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biopet.biopet
Commits
d49e8e65
Commit
d49e8e65
authored
Apr 15, 2015
by
Peter van 't Hof
Browse files
Safer class name, now checked by the compiler
parent
61232d12
Changes
12
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
View file @
d49e8e65
...
...
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard AddOrReplaceReadGroups */
class
AddOrReplaceReadGroups
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"
picard.sam.AddOrReplaceReadGroups
"
javaMainClass
=
new
picard
.
sam
.
AddOrReplaceReadGroups
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze."
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
View file @
d49e8e65
...
...
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard CalculateHsMetrics */
class
CalculateHsMetrics
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"
picard.analysis.directed.CalculateHsMetrics
"
javaMainClass
=
new
picard
.
analysis
.
directed
.
CalculateHsMetrics
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze. Must be coordinate sorted."
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
View file @
d49e8e65
...
...
@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard CollectAlignmentSummaryMetrics */
class
CollectAlignmentSummaryMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
{
javaMainClass
=
"
picard.analysis.CollectAlignmentSummaryMetrics
"
javaMainClass
=
new
picard
.
analysis
.
CollectAlignmentSummaryMetrics
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze. Must be coordinate sorted."
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
View file @
d49e8e65
...
...
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard CollectGcBiasMetrics */
class
CollectGcBiasMetrics
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"
picard.analysis.CollectGcBiasMetrics
"
javaMainClass
=
new
picard
.
analysis
.
CollectGcBiasMetrics
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze. Must be coordinate sorted."
,
required
=
true
)
var
input
:
Seq
[
File
]
=
Nil
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
View file @
d49e8e65
...
...
@@ -24,7 +24,7 @@ import scala.collection.immutable.Nil
/** Extension for picard CollectInsertSizeMetrics */
class
CollectInsertSizeMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
{
javaMainClass
=
"
picard.analysis.CollectInsertSizeMetrics
"
javaMainClass
=
new
picard
.
analysis
.
CollectInsertSizeMetrics
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze. Must be coordinate sorted."
,
required
=
true
)
var
input
:
File
=
null
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
View file @
d49e8e65
...
...
@@ -26,7 +26,7 @@ import picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
*/
class
CollectRnaSeqMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
{
javaMainClass
=
"
picard.analysis.CollectRnaSeqMetrics
"
javaMainClass
=
new
picard
.
analysis
.
CollectRnaSeqMetrics
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze"
,
required
=
true
)
var
input
:
File
=
null
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
View file @
d49e8e65
...
...
@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
class
GatherBamFiles
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"
picard.sam.GatherBamFiles
"
javaMainClass
=
new
picard
.
sam
.
GatherBamFiles
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze."
,
required
=
true
)
var
input
:
List
[
File
]
=
Nil
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
View file @
d49e8e65
...
...
@@ -22,7 +22,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard MarkDuplicates */
class
MarkDuplicates
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
{
javaMainClass
=
"picard.sam.MarkDuplicates"
javaMainClass
=
new
picard
.
sam
.
MarkDuplicates
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze. Must be coordinate sorted."
,
required
=
true
)
var
input
:
List
[
File
]
=
Nil
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
View file @
d49e8e65
...
...
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard MergeSamFiles */
class
MergeSamFiles
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"
picard.sam.MergeSamFiles
"
javaMainClass
=
new
picard
.
sam
.
MergeSamFiles
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze."
,
required
=
true
)
var
input
:
List
[
File
]
=
Nil
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
View file @
d49e8e65
...
...
@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
class
ReorderSam
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"
picard.sam.ReorderSam
"
javaMainClass
=
new
picard
.
sam
.
ReorderSam
().
getClass
.
getName
@Input
(
doc
=
"Input SAM or BAM file"
,
required
=
true
)
var
input
:
File
=
null
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
View file @
d49e8e65
...
...
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard SamToFastq */
class
SamToFastq
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"
picard.sam.SamToFastq
"
javaMainClass
=
new
picard
.
sam
.
SamToFastq
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze."
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
View file @
d49e8e65
...
...
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard SortSam */
class
SortSam
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"
picard.sam.SortSam
"
javaMainClass
=
new
picard
.
sam
.
SortSam
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze."
,
required
=
true
)
var
input
:
File
=
_
...
...
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