantizing_levels: Option[Int] = None
/**
* Short name of quantizing_levels
* @return Short name of quantizing_levels
*/
def ql = this.quantizing_levels
/**
* Short name of quantizing_levels
* @param value Short name of quantizing_levels
*/
def ql_=(value: Option[Int]) { this.quantizing_levels = value }
/** the binary tag covariate name if using it */
@Argument(fullName = "binary_tag_name", shortName = "bintag", doc = "the binary tag covariate name if using it", required = false, exclusiveOf = "", validation = "")
var binary_tag_name: String = _
/**
* Short name of binary_tag_name
* @return Short name of binary_tag_name
*/
def bintag = this.binary_tag_name
/**
* Short name of binary_tag_name
* @param value Short name of binary_tag_name
*/
def bintag_=(value: String) { this.binary_tag_name = value }
/** Sort the rows in the tables of reports */
@Argument(fullName = "sort_by_all_columns", shortName = "sortAllCols", doc = "Sort the rows in the tables of reports", required = false, exclusiveOf = "", validation = "")
var sort_by_all_columns: Boolean = _
/**
* Short name of sort_by_all_columns
* @return Short name of sort_by_all_columns
*/
def sortAllCols = this.sort_by_all_columns
/**
* Short name of sort_by_all_columns
* @param value Short name of sort_by_all_columns
*/
def sortAllCols_=(value: Boolean) { this.sort_by_all_columns = value }
/** If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid. */
@Argument(fullName = "default_platform", shortName = "dP", doc = "If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.", required = false, exclusiveOf = "", validation = "")
var default_platform: String = _