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biopet.biopet
Commits
8df86298
Commit
8df86298
authored
Jun 07, 2017
by
Peter van 't Hof
Browse files
Adding index step
parent
bf2e950a
Changes
2
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
View file @
8df86298
...
...
@@ -56,5 +56,5 @@ object SambambaIndex {
apply
(
root
,
input
,
new
File
(
swapExtension
(
input
.
getAbsolutePath
)))
}
private
def
swapExtension
(
inputFile
:
String
)
=
inputFile
.
stripSuffix
(
".bam"
)
+
".
bam.
bai"
private
def
swapExtension
(
inputFile
:
String
)
=
inputFile
.
stripSuffix
(
".bam"
)
+
".bai"
}
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
8df86298
...
...
@@ -23,13 +23,7 @@ import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie, Bowtie2}
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.hisat.Hisat2
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.extensions.taxextract.TaxExtractExtract
...
...
@@ -45,7 +39,7 @@ import org.broadinstitute.gatk.utils.commandline
import
scala.math._
import
Mapping.DuplicatesMethod
import
nl.lumc.sasc.biopet.extensions.sambamba.SambambaMarkdup
import
nl.lumc.sasc.biopet.extensions.sambamba.
{
SambambaIndex
,
SambambaMarkdup
}
/**
* This pipeline doing a alignment to a given reference genome
...
...
@@ -358,6 +352,7 @@ class Mapping(val parent: Configurable)
case
DuplicatesMethod
.
Sambamba
=>
bamFile
=
new
File
(
outputDir
,
outputName
+
".dedup.bam"
)
add
(
SambambaMarkdup
(
this
,
mergedBamFile
,
finalBamFile
,
!
keepFinalBamFile
))
add
(
SambambaIndex
(
this
,
finalBamFile
))
case
DuplicatesMethod
.
None
=>
}
...
...
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