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biopet.biopet
Commits
179d9f01
Commit
179d9f01
authored
Oct 07, 2014
by
bow
Browse files
Add WipeReads to main command line interface
parent
9e5f2608
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
View file @
179d9f01
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.basty.Basty
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
...
...
@@ -31,6 +32,7 @@ object BiopetExecutable {
)
val
tools
:
Map
[
String
,
ToolCommand
]
=
Map
(
"WipeReads"
->
WipeReads
)
/**
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/WipeReads.scala
View file @
179d9f01
...
...
@@ -19,6 +19,7 @@ import org.apache.commons.io.FilenameUtils.getExtension
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
// TODO: finish implementation for usage in pipelines
...
...
@@ -39,7 +40,7 @@ class WipeReads(val root: Configurable) extends BiopetJavaCommandLineFunction {
}
object
WipeReads
{
object
WipeReads
extends
ToolCommand
{
/** Container type for command line flags */
type
OptionMap
=
Map
[
String
,
Any
]
...
...
@@ -392,28 +393,29 @@ object WipeReads {
val
usage
:
String
=
"""
|
u
sage: java -
cp
BiopetFramework.jar
nl.lumc.sasc.biopet.core.apps.WipeRead
s [options] -I input -l regions -o output
|
U
sage: java -
jar
BiopetFramework.jar
tool %
s [options] -I input -l regions -o output
|
|
WipeRead
s - Tool for reads removal from an indexed BAM file
|
%
s - Tool for reads removal from an indexed BAM file
|
|positional arguments:
| -I,--inputBAM Input BAM file, must be indexed with '.bam.bai' or 'bai' extension
|Positional arguments:
| -I,--inputBAM Input BAM file, must be indexed with
| '.bam.bai' or 'bai' extension
| -l,--targetRegions Input BED file
| -o,--outputBAM Output BAM file
|
|
o
ptional arguments:
| -RG,--readGroup Read groups to remove; set multiple read
groups using commas
| (default: all)
|
O
ptional arguments:
| -RG,--readGroup Read groups to remove; set multiple read
|
groups using commas
(default: all)
| -Q,--minMapQ Minimum MAPQ value of reads in target region
| (default: 0)
| --makeIndex Write BAM output file index
| (default: true)
| --limitToRegion Whether to remove only reads in the target
regions and and
| keep the same reads if they
map to other regions
| (default: not set)
| --limitToRegion Whether to remove only reads in the target
|
regions and and
keep the same reads if they
|
map to other regions
(default: not set)
|
|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
|the given ones, they will also be removed.
"""
.
stripMargin
"""
.
stripMargin
.
format
(
toolName
,
toolName
)
}
\ No newline at end of file
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