Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
134d77a4
Commit
134d77a4
authored
Nov 29, 2016
by
Sander Bollen
Browse files
use fixed values method
parent
68cd247e
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
View file @
134d77a4
...
...
@@ -82,7 +82,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
var
includeDeletions
:
Boolean
=
config
(
"include_deletions"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
var
includeRefNSites
:
Boolean
=
config
(
"include_
R
ef
NS
ites"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
var
includeRefNSites
:
Boolean
=
config
(
"include_
r
ef
_n_s
ites"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
var
printBinEndpointsAndExit
:
Boolean
=
config
(
"print_bin_endpoint_and_exit"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
...
...
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
View file @
134d77a4
...
...
@@ -13,15 +13,25 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
def
name
=
"xhmm"
private
var
targets
:
Option
[
File
]
=
N
on
e
private
var
targets
:
File
=
c
on
fig
(
"amplicon_bed"
)
val
xhmmDir
=
new
File
(
outputDir
,
"xhmm"
)
override
def
init
()
=
{
super
.
init
()
targets
=
config
(
"amplicon_bed"
)
if
(
targets
.
isEmpty
)
{
throw
new
IllegalStateException
(
"You must provide a BED file in key 'amplicon_bed' in your config to use XHMM"
)
}
override
def
fixedValues
:
Map
[
String
,
Any
]
=
{
super
.
fixedValues
++
Map
(
"depth_of_coverage"
->
Map
(
"downsampling_type"
->
"BY_SAMPLE"
,
"downsample_to_coverage"
->
5000
,
"omit_depth_output_at_each_base"
->
true
,
"omit_locus_table"
->
true
,
"min_base_quality"
->
0
,
"min_mapping_quality"
->
20
,
"start"
->
1
,
"stop"
->
5000
,
"n_bins"
->
200
,
"include_ref_n_sites"
->
true
,
"count_type"
->
"COUNT_FRAGMENTS"
)
)
}
def
biopetScript
()
=
{
...
...
@@ -117,19 +127,8 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
private
def
depthOfCoverage
(
bamFile
:
File
)
:
DepthOfCoverage
=
{
val
dp
=
new
DepthOfCoverage
(
this
)
dp
.
input_file
=
List
(
bamFile
)
dp
.
intervals
=
targets
.
toList
dp
.
downsampling_type
=
Some
(
"BY_SAMPLE"
)
dp
.
downsample_to_coverage
=
5000
dp
.
intervals
=
List
(
targets
)
dp
.
out
=
swapExt
(
xhmmDir
,
bamFile
,
".bam"
,
".dcov"
)
dp
.
omitDepthOutputAtEachBase
=
true
dp
.
omitLocusTable
=
true
dp
.
minBaseQuality
=
0
dp
.
minMappingQuality
=
20
dp
.
start
=
1
dp
.
stop
=
5000
dp
.
nBins
=
200
dp
.
includeRefNSites
=
true
dp
.
countType
=
Some
(
"COUNT_FRAGMENTS"
)
dp
}
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new 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