Commit 179d9f01 authored by bow's avatar bow
Browse files

Add WipeReads to main command line interface

parent 9e5f2608
package nl.lumc.sasc.biopet.core package nl.lumc.sasc.biopet.core
import nl.lumc.sasc.biopet.core.apps.WipeReads
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.basty.Basty import nl.lumc.sasc.biopet.pipelines.basty.Basty
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
...@@ -31,6 +32,7 @@ object BiopetExecutable { ...@@ -31,6 +32,7 @@ object BiopetExecutable {
) )
val tools: Map[String, ToolCommand] = Map( val tools: Map[String, ToolCommand] = Map(
"WipeReads" -> WipeReads
) )
/** /**
......
...@@ -19,6 +19,7 @@ import org.apache.commons.io.FilenameUtils.getExtension ...@@ -19,6 +19,7 @@ import org.apache.commons.io.FilenameUtils.getExtension
import org.broadinstitute.gatk.utils.commandline.{ Input, Output } import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
// TODO: finish implementation for usage in pipelines // TODO: finish implementation for usage in pipelines
...@@ -39,7 +40,7 @@ class WipeReads(val root: Configurable) extends BiopetJavaCommandLineFunction { ...@@ -39,7 +40,7 @@ class WipeReads(val root: Configurable) extends BiopetJavaCommandLineFunction {
} }
object WipeReads { object WipeReads extends ToolCommand {
/** Container type for command line flags */ /** Container type for command line flags */
type OptionMap = Map[String, Any] type OptionMap = Map[String, Any]
...@@ -392,28 +393,29 @@ object WipeReads { ...@@ -392,28 +393,29 @@ object WipeReads {
val usage: String = val usage: String =
""" """
|usage: java -cp BiopetFramework.jar nl.lumc.sasc.biopet.core.apps.WipeReads [options] -I input -l regions -o output |Usage: java -jar BiopetFramework.jar tool %s [options] -I input -l regions -o output
| |
|WipeReads - Tool for reads removal from an indexed BAM file |%s - Tool for reads removal from an indexed BAM file
| |
|positional arguments: |Positional arguments:
| -I,--inputBAM Input BAM file, must be indexed with '.bam.bai' or 'bai' extension | -I,--inputBAM Input BAM file, must be indexed with
| '.bam.bai' or 'bai' extension
| -l,--targetRegions Input BED file | -l,--targetRegions Input BED file
| -o,--outputBAM Output BAM file | -o,--outputBAM Output BAM file
| |
|optional arguments: |Optional arguments:
| -RG,--readGroup Read groups to remove; set multiple read groups using commas | -RG,--readGroup Read groups to remove; set multiple read
| (default: all) | groups using commas (default: all)
| -Q,--minMapQ Minimum MAPQ value of reads in target region | -Q,--minMapQ Minimum MAPQ value of reads in target region
| (default: 0) | (default: 0)
| --makeIndex Write BAM output file index | --makeIndex Write BAM output file index
| (default: true) | (default: true)
| --limitToRegion Whether to remove only reads in the target regions and and | --limitToRegion Whether to remove only reads in the target
| keep the same reads if they map to other regions | regions and and keep the same reads if they
| (default: not set) | map to other regions (default: not set)
| |
|This tool will remove BAM records that overlaps a set of given regions. |This tool will remove BAM records that overlaps a set of given regions.
|By default, if the removed reads are also mapped to other regions outside |By default, if the removed reads are also mapped to other regions outside
|the given ones, they will also be removed. |the given ones, they will also be removed.
""".stripMargin """.stripMargin.format(toolName, toolName)
} }
\ No newline at end of file
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