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Mirrors
biopet.biopet
Commits
e82756e6
Commit
e82756e6
authored
Jul 18, 2017
by
Peter van 't Hof
Browse files
Switch to output classes for Arg parsing
parent
29b937d4
Changes
55
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
View file @
e82756e6
...
...
@@ -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 @
e82756e6
...
...
@@ -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 @
e82756e6
...
...
@@ -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 @
e82756e6
...
...
@@ -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 @
e82756e6
...
...
@@ -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 @
e82756e6
...
...
@@ -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 @
e82756e6
...
...
@@ -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 @
e82756e6
...
...
@@ -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 @
e82756e6
...
...
@@ -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 @
e82756e6
...
...
@@ -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 @
e82756e6
...
...
@@ -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 @
e82756e6
...
...
@@ -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._
...
...
@@ -111,9 +111,8 @@ object FastqSync extends ToolCommand {
inputFastq2
:
File
=
new
File
(
""
),
outputFastq1
:
File
=
new
File
(
""
),
outputFastq2
:
File
=
new
File
(
""
))
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 @
e82756e6
...
...
@@ -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"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
View file @
e82756e6
...
...
@@ -14,19 +14,18 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
PrintWriter
,
File
}
import
java.io.
{
File
,
PrintWriter
}
import
htsjdk.samtools.
{
QueryInterval
,
SAMRecord
,
SamReaderFactory
,
ValidationStringency
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
scala.collection.JavaConversions._
import
scala.io.Source
object
FindRepeatsPacBio
extends
ToolCommand
{
case
class
Args
(
inputBam
:
File
=
null
,
outputFile
:
Option
[
File
]
=
None
,
inputBed
:
File
=
null
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'I'
,
"inputBam"
)
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputBam
=
x
)
}
text
"Path to input file"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
View file @
e82756e6
...
...
@@ -24,7 +24,7 @@ import htsjdk.variant.variantcontext.writer.{
}
import
htsjdk.variant.variantcontext.
{
Allele
,
GenotypeBuilder
,
VariantContextBuilder
}
import
htsjdk.variant.vcf._
import
nl.lumc.sasc.biopet.utils.
{
FastaUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
FastaUtils
,
ToolCommand
}
import
scala.collection.JavaConversions._
import
scala.io.Source
...
...
@@ -41,9 +41,8 @@ object GensToVcf extends ToolCommand {
referenceFasta
:
File
=
null
,
contig
:
String
=
null
,
sortInput
:
Boolean
=
false
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'g'
,
"inputGenotypes"
)
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputGenotypes
=
x
)
}
text
"Input genotypes"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GtfToRefflat.scala
View file @
e82756e6
package
nl.lumc.sasc.biopet.tools
import
nl.lumc.sasc.biopet.utils.
{
FastaUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
FastaUtils
,
ToolCommand
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.annotation.
{
Exon
,
Feature
,
Gene
,
Transcript
}
...
...
@@ -14,9 +14,8 @@ import scala.io.Source
object
GtfToRefflat
extends
ToolCommand
{
case
class
Args
(
refFlat
:
File
=
null
,
gtfFile
:
File
=
null
,
referenceFasta
:
Option
[
File
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'r'
,
"refFlat"
)
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
refFlat
=
x
)
}
text
"Input refFlat file. Mandatory"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala
View file @
e82756e6
...
...
@@ -18,7 +18,7 @@ import java.io.{File, PrintWriter}
import
htsjdk.variant.variantcontext.VariantContext
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.utils.
{
VcfUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
,
VcfUtils
}
import
nl.lumc.sasc.biopet.utils.intervals.BedRecord
import
scala.collection.JavaConversions._
...
...
@@ -35,9 +35,8 @@ object GvcfToBed extends ToolCommand {
sample
:
Option
[
String
]
=
None
,
minGenomeQuality
:
Int
=
0
,
inverse
:
Boolean
=
false
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'I'
,
"inputVcf"
)
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputVcf
=
x
)
}
text
"Input vcf file"
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
View file @
e82756e6
...
...
@@ -20,7 +20,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils._
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
scala.collection.mutable
import
scala.collection.mutable.ListBuffer
...
...
@@ -60,9 +60,8 @@ object KrakenReportToJson extends ToolCommand {
case
class
Args
(
krakenreport
:
File
=
null
,
outputJson
:
Option
[
File
]
=
None
,
skipNames
:
Boolean
=
false
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
head
(
s
"""
|$commandName - Convert Kraken-report (full) output to JSON
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
View file @
e82756e6
...
...
@@ -23,7 +23,7 @@ import htsjdk.variant.variantcontext.writer.{
}
import
htsjdk.variant.variantcontext.
{
Allele
,
VariantContext
,
VariantContextBuilder
}
import
htsjdk.variant.vcf.
{
VCFFileReader
,
VCFHeader
}
import
nl.lumc.sasc.biopet.utils.
{
FastaUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
FastaUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
scala.collection.JavaConversions._
...
...
@@ -32,9 +32,8 @@ import scala.collection.{SortedMap, mutable}
object
MergeAlleles
extends
ToolCommand
{
case
class
Args
(
inputFiles
:
List
[
File
]
=
Nil
,
outputFile
:
File
=
null
,
reference
:
File
=
null
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'I'
,
"inputVcf"
)
minOccurs
2
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFiles
=
x
::
c
.
inputFiles
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala
View file @
e82756e6
...
...
@@ -14,9 +14,9 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
PrintWriter
,
File
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
scala.io.Source
...
...
@@ -27,9 +27,8 @@ object MergeOtuMaps extends ToolCommand {
case
class
Args
(
inputFiles
:
List
[
File
]
=
Nil
,
outputFile
:
File
=
null
,
skipPrefix
:
List
[
String
]
=
Nil
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'I'
,
"input"
)
minOccurs
2
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFiles
=
x
::
c
.
inputFiles
)
...
...
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