Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
What's new
7
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Open sidebar
Mirrors
biopet.biopet
Commits
0b4c76c5
Commit
0b4c76c5
authored
Dec 09, 2016
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Plain Diff
Merge branch 'fix-xhmm' into 'develop'
fix biopet-495 See merge request !496
parents
5c13638f
e735b32d
Changes
3
Hide whitespace changes
Inline
Side-by-side
Showing
3 changed files
with
28 additions
and
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
_s
ummary
"
)
_intervalStatisticsFile
=
new
File
(
out
+
".sample_
interval
_s
tatistics
"
)
_geneSummaryFile
=
new
File
(
out
+
".sample_
gene
_s
ummary
"
)
_geneStatisticsFile
=
new
File
(
out
+
".sample_
gene
_s
tatistics
"
)
_cumulativeCoverageCountsFile
=
new
File
(
out
+
".sample_
cumulative
_c
overage
_c
ounts
"
)
_cumulativeCoverageProportionsFile
=
new
File
(
out
+
".sample_
cumulative
_c
overage
_p
roportions
"
)
_summaryFile
=
summary
File
_statisticsFile
=
statistics
File
_intervalSummaryFile
=
interval
S
ummary
File
_intervalStatisticsFile
=
interval
S
tatistics
File
_geneSummaryFile
=
gene
S
ummary
File
_geneStatisticsFile
=
gene
S
tatistics
File
_cumulativeCoverageCountsFile
=
cumulative
C
overage
C
ounts
File
_cumulativeCoverageProportionsFile
=
cumulative
C
overage
P
roportions
File
}
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
=
outputXcnv
AuxFile
}
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
)
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment