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biopet.biopet
Commits
59467664
Commit
59467664
authored
Sep 13, 2015
by
Peter van 't Hof
Browse files
Added a tool package
parent
405222b6
Changes
38
Hide whitespace changes
Inline
Side-by-side
protected/biopet-protected-package/pom.xml
View file @
59467664
...
...
@@ -24,7 +24,7 @@
<properties>
<sting.shade.phase>
package
</sting.shade.phase>
<app.main.class>
nl.lumc.sasc.biopet.
core.
BiopetExecutableProtected
</app.main.class>
<app.main.class>
nl.lumc.sasc.biopet.BiopetExecutableProtected
</app.main.class>
</properties>
<dependencies>
...
...
protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala
View file @
59467664
...
...
@@ -5,8 +5,7 @@
*/
package
nl.lumc.sasc.biopet
import
nl.lumc.sasc.biopet.core.BiopetExecutable
import
nl.lumc.sasc.biopet.utils.MainCommand
import
nl.lumc.sasc.biopet.utils.
{
BiopetExecutable
,
MainCommand
}
object
BiopetExecutableProtected
extends
BiopetExecutable
{
def
pipelines
:
List
[
MainCommand
]
=
BiopetExecutablePublic
.
pipelines
:::
List
(
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
59467664
...
...
@@ -17,9 +17,8 @@ package nl.lumc.sasc.biopet.core.report
import
java.io._
import
nl.lumc.sasc.biopet.core.ToolCommandFuntion
import
nl.lumc.sasc.biopet.tools.ToolCommand
import
nl.lumc.sasc.biopet.utils.summary.Summary
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
IoUtils
}
import
nl.lumc.sasc.biopet.utils.
{
ToolCommand
,
Logging
,
IoUtils
}
import
org.broadinstitute.gatk.utils.commandline.Input
import
org.fusesource.scalate.
{
TemplateEngine
,
TemplateSource
}
import
scala.collection.mutable
...
...
public/biopet-public-package/pom.xml
View file @
59467664
...
...
@@ -35,7 +35,7 @@
<properties>
<sting.shade.phase>
package
</sting.shade.phase>
<app.main.class>
nl.lumc.sasc.biopet.
core.
BiopetExecutablePublic
</app.main.class>
<app.main.class>
nl.lumc.sasc.biopet.BiopetExecutablePublic
</app.main.class>
</properties>
<dependencies>
...
...
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
View file @
59467664
...
...
@@ -15,8 +15,7 @@
*/
package
nl.lumc.sasc.biopet
import
nl.lumc.sasc.biopet.core.BiopetExecutable
import
nl.lumc.sasc.biopet.utils.MainCommand
import
nl.lumc.sasc.biopet.utils.
{
BiopetExecutable
,
MainCommand
}
object
BiopetExecutablePublic
extends
BiopetExecutable
{
def
publicPipelines
:
List
[
MainCommand
]
=
List
(
...
...
public/biopet-tools-package/pom.xml
0 → 100644
View file @
59467664
<?xml version="1.0" encoding="UTF-8"?>
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation=
"http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
>
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.5.0-SNAPSHOT
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
<artifactId>
BiopetToolsPackage
</artifactId>
<properties>
<sting.shade.phase>
package
</sting.shade.phase>
<app.main.class>
nl.lumc.sasc.biopet.BiopetToolsExecutable
</app.main.class>
</properties>
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetTools
</artifactId>
<version>
${project.version}
</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>
org.apache.maven.plugins
</groupId>
<artifactId>
maven-shade-plugin
</artifactId>
<version>
2.4.1
</version>
<configuration>
<!--suppress MavenModelInspection -->
<finalName>
BiopetTools-${project.version}-${git.commit.id.abbrev}
</finalName>
<transformers>
<transformer
implementation=
"org.apache.maven.plugins.shade.resource.ManifestResourceTransformer"
>
<manifestEntries>
<Main-Class>
${app.main.class}
</Main-Class>
<!--suppress MavenModelInspection -->
<X-Compile-Source-JDK>
${maven.compile.source}
</X-Compile-Source-JDK>
<!--suppress MavenModelInspection -->
<X-Compile-Target-JDK>
${maven.compile.target}
</X-Compile-Target-JDK>
</manifestEntries>
</transformer>
</transformers>
<filters>
</filters>
</configuration>
<executions>
<execution>
<phase>
package
</phase>
<goals>
<goal>
shade
</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
\ No newline at end of file
public/biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
0 → 100644
View file @
59467664
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet
import
nl.lumc.sasc.biopet.utils.
{
BiopetExecutable
,
MainCommand
}
object
BiopetToolsExecutable
extends
BiopetExecutable
{
def
pipelines
:
List
[
MainCommand
]
=
Nil
def
tools
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeTables
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
WipeReads
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
ExtractAlignedFastq
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSync
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BiopetFlagstat
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
CheckAllelesVcfInBam
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfToTsv
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfFilter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfStats
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FindRepeatsPacBio
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MpileupToVcf
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSplitter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BedtoolsCoverageToCounts
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCountFastq
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCreateLibrary
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCreateTagCounts
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BastyGenerateFasta
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeAlleles
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SamplesTsvToJson
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SeqStat
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VepNormalizer
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
AnnotateVcfWithBed
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfWithVcf
)
}
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
View file @
59467664
...
...
@@ -20,6 +20,7 @@ import java.io.File
import
htsjdk.variant.variantcontext.VariantContextBuilder
import
htsjdk.variant.variantcontext.writer.
{
AsyncVariantContextWriter
,
VariantContextWriterBuilder
}
import
htsjdk.variant.vcf.
{
VCFFileReader
,
VCFHeaderLineCount
,
VCFHeaderLineType
,
VCFInfoHeaderLine
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.intervals.
{
BedRecord
,
BedRecordList
}
import
scala.collection.JavaConversions._
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
View file @
59467664
...
...
@@ -21,6 +21,7 @@ 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.VcfUtils._
import
scala.collection.JavaConversions._
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
View file @
59467664
...
...
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
htsjdk.samtools.
{
SAMSequenceRecord
,
SamReaderFactory
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
scala.io.Source
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
View file @
59467664
...
...
@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
scala.collection.
{
SortedMap
,
mutable
}
import
scala.io.Source
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
View file @
59467664
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
htsjdk.samtools.
{
SAMRecord
,
SamReaderFactory
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.
{
ToolCommand
,
ConfigUtils
}
import
scala.collection.JavaConversions._
import
scala.collection.mutable
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
View file @
59467664
...
...
@@ -21,6 +21,7 @@ import htsjdk.samtools.{ QueryInterval, SAMRecord, SamReader, SamReaderFactory }
import
htsjdk.variant.variantcontext.
{
VariantContext
,
VariantContextBuilder
}
import
htsjdk.variant.variantcontext.writer.
{
AsyncVariantContextWriter
,
VariantContextWriterBuilder
}
import
htsjdk.variant.vcf.
{
VCFFileReader
,
VCFHeaderLineCount
,
VCFHeaderLineType
,
VCFInfoHeaderLine
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
scala.collection.JavaConversions._
import
scala.collection.mutable
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
View file @
59467664
...
...
@@ -20,6 +20,7 @@ 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
scala.collection.JavaConverters._
import
scala.collection.mutable.
{
Set
=>
MSet
}
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
View file @
59467664
...
...
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.samtools.fastq.
{
AsyncFastqWriter
,
BasicFastqWriter
,
FastqReader
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
object
FastqSplitter
extends
ToolCommand
{
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
View file @
59467664
...
...
@@ -18,6 +18,7 @@ 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
scala.annotation.tailrec
import
scala.collection.JavaConverters._
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
View file @
59467664
...
...
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
PrintWriter
,
File
}
import
htsjdk.samtools.
{
QueryInterval
,
SAMRecord
,
SamReaderFactory
,
ValidationStringency
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
scala.collection.JavaConversions._
import
scala.io.Source
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
View file @
59467664
...
...
@@ -21,6 +21,7 @@ import htsjdk.samtools.reference.FastaSequenceFile
import
htsjdk.variant.variantcontext.writer.
{
AsyncVariantContextWriter
,
VariantContextWriterBuilder
}
import
htsjdk.variant.variantcontext.
{
Allele
,
VariantContext
,
VariantContextBuilder
}
import
htsjdk.variant.vcf.
{
VCFFileReader
,
VCFHeader
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
scala.collection.JavaConversions._
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
View file @
59467664
...
...
@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
BufferedWriter
,
File
,
FileWriter
,
OutputStreamWriter
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
scala.collection.mutable.
{
Set
=>
MutSet
}
import
scala.io.
{
BufferedSource
,
Source
}
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
View file @
59467664
...
...
@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
scala.collection.mutable
import
scala.collection.mutable.ArrayBuffer
import
scala.io.Source
...
...
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