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biopet.biopet
Commits
706ca942
Commit
706ca942
authored
Sep 13, 2015
by
Peter van 't Hof
Browse files
Fix compile errors
parent
7d112c68
Changes
20
Hide whitespace changes
Inline
Side-by-side
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
View file @
706ca942
...
...
@@ -15,21 +15,12 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
java.io.File
import
htsjdk.samtools.
{
SAMSequenceRecord
,
SamReaderFactory
}
import
htsjdk.samtools.reference.IndexedFastaSequenceFile
import
htsjdk.variant.variantcontext.VariantContext
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommand
,
ToolCommandFuntion
}
import
nl.lumc.sasc.biopet.utils.VcfUtils._
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFuntion
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
import
scala.collection.mutable.ListBuffer
import
scala.collection.parallel.ParMap
class
BastyGenerateFasta
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Reference
{
javaMainClass
=
getClass
.
getName
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
View file @
706ca942
...
...
@@ -15,15 +15,12 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
java.io.File
import
htsjdk.samtools.
{
SAMSequenceRecord
,
SamReaderFactory
}
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
,
ToolCommandFuntion
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.io.Source
/**
* @deprecated Use picard.util.BedToIntervalList instead
*/
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
View file @
706ca942
...
...
@@ -15,15 +15,12 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
,
ToolCommandFuntion
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.
{
mutable
,
SortedMap
}
import
scala.io.Source
class
BedtoolsCoverageToCounts
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
getClass
.
getName
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
View file @
706ca942
...
...
@@ -15,18 +15,14 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
java.io.File
import
htsjdk.samtools.
{
SAMRecord
,
SamReaderFactory
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
,
ToolCommandFuntion
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
import
scala.collection.mutable
class
BiopetFlagstat
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Summarizable
{
javaMainClass
=
getClass
.
getName
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
View file @
706ca942
...
...
@@ -17,9 +17,8 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.samtools.fastq.
{
AsyncFastqWriter
,
BasicFastqWriter
,
FastqReader
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
,
ToolCommandFuntion
}
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
View file @
706ca942
...
...
@@ -17,14 +17,11 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.samtools.fastq.
{
AsyncFastqWriter
,
BasicFastqWriter
,
FastqReader
,
FastqRecord
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.
core.
{
ToolCommand
,
ToolCommandFuntion
}
import
nl.lumc.sasc.biopet.
utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.annotation.tailrec
import
scala.collection.JavaConverters._
import
scala.io.Source
import
scala.util.matching.Regex
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
View file @
706ca942
...
...
@@ -17,18 +17,10 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.samtools.reference.FastaSequenceFile
import
htsjdk.variant.variantcontext.
{
Allele
,
VariantContext
,
VariantContextBuilder
}
import
htsjdk.variant.variantcontext.writer.
{
AsyncVariantContextWriter
,
VariantContextWriterBuilder
}
import
htsjdk.variant.vcf.
{
VCFFileReader
,
VCFHeader
}
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
,
ToolCommandFuntion
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
import
scala.collection.
{
mutable
,
SortedMap
}
import
scala.collection.mutable.
{
Map
,
Set
}
class
MergeAlleles
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
getClass
.
getName
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
View file @
706ca942
...
...
@@ -15,14 +15,13 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
BufferedWriter
,
File
,
FileWriter
,
OutputStreamWriter
}
import
java.io.
File
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
,
ToolCommandFuntion
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.mutable.
{
Set
=>
MutSet
}
import
scala.io.
{
BufferedSource
,
Source
}
/**
* Biopet wrapper for the [[MergeTables]] command line tool.
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
View file @
706ca942
...
...
@@ -15,20 +15,16 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
java.io.File
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommand
,
ToolCommandFuntion
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFuntion
}
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
import
scala.collection.mutable
import
scala.collection.mutable.ArrayBuffer
import
scala.io.Source
import
scala.math.
{
floor
,
round
}
class
MpileupToVcf
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Reference
{
javaMainClass
=
getClass
.
getName
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
View file @
706ca942
...
...
@@ -17,9 +17,8 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.samtools.fastq.
{
AsyncFastqWriter
,
BasicFastqWriter
,
FastqReader
,
FastqRecord
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
,
ToolCommandFuntion
}
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
...
...
@@ -51,7 +50,7 @@ class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
optional
(
"-s"
,
prefixSeq
)
}
object
PrefixFastq
extends
ToolCommand
{
object
PrefixFastq
{
/**
* Create a PrefixFastq class object with a sufix ".prefix.fastq" in the output folder
*
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
View file @
706ca942
...
...
@@ -15,16 +15,12 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
FileReader
,
PrintWriter
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
,
ToolCommandFuntion
}
import
org.biojava3.sequencing.io.fastq.
{
Fastq
,
SangerFastqReader
,
StreamListener
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.
{
mutable
,
SortedMap
}
import
scala.collection.mutable.Map
class
SageCountFastq
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
getClass
.
getName
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
View file @
706ca942
...
...
@@ -15,19 +15,12 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
,
ToolCommandFuntion
}
import
org.biojava3.core.sequence.DNASequence
import
org.biojava3.core.sequence.io.FastaReaderHelper
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
import
scala.collection.
{
mutable
,
SortedMap
}
import
scala.collection.mutable.
{
Map
,
Set
}
import
scala.util.matching.Regex
class
SageCreateLibrary
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
getClass
.
getName
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
View file @
706ca942
...
...
@@ -15,16 +15,12 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
,
ToolCommandFuntion
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.
{
mutable
,
SortedMap
}
import
scala.collection.mutable.Map
import
scala.io.Source
class
SageCreateTagCounts
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
getClass
.
getName
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
View file @
706ca942
...
...
@@ -2,6 +2,12 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Seqstat function class for usage in Biopet pipelines
*
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
View file @
706ca942
...
...
@@ -2,9 +2,9 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by pjvanthof on 22/08/15.
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
706ca942
...
...
@@ -17,14 +17,9 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.variant.variantcontext.writer.
{
AsyncVariantContextWriter
,
VariantContextWriterBuilder
}
import
htsjdk.variant.variantcontext.
{
GenotypeType
,
VariantContext
}
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
import
scala.io.Source
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
VcfFilter
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
getClass
.
getName
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
706ca942
...
...
@@ -15,23 +15,14 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
FileOutputStream
,
PrintWriter
}
import
htsjdk.samtools.reference.FastaSequenceFile
import
htsjdk.samtools.util.Interval
import
htsjdk.variant.variantcontext.
{
Allele
,
Genotype
,
VariantContext
}
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.core.Reference
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFuntion
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
import
scala.collection.mutable
import
scala.io.Source
import
scala.sys.process.
{
Process
,
ProcessLogger
}
import
scala.util.Random
/**
* This tool will generate statistics from a vcf file
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
View file @
706ca942
...
...
@@ -16,16 +16,10 @@
package
nl.lumc.sasc.biopet.tools
import
java.io.File
import
java.util
import
htsjdk.variant.variantcontext.writer.
{
AsyncVariantContextWriter
,
VariantContextWriterBuilder
}
import
htsjdk.variant.variantcontext.
{
VariantContext
,
VariantContextBuilder
}
import
htsjdk.variant.vcf._
import
nl.lumc.sasc.biopet.utils.VcfUtils.scalaListToJavaObjectArrayList
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Biopet extension for tool VcfWithVcf
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
View file @
706ca942
...
...
@@ -17,15 +17,9 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.tribble.TribbleException
import
htsjdk.variant.variantcontext.writer.
{
AsyncVariantContextWriter
,
VariantContextWriterBuilder
}
import
htsjdk.variant.variantcontext.
{
VariantContext
,
VariantContextBuilder
}
import
htsjdk.variant.vcf._
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
import
scala.collection.mutable.
{
Map
=>
MMap
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* This tool parses a VEP annotated VCF into a standard VCF file.
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
View file @
706ca942
...
...
@@ -17,17 +17,9 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
com.google.common.hash.
{
BloomFilter
,
Funnel
}
import
htsjdk.samtools.util.
{
Interval
,
IntervalTreeMap
}
import
htsjdk.samtools.
{
QueryInterval
,
SAMFileWriter
,
SAMFileWriterFactory
,
SAMRecord
,
SamReader
,
SamReaderFactory
,
ValidationStringency
}
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import
org.apache.commons.io.FilenameUtils.getExtension
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConverters._
import
scala.io.Source
import
scala.math.
{
max
,
min
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
// TODO: finish implementation for usage in pipelines
/**
...
...
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