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Mirrors
biopet.biopet
Commits
c913b602
Commit
c913b602
authored
Jul 25, 2017
by
Peter van 't Hof
Committed by
GitHub
Jul 25, 2017
Browse files
Merge pull request #165 from biopet/fix-BIOPET-750
Adding spark support for VcfStats
parents
dc145917
db65e3d7
Changes
67
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
View file @
c913b602
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.summary.Summary
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Question
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ConfigUtils
,
Question
,
ToolCommand
}
import
scala.io.Source
...
...
@@ -30,9 +30,8 @@ trait TemplateTool extends ToolCommand {
runScript
:
Option
[
File
]
=
None
,
expert
:
Boolean
=
false
,
template
:
Option
[
File
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'o'
,
"outputConfig"
)
required
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
outputConfig
=
x
)
}
text
"Path to output config"
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/pipelinestatus/PipelineStatus.scala
View file @
c913b602
...
...
@@ -20,7 +20,7 @@ import akka.actor.ActorSystem
import
akka.stream.ActorMaterializer
import
nl.lumc.sasc.biopet.utils.pim._
import
nl.lumc.sasc.biopet.utils.pim.
{
Job
=>
PimJob
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ConfigUtils
,
ToolCommand
}
import
play.api.libs.ws.ahc.AhcWSClient
import
scala.concurrent.ExecutionContext.Implicits.global
...
...
@@ -41,9 +41,8 @@ object PipelineStatus extends ToolCommand {
compressPlots
:
Boolean
=
true
,
pimHost
:
Option
[
String
]
=
None
,
pimRunId
:
Option
[
String
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'd'
,
"pipelineDir"
)
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
pipelineDir
=
x
)
}
text
"Output directory of the pipeline"
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
c913b602
...
...
@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.core.report
import
java.io._
import
nl.lumc.sasc.biopet.core.ToolCommandFunction
import
nl.lumc.sasc.biopet.utils.summary.db.Schema.
{
Library
,
Module
,
Pipeline
,
Sample
,
Run
}
import
nl.lumc.sasc.biopet.utils.summary.db.Schema.
{
Library
,
Module
,
Pipeline
,
Run
,
Sample
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.
{
LibraryId
,
SampleId
}
import
nl.lumc.sasc.biopet.utils.
{
IoUtils
,
Logging
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
IoUtils
,
Logging
,
ToolCommand
}
import
org.broadinstitute.gatk.utils.commandline.Input
import
org.fusesource.scalate.TemplateEngine
...
...
@@ -82,9 +82,8 @@ trait ReportBuilder extends ToolCommand {
outputDir
:
File
=
null
,
runId
:
Int
=
0
,
pageArgs
:
mutable.Map
[
String
,
Any
]
=
mutable
.
Map
())
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
head
(
s
"""
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
View file @
c913b602
...
...
@@ -20,7 +20,7 @@ package nl.lumc.sasc.biopet.extensions.clever
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
...
...
@@ -48,9 +48,8 @@ class CleverFixVCF(val parent: Configurable) extends BiopetJavaCommandLineFuncti
object
CleverFixVCF
extends
ToolCommand
{
case
class
Args
(
inputVCF
:
File
=
null
,
sampleLabel
:
String
=
""
,
outputVCF
:
File
=
null
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'i'
,
"inputvcf"
)
required
()
valueName
"<vcffile/path>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputVCF
=
x
)
}
text
"Please specify the input Clever VCF file"
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
View file @
c913b602
...
...
@@ -18,7 +18,7 @@ import java.io.{File, PrintWriter}
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
BamUtils
,
ToolCommand
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
class
PindelConfig
(
val
parent
:
Configurable
)
extends
BiopetJavaCommandLineFunction
{
...
...
@@ -46,9 +46,8 @@ object PindelConfig extends ToolCommand {
sampleLabel
:
Option
[
String
]
=
None
,
insertSize
:
Option
[
Int
]
=
None
,
output
:
Option
[
File
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'i'
,
"inputbam"
)
required
()
valueName
"<bamfile/path>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputBam
=
x
)
}
text
"Please specify the input bam file"
...
...
biopet-package/pom.xml
View file @
c913b602
...
...
@@ -155,6 +155,20 @@
</transformer>
</transformers>
<filters>
<filter>
<artifact>
*:*
</artifact>
<excludes>
<exclude>
META-INF/*.SF
</exclude>
<exclude>
META-INF/*.DSA
</exclude>
<exclude>
META-INF/*.RSA
</exclude>
</excludes>
</filter>
<filter>
<artifact>
javax.servlet:servlet-api:2.5
</artifact>
<excludes>
<exclude>
*.*
</exclude>
</excludes>
</filter>
</filters>
</configuration>
<executions>
...
...
biopet-tools/pom.xml
View file @
c913b602
...
...
@@ -29,6 +29,11 @@
<artifactId>
BiopetTools
</artifactId>
<dependencies>
<dependency>
<groupId>
org.apache.spark
</groupId>
<artifactId>
spark-core_2.11
</artifactId>
<version>
2.2.0
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetUtils
</artifactId>
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
View file @
c913b602
...
...
@@ -22,7 +22,7 @@ import htsjdk.variant.variantcontext.writer.{
VariantContextWriterBuilder
}
import
htsjdk.variant.vcf.
{
VCFFileReader
,
VCFHeaderLineCount
,
VCFHeaderLineType
,
VCFInfoHeaderLine
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.intervals.
{
BedRecord
,
BedRecordList
}
import
scala.collection.JavaConversions._
...
...
@@ -51,9 +51,8 @@ object AnnotateVcfWithBed extends ToolCommand {
fieldName
:
String
=
null
,
fieldDescription
:
String
=
""
,
fieldType
:
String
=
"String"
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'I'
,
"inputFile"
)
required
()
unbounded
()
valueName
"<vcf file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFile
=
x
)
}
text
"Input VCF file. Mandatory field"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
View file @
c913b602
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
htsjdk.samtools.
{
SAMRecord
,
SamReaderFactory
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ConfigUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.intervals.
{
BedRecord
,
BedRecordList
}
import
picard.annotation.
{
Gene
,
GeneAnnotationReader
}
...
...
@@ -35,9 +35,8 @@ object BaseCounter extends ToolCommand {
outputDir
:
File
=
null
,
bamFile
:
File
=
null
,
prefix
:
String
=
"output"
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'r'
,
"refFlat"
)
required
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
refFlat
=
x
)
}
text
"refFlat file. Mandatory"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
View file @
c913b602
...
...
@@ -20,7 +20,7 @@ import htsjdk.samtools.SamReaderFactory
import
htsjdk.samtools.reference.IndexedFastaSequenceFile
import
htsjdk.variant.variantcontext.VariantContext
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.VcfUtils._
import
scala.collection.JavaConversions._
...
...
@@ -38,9 +38,8 @@ object BastyGenerateFasta extends ToolCommand {
minAD
:
Int
=
8
,
minDepth
:
Int
=
8
,
reference
:
File
=
null
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'V'
,
"inputVcf"
)
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputVcf
=
x
)
}
text
"vcf file, needed for outputVariants and outputConsensusVariants"
validate
{
x
=>
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
View file @
c913b602
...
...
@@ -16,10 +16,10 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
htsjdk.samtools.
{
SAMSequenceRecord
,
SamReaderFactory
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
scala.collection.JavaConversions._
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
scala.collection.JavaConversions._
import
scala.io.Source
/**
...
...
@@ -28,9 +28,8 @@ import scala.io.Source
object
BedToInterval
extends
ToolCommand
{
case
class
Args
(
inputFile
:
File
=
null
,
outputFile
:
File
=
null
,
bamFile
:
File
=
null
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'I'
,
"inputFile"
)
required
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFile
=
x
)
}
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
View file @
c913b602
...
...
@@ -16,15 +16,15 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
scala.collection.
{
SortedMap
,
mutable
}
import
scala.io.Source
object
BedtoolsCoverageToCounts
extends
ToolCommand
{
case
class
Args
(
input
:
File
=
null
,
output
:
File
=
null
)
extends
AbstractArgs
case
class
Args
(
input
:
File
=
null
,
output
:
File
=
null
)
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'I'
,
"input"
)
required
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
input
=
x
)
}
text
"Coverage file produced with bedtools"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
View file @
c913b602
...
...
@@ -23,7 +23,7 @@ import htsjdk.variant.variantcontext.writer.{
VariantContextWriterBuilder
}
import
htsjdk.variant.vcf.
{
VCFFileReader
,
VCFHeaderLineCount
,
VCFHeaderLineType
,
VCFInfoHeaderLine
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
scala.collection.JavaConversions._
import
scala.collection.mutable
...
...
@@ -49,9 +49,8 @@ object CheckAllelesVcfInBam extends ToolCommand {
samples
:
List
[
String
]
=
Nil
,
bamFiles
:
List
[
File
]
=
Nil
,
minMapQual
:
Int
=
1
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'I'
,
"inputFile"
)
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFile
=
x
)
}
text
"VCF file"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala
View file @
c913b602
...
...
@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
scala.io.Source
...
...
@@ -31,9 +31,8 @@ object DownloadNcbiAssembly extends ToolCommand {
contigNameHeader
:
Option
[
String
]
=
None
,
mustHaveOne
:
List
[(
String
,
String
)]
=
List
(),
mustNotHave
:
List
[(
String
,
String
)]
=
List
())
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'a'
,
"assembly_report"
)
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
assemblyReport
=
x
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
View file @
c913b602
...
...
@@ -19,7 +19,7 @@ import java.io.File
import
htsjdk.samtools.
{
QueryInterval
,
SamReaderFactory
,
ValidationStringency
}
import
htsjdk.samtools.fastq.
{
BasicFastqWriter
,
FastqReader
,
FastqRecord
}
import
htsjdk.samtools.util.Interval
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
scala.collection.JavaConverters._
import
scala.collection.mutable.
{
Set
=>
MSet
}
...
...
@@ -181,10 +181,9 @@ object ExtractAlignedFastq extends ToolCommand {
outputFastq2
:
Option
[
File
]
=
None
,
minMapQ
:
Int
=
0
,
commonSuffixLength
:
Int
=
0
)
extends
AbstractArgs
/** Command line argument parser */
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
head
(
s
"""
|$commandName - Select aligned FASTQ records
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractTagsFromGtf.scala
View file @
c913b602
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.annotation.Feature
import
scala.io.Source
...
...
@@ -15,9 +15,8 @@ object ExtractTagsFromGtf extends ToolCommand {
gtfFile
:
File
=
null
,
tags
:
List
[
String
]
=
Nil
,
feature
:
Option
[
String
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'o'
,
"output"
)
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
outputFile
=
x
)
}
text
"Input refFlat file. Mandatory"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqFilter.scala
View file @
c913b602
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.samtools.fastq.
{
AsyncFastqWriter
,
BasicFastqWriter
,
FastqReader
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
scala.util.matching.Regex
import
scala.collection.JavaConversions._
...
...
@@ -33,9 +33,8 @@ object FastqFilter extends ToolCommand {
* @param outputFile output fastq files
*/
case
class
Args
(
inputFile
:
File
=
null
,
outputFile
:
File
=
null
,
idRegex
:
Option
[
Regex
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'I'
,
"inputFile"
)
required
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFile
=
x
)
}
text
"Path to input file"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
View file @
c913b602
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.samtools.fastq.
{
AsyncFastqWriter
,
BasicFastqWriter
,
FastqReader
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
object
FastqSplitter
extends
ToolCommand
{
...
...
@@ -26,9 +26,9 @@ object FastqSplitter extends ToolCommand {
* @param inputFile input fastq file
* @param outputFile output fastq files
*/
case
class
Args
(
inputFile
:
File
=
null
,
outputFile
:
List
[
File
]
=
Nil
)
extends
AbstractArgs
case
class
Args
(
inputFile
:
File
=
null
,
outputFile
:
List
[
File
]
=
Nil
)
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'I'
,
"inputFile"
)
required
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFile
=
x
)
}
text
"Path to input file"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
View file @
c913b602
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.samtools.fastq.
{
AsyncFastqWriter
,
BasicFastqWriter
,
FastqReader
,
FastqRecord
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
scala.annotation.tailrec
import
scala.collection.JavaConverters._
...
...
@@ -113,9 +113,8 @@ object FastqSync extends ToolCommand {
inputFastq2
:
File
=
null
,
outputFastq1
:
File
=
null
,
outputFastq2
:
File
=
null
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
head
(
s
"""
|$commandName - Sync paired-end FASTQ files.
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala
View file @
c913b602
...
...
@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintStream
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
scala.collection.mutable.ListBuffer
import
scala.io.Source
...
...
@@ -35,9 +35,8 @@ object FindOverlapMatch extends ToolCommand {
filterSameNames
:
Boolean
=
true
,
rowSampleRegex
:
Option
[
Regex
]
=
None
,
columnSampleRegex
:
Option
[
Regex
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'i'
,
"input"
)
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputMetrics
=
x
)
}
text
"Input should be a table where the first row and column have the ID's, those can be different"
...
...
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