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biopet.biopet
Commits
9c71efa3
Commit
9c71efa3
authored
Oct 09, 2015
by
Sander van der Zeeuw
Browse files
style changes, bamMetrics changed in bammetrics
parent
cfdfd0b9
Changes
3
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
View file @
9c71efa3
...
...
@@ -3,12 +3,12 @@ package nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
In
put
,
Out
put
}
import
org.broadinstitute.gatk.utils.commandline.
{
Out
put
,
In
put
}
/**
* Created by sajvanderzeeuw on 6-10-15.
*/
class
BuildBamIndex
(
val
root
:
Configurable
)
extends
Picard
{
class
BuildBamIndex
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
new
picard
.
sam
.
BuildBamIndex
().
getClass
.
getName
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
View file @
9c71efa3
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.samtools
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by pjvanthof on 22/09/15.
...
...
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
9c71efa3
...
...
@@ -127,7 +127,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
val
bamMetricsFilter
=
BamMetrics
(
qscript
,
bamFileFilter
,
new
File
(
sampleDir
,
"metrics-filter"
),
sampleId
=
Some
(
sampleId
))
addAll
(
bamMetricsFilter
.
functions
)
bamMetricsFilter
.
summaryName
=
"bam
M
etrics-filter"
bamMetricsFilter
.
summaryName
=
"bam
m
etrics-filter"
addSummaryQScript
(
bamMetricsFilter
)
addAll
(
Bam2Wig
(
qscript
,
bamFile
).
functions
)
...
...
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