Commit ee058d6a authored by bow's avatar bow
Browse files

Add ReorderSam (to ensure correct sam header ordering)

parent 119ff147
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
class ReorderSam(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.GatherBamFiles"
@Input(doc = "Input SAM or BAM file", required = true)
var input: File = null
@Input(doc = "Reference sequence to reorder reads to match", required = true)
var reference: File = null
@Output(doc = "Output SAM or BAM file", required = true)
var output: File = null
@Argument(doc = "Allow incomplete dict concordance", required = false)
var allowIncompleteDictConcordance: Boolean = config("allow_incomplete_dict_concordance", default= false)
@Argument(doc = "Allow contig length discordance", required = false)
var allowContigLengthDiscordance: Boolean = config("allow_contig_length_discordance", default= false)
override def commandLine = super.commandLine +
conditional(allowIncompleteDictConcordance, "ALLOW_INCOMPLETE_DICT_CONCORDANCE=TRUE") +
conditional(allowContigLengthDiscordance, "ALLOW_CONTIG_LENGTH_DISCORDANCE=TRUE") +
required("REFERENCE=", reference, spaceSeparated = false) +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false)
}
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