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biopet.biopet
Commits
76383bf1
Commit
76383bf1
authored
Dec 29, 2015
by
Peter van 't Hof
Browse files
Move Bowtie2 to package bowtie
parent
394f32a2
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie2.scala
→
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/
bowtie/
Bowtie2.scala
View file @
76383bf1
package
nl.lumc.sasc.biopet.extensions
package
nl.lumc.sasc.biopet.extensions
.bowtie
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Extension for bowtie 2
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
76383bf1
...
...
@@ -20,7 +20,7 @@ import java.util.Date
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.bowtie.Bowtie
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie
2
,
Bowtie
}
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
import
nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
...
...
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