@@ -21,17 +22,13 @@ class IndelRealigner(val root: Configurable) extends CommandLineGATK with Scatte
@Input(fullName="knownAlleles",shortName="known",doc="Input VCF file(s) with known indels",required=false,exclusiveOf="",validation="")
varknownAlleles:Seq[File]=Nil
/** Dependencies on any indexes of knownAlleles */
@Input(fullName="knownAllelesIndexes",shortName="",doc="Dependencies on any indexes of knownAlleles",required=false,exclusiveOf="",validation="")
privatevarknownAllelesIndexes:Seq[File]=Nil
/** Intervals file output from RealignerTargetCreator */
@Input(fullName="targetIntervals",shortName="targetIntervals",doc="Intervals file output from RealignerTargetCreator",required=true,exclusiveOf="",validation="")
vartargetIntervals:File=_
/** LOD threshold above which the cleaner will clean */
@Argument(fullName="LODThresholdForCleaning",shortName="LOD",doc="LOD threshold above which the cleaner will clean",required=false,exclusiveOf="",validation="")
@Argument(fullName="LODThresholdForCleaningFormat",shortName="",doc="Format string for LODThresholdForCleaning",required=false,exclusiveOf="",validation="")
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@@ -42,11 +39,6 @@ class IndelRealigner(val root: Configurable) extends CommandLineGATK with Scatte
@Gather(classOf[BamGatherFunction])
varout:File=_
/** Automatically generated index for out */
@Output(fullName="outIndex",shortName="",doc="Automatically generated index for out",required=false,exclusiveOf="",validation="")
@Gather(enabled=false)
privatevaroutIndex:File=_
/** Automatically generated md5 for out */
@Output(fullName="outMD5",shortName="",doc="Automatically generated md5 for out",required=false,exclusiveOf="",validation="")
@Gather(enabled=false)
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@@ -54,11 +46,11 @@ class IndelRealigner(val root: Configurable) extends CommandLineGATK with Scatte
/** Determines how to compute the possible alternate consenses */
@Argument(fullName="consensusDeterminationModel",shortName="model",doc="Determines how to compute the possible alternate consenses",required=false,exclusiveOf="",validation="")
/** Percentage of mismatches at a locus to be considered having high entropy (0.0 < entropy <= 1.0) */
@Argument(fullName="entropyThreshold",shortName="entropy",doc="Percentage of mismatches at a locus to be considered having high entropy (0.0 < entropy <= 1.0)",required=false,exclusiveOf="",validation="")
@Argument(fullName="entropyThresholdFormat",shortName="",doc="Format string for entropyThreshold",required=false,exclusiveOf="",validation="")
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@@ -66,51 +58,51 @@ class IndelRealigner(val root: Configurable) extends CommandLineGATK with Scatte
/** max reads allowed to be kept in memory at a time by the SAMFileWriter */
@Argument(fullName="maxReadsInMemory",shortName="maxInMemory",doc="max reads allowed to be kept in memory at a time by the SAMFileWriter",required=false,exclusiveOf="",validation="")
/** maximum insert size of read pairs that we attempt to realign */
@Argument(fullName="maxIsizeForMovement",shortName="maxIsize",doc="maximum insert size of read pairs that we attempt to realign",required=false,exclusiveOf="",validation="")
/** Maximum positional move in basepairs that a read can be adjusted during realignment */
@Argument(fullName="maxPositionalMoveAllowed",shortName="maxPosMove",doc="Maximum positional move in basepairs that a read can be adjusted during realignment",required=false,exclusiveOf="",validation="")
/** Max alternate consensuses to try (necessary to improve performance in deep coverage) */
@Argument(fullName="maxConsensuses",shortName="maxConsensuses",doc="Max alternate consensuses to try (necessary to improve performance in deep coverage)",required=false,exclusiveOf="",validation="")
/** Max reads used for finding the alternate consensuses (necessary to improve performance in deep coverage) */
@Argument(fullName="maxReadsForConsensuses",shortName="greedy",doc="Max reads used for finding the alternate consensuses (necessary to improve performance in deep coverage)",required=false,exclusiveOf="",validation="")
/** Max reads allowed at an interval for realignment */
@Argument(fullName="maxReadsForRealignment",shortName="maxReads",doc="Max reads allowed at an interval for realignment",required=false,exclusiveOf="",validation="")
/** Don't output the original cigar or alignment start tags for each realigned read in the output bam */
@Argument(fullName="noOriginalAlignmentTags",shortName="noTags",doc="Don't output the original cigar or alignment start tags for each realigned read in the output bam",required=false,exclusiveOf="",validation="")
/** Generate one output file for each input (-I) bam file (not compatible with -output) */
@Argument(fullName="nWayOut",shortName="nWayOut",doc="Generate one output file for each input (-I) bam file (not compatible with -output)",required=false,exclusiveOf="",validation="")
varnWayOut:String=_
varnWayOut:Option[String]=config("nWayOut")
/** Generate md5sums for BAMs */
@Argument(fullName="generate_nWayOut_md5s",shortName="",doc="Generate md5sums for BAMs",required=false,exclusiveOf="",validation="")
/** Do early check of reads against existing consensuses */
@Argument(fullName="check_early",shortName="check_early",doc="Do early check of reads against existing consensuses",required=false,exclusiveOf="",validation="")
/** Don't output the usual PG tag in the realigned bam file header. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests. */
@Argument(fullName="noPGTag",shortName="noPG",doc="Don't output the usual PG tag in the realigned bam file header. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.",required=false,exclusiveOf="",validation="")
/** Keep older PG tags left in the bam header by previous runs of this tool (by default, all these historical tags will be replaced by the latest tag generated in the current run). */
@Argument(fullName="keepPGTags",shortName="keepPG",doc="Keep older PG tags left in the bam header by previous runs of this tool (by default, all these historical tags will be replaced by the latest tag generated in the current run).",required=false,exclusiveOf="",validation="")
/** Output file (text) for the indels found; FOR DEBUGGING PURPOSES ONLY */
@Output(fullName="indelsFileForDebugging",shortName="indels",doc="Output file (text) for the indels found; FOR DEBUGGING PURPOSES ONLY",required=false,exclusiveOf="",validation="")
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@@ -129,22 +121,22 @@ class IndelRealigner(val root: Configurable) extends CommandLineGATK with Scatte
/** 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="")
/** 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="")
/** 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="")
@@ -22,64 +22,54 @@ class PrintReads(val root: Configurable) extends CommandLineGATK with ScatterGat
@Gather(classOf[BamGatherFunction])
varout:File=_
/** Automatically generated index for out */
@Output(fullName="outIndex",shortName="",doc="Automatically generated index for out",required=false,exclusiveOf="",validation="")
@Gather(enabled=false)
privatevaroutIndex:File=_
/** Automatically generated md5 for out */
@Output(fullName="outMD5",shortName="",doc="Automatically generated md5 for out",required=false,exclusiveOf="",validation="")
@Gather(enabled=false)
privatevaroutMD5:File=_
/** Exclude all reads with this read group from the output */
@Argument(fullName="readGroup",shortName="readGroup",doc="Exclude all reads with this read group from the output",required=false,exclusiveOf="",validation="")
/** Exclude all reads with this platform from the output */
@Argument(fullName="platform",shortName="platform",doc="Exclude all reads with this platform from the output",required=false,exclusiveOf="",validation="")
varplatform:String=_
varplatform:Option[String]=config("platform")
/** Print the first n reads from the file, discarding the rest */
@Argument(fullName="number",shortName="n",doc="Print the first n reads from the file, discarding the rest",required=false,exclusiveOf="",validation="")
varnumber:Option[Int]=None
varnumber:Option[Int]=config("number")
/** File containing a list of samples (one per line). Can be specified multiple times */
@Argument(fullName="sample_file",shortName="sf",doc="File containing a list of samples (one per line). Can be specified multiple times",required=false,exclusiveOf="",validation="")
/** Sample name to be included in the analysis. Can be specified multiple times. */
@Argument(fullName="sample_name",shortName="sn",doc="Sample name to be included in the analysis. Can be specified multiple times.",required=false,exclusiveOf="",validation="")
/** 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="")
/** 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="")
/** 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="")