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biopet.biopet
Commits
0b4c76c5
Commit
0b4c76c5
authored
Dec 09, 2016
by
Peter van 't Hof
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Merge branch 'fix-xhmm' into 'develop'
fix biopet-495 See merge request !496
parents
5c13638f
e735b32d
Changes
3
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3 changed files
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28 additions
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28 deletions
+28
-28
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
...nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
+24
-24
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
...la/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
+3
-3
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
...umc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
+1
-1
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
View file @
0b4c76c5
...
...
@@ -18,31 +18,31 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
@Output
(
fullName
=
"out"
,
shortName
=
"o"
,
doc
=
"File name base to which coverage metric should be written"
)
var
out
:
File
=
_
@Output
private
var
_summaryFile
:
File
=
_
@Output
private
var
_statisticsFile
:
File
=
_
@Output
private
var
_intervalSummaryFile
:
File
=
_
@Output
private
var
_intervalStatisticsFile
:
File
=
_
@Output
private
var
_geneSummaryFile
:
File
=
_
@Output
private
var
_geneStatisticsFile
:
File
=
_
@Output
private
var
_cumulativeCoverageCountsFile
:
File
=
_
@Output
private
var
_cumulativeCoverageProportionsFile
:
File
=
_
@Output
var
summaryFile
=
_summaryFile
@Output
var
statisticsFile
=
_statisticsFile
@Output
var
intervalSummaryFile
=
_intervalSummaryFile
@Output
var
intervalStatisticsFile
=
_intervalStatisticsFile
@Output
var
geneSummaryFile
=
_geneSummaryFile
@Output
var
geneStatisticsFile
=
_geneStatisticsFile
@Output
var
culumativeCoverageCountsFile
=
_cumulativeCoverageCountsFile
@Output
var
cumulativeCoverageProportionsFile
=
_cumulativeCoverageProportionsFile
def
summaryFile
=
new
File
(
out
+
".sample_summary"
)
def
statisticsFile
=
new
File
(
out
+
".sample_statistics"
)
def
intervalSummaryFile
=
new
File
(
out
+
".sample_interval_summary"
)
def
intervalStatisticsFile
=
new
File
(
out
+
".sample_interval_statistics"
)
def
geneSummaryFile
=
new
File
(
out
+
".sample_gene_summary"
)
def
geneStatisticsFile
=
new
File
(
out
+
".sample_gene_statistics"
)
def
cumulativeCoverageCountsFile
=
new
File
(
out
+
".sample_cumulative_coverage_counts"
)
def
cumulativeCoverageProportionsFile
=
new
File
(
out
+
".sample_cumulative_coverage_proportions"
)
@Input
(
required
=
false
)
var
calculateCoverageOverGenes
:
Option
[
File
]
=
config
(
"calculate_coverage_over_genes"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
...
...
@@ -92,14 +92,14 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
if
(
out
==
null
)
{
throw
new
IllegalStateException
(
"You must set the <out> variable"
)
}
_summaryFile
=
new
File
(
out
+
".sample_summary"
)
_statisticsFile
=
new
File
(
out
+
".sample_statistics"
)
_intervalSummaryFile
=
new
File
(
out
+
".sample_interval_summary"
)
_intervalStatisticsFile
=
new
File
(
out
+
".sample_interval_statistics"
)
_geneSummaryFile
=
new
File
(
out
+
".sample_gene_summary"
)
_geneStatisticsFile
=
new
File
(
out
+
".sample_gene_statistics"
)
_cumulativeCoverageCountsFile
=
new
File
(
out
+
".sample_cumulative_coverage_counts"
)
_cumulativeCoverageProportionsFile
=
new
File
(
out
+
".sample_cumulative_coverage_proportions"
)
_summaryFile
=
summaryFile
_statisticsFile
=
statisticsFile
_intervalSummaryFile
=
intervalSummaryFile
_intervalStatisticsFile
=
intervalStatisticsFile
_geneSummaryFile
=
geneSummaryFile
_geneStatisticsFile
=
geneStatisticsFile
_cumulativeCoverageCountsFile
=
cumulativeCoverageCountsFile
_cumulativeCoverageProportionsFile
=
cumulativeCoverageProportionsFile
}
override
def
cmdLine
=
{
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
View file @
0b4c76c5
...
...
@@ -22,10 +22,10 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
@Input
var
r
:
File
=
_
@Output
private
var
_outputXcnvAuxFile
:
File
=
_
@Output
var
outputXcnvAuxFile
=
_outputXcnvAuxFile
def
outputXcnvAuxFile
=
new
File
(
outputXcnv
.
getAbsolutePath
+
".aux"
)
var
xhmmAnalysisName
:
String
=
_
...
...
@@ -34,7 +34,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
if
(
outputXcnv
==
null
)
{
throw
new
IllegalStateException
(
"Must set output file"
)
}
_outputXcnvAuxFile
=
new
File
(
outputXcnv
.
getAbsolutePath
+
".aux"
)
_outputXcnvAuxFile
=
outputXcnvAuxFile
}
def
cmdLine
=
{
...
...
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
View file @
0b4c76c5
...
...
@@ -36,7 +36,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
def
biopetScript
()
=
{
val
depths
=
inputBams
.
map
{
keyValuePair
=>
DepthOfCoverage
(
this
,
List
(
keyValuePair
.
_2
),
swapExt
(
xhmmDir
,
".bam"
,
".dcov"
),
List
(
targets
))
DepthOfCoverage
(
this
,
List
(
keyValuePair
.
_2
),
swapExt
(
xhmmDir
,
keyValuePair
.
_2
,
".bam"
,
".dcov"
),
List
(
targets
))
}.
toList
addAll
(
depths
)
...
...
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