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biopet.biopet
Commits
d7260ac8
Commit
d7260ac8
authored
Oct 13, 2014
by
Peter van 't Hof
Browse files
Reorganize tools
Fix for #29
parent
5edfb6af
Changes
11
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
View file @
d7260ac8
...
...
@@ -18,9 +18,9 @@ object BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
yamsvp
.
Yamsvp
),
"tool"
->
List
(
nl
.
lumc
.
sasc
.
biopet
.
core
.
app
s
.
WipeReads
,
nl
.
lumc
.
sasc
.
biopet
.
core
.
app
s
.
BiopetFlagstat
,
nl
.
lumc
.
sasc
.
biopet
.
core
.
app
s
.
CheckAllelesVcfInBam
)
nl
.
lumc
.
sasc
.
biopet
.
tool
s
.
WipeReads
,
nl
.
lumc
.
sasc
.
biopet
.
tool
s
.
BiopetFlagstat
,
nl
.
lumc
.
sasc
.
biopet
.
tool
s
.
CheckAllelesVcfInBam
)
)
/**
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
d7260ac8
...
...
@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.scripts.CoverageStats
import
org.broadinstitute.gatk.queue.QScript
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
java.io.File
import
nl.lumc.sasc.biopet.
core.app
s.
{
BedToInterval
,
BiopetFlagstat
}
import
nl.lumc.sasc.biopet.
tool
s.
{
BedToInterval
,
BiopetFlagstat
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
CollectInsertSizeMetrics
,
CollectGcBiasMetrics
,
CalculateHsMetrics
,
CollectAlignmentSummaryMetrics
}
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
d7260ac8
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
java.io.File
import
nl.lumc.sasc.biopet.
core.app
s.
{
MpileupToVcf
,
VcfFilter
}
import
nl.lumc.sasc.biopet.
tool
s.
{
MpileupToVcf
,
VcfFilter
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.
{
AnalyzeCovariates
,
BaseRecalibrator
,
GenotypeGVCFs
,
HaplotypeCaller
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
,
SelectVariants
,
CombineVariants
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
d7260ac8
...
...
@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
java.io.File
import
java.util.Date
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.
core.app
s.FastqSplitter
import
nl.lumc.sasc.biopet.
tool
s.FastqSplitter
import
nl.lumc.sasc.biopet.extensions.aligners.
{
Bwa
,
Star
,
Bowtie
,
Stampy
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
SortSam
,
MergeSamFiles
,
AddOrReplaceReadGroups
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
core/app
s/BedToInterval.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
tool
s/BedToInterval.scala
View file @
d7260ac8
package
nl.lumc.sasc.biopet.
core.app
s
package
nl.lumc.sasc.biopet.
tool
s
import
htsjdk.samtools.SAMFileReader
import
htsjdk.samtools.SAMSequenceRecord
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
core/app
s/BiopetFlagstat.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
tool
s/BiopetFlagstat.scala
View file @
d7260ac8
package
nl.lumc.sasc.biopet.
core.app
s
package
nl.lumc.sasc.biopet.
tool
s
import
htsjdk.samtools.SAMFileReader
import
htsjdk.samtools.SAMRecord
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
core/app
s/CheckAllelesVcfInBam.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
tool
s/CheckAllelesVcfInBam.scala
View file @
d7260ac8
package
nl.lumc.sasc.biopet.
core.app
s
package
nl.lumc.sasc.biopet.
tool
s
import
htsjdk.samtools.SAMFileReader
import
htsjdk.samtools.SAMRecord
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
core/app
s/FastqSplitter.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
tool
s/FastqSplitter.scala
View file @
d7260ac8
package
nl.lumc.sasc.biopet.
core.app
s
package
nl.lumc.sasc.biopet.
tool
s
import
java.io.
{
BufferedInputStream
,
File
,
FileInputStream
,
PrintWriter
}
import
java.util.zip.GZIPInputStream
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
core/app
s/MpileupToVcf.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
tool
s/MpileupToVcf.scala
View file @
d7260ac8
package
nl.lumc.sasc.biopet.
core.app
s
package
nl.lumc.sasc.biopet.
tool
s
import
java.io.File
import
java.io.PrintWriter
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
core/app
s/VcfFilter.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
tool
s/VcfFilter.scala
View file @
d7260ac8
package
nl.lumc.sasc.biopet.
core.app
s
package
nl.lumc.sasc.biopet.
tool
s
import
htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
import
htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
core/app
s/WipeReads.scala
→
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/
tool
s/WipeReads.scala
View file @
d7260ac8
...
...
@@ -2,7 +2,7 @@
* Copyright (c) 2014 Leiden University Medical Center - Sequencing Analysis Support Core <sasc@lumc.nl>
* @author Wibowo Arindrarto <w.arindrarto@lumc.nl>
*/
package
nl.lumc.sasc.biopet.
core.app
s
package
nl.lumc.sasc.biopet.
tool
s
import
java.io.
{
File
,
IOException
}
...
...
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