/** 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="")
varignoreLastModificationTimes:Boolean=_
/**
* Short name of ignoreLastModificationTimes
* @return Short name of ignoreLastModificationTimes
*/
defignoreLMT=this.ignoreLastModificationTimes
/**
* Short name of ignoreLastModificationTimes
* @param value Short name of ignoreLastModificationTimes
/** 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="")
varfilter_reads_with_N_cigar:Boolean=_
/**
* Short name of filter_reads_with_N_cigar
* @return Short name of filter_reads_with_N_cigar
*/
deffilterRNC=this.filter_reads_with_N_cigar
/**
* Short name of filter_reads_with_N_cigar
* @param value Short name of filter_reads_with_N_cigar
/** 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="")
varfilter_mismatching_base_and_quals:Boolean=_
/**
* Short name of filter_mismatching_base_and_quals
* @return Short name of filter_mismatching_base_and_quals
/** 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="")
varfilter_bases_not_stored:Boolean=_
/**
* Short name of filter_bases_not_stored
* @return Short name of filter_bases_not_stored
*/
deffilterNoBases=this.filter_bases_not_stored
/**
* Short name of filter_bases_not_stored
* @param value Short name of filter_bases_not_stored
@@ -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="")
varrecal_file:File=_
/**
* Short name of recal_file
* @return Short name of recal_file
*/
defrecalFile=this.recal_file
/**
* Short name of recal_file
* @param value Short name of recal_file
*/
defrecalFile_=(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="")
privatevarrecal_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="")
/** 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])
varout:File=_
/**
* Short name of out
* @return Short name of out
*/
defo=this.out
/**
* Short name of out
* @param value Short name of out
*/
defo_=(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="")
/** 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="")
/** 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="")
/** 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="")
varmode: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="")
varfilter_reads_with_N_cigar:Boolean=_
/**
* Short name of filter_reads_with_N_cigar
* @return Short name of filter_reads_with_N_cigar
*/
deffilterRNC=this.filter_reads_with_N_cigar
/**
* Short name of filter_reads_with_N_cigar
* @param value Short name of filter_reads_with_N_cigar
/** 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="")
varfilter_mismatching_base_and_quals:Boolean=_
/**
* Short name of filter_mismatching_base_and_quals
* @return Short name of filter_mismatching_base_and_quals
/** 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="")
varfilter_bases_not_stored:Boolean=_
/**
* Short name of filter_bases_not_stored
* @return Short name of filter_bases_not_stored
*/
deffilterNoBases=this.filter_bases_not_stored
/**
* Short name of filter_bases_not_stored
* @param value Short name of filter_bases_not_stored
@Argument(fullName="list",shortName="ls",doc="List the available covariates and exit",required=false,exclusiveOf="",validation="")
varlist:Boolean=_
/**
* Short name of list
* @return Short name of list
*/
defls=this.list
/**
* Short name of list
* @param value Short name of list
*/
defls_=(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="")
varcovariate:Seq[String]=Nil
/**
* Short name of covariate
* @return Short name of covariate
*/
defcov=this.covariate
/**
* Short name of covariate
* @param value Short name of covariate
*/
defcov_=(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="")
/** 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="")
@@ -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="")
/** 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="")
varsolid_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="")
varmismatches_context_size:Option[Int]=None
/**
* Short name of mismatches_context_size
* @return Short name of mismatches_context_size
*/
defmcs=this.mismatches_context_size
/**
* Short name of mismatches_context_size
* @param value Short name of mismatches_context_size
/** 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="")
/** 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="")
/** 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="")
varmismatches_default_quality:Option[Byte]=None
/**
* Short name of mismatches_default_quality
* @return Short name of mismatches_default_quality
*/
defmdq=this.mismatches_default_quality
/**
* Short name of mismatches_default_quality
* @param value Short name of mismatches_default_quality
/** 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="")
varinsertions_default_quality:Option[Byte]=None
/**
* Short name of insertions_default_quality
* @return Short name of insertions_default_quality
*/
defidq=this.insertions_default_quality
/**
* Short name of insertions_default_quality
* @param value Short name of insertions_default_quality
/** 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="")
vardeletions_default_quality:Option[Byte]=None
/**
* Short name of deletions_default_quality
* @return Short name of deletions_default_quality
*/
defddq=this.deletions_default_quality
/**
* Short name of deletions_default_quality
* @param value Short name of deletions_default_quality
/** 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="")
/** 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="")
@Argument(fullName="sort_by_all_columns",shortName="sortAllCols",doc="Sort the rows in the tables of reports",required=false,exclusiveOf="",validation="")
/** 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="")