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biopet.biopet
Commits
e2dcb312
Commit
e2dcb312
authored
Apr 24, 2017
by
Peter van 't Hof
Browse files
Fixing var names
parent
0e1722a0
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
e2dcb312
...
...
@@ -78,10 +78,10 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
// TODO: hide sampleId and libId from the command line so they do not interfere with our config values
/** Readgroup Platform */
protected
var
p
latform
:
String
=
config
(
"platform"
,
default
=
"illumina"
)
protected
var
readgroupP
latform
:
String
=
config
(
"
readgroup_
platform"
,
default
=
"illumina"
)
/** Readgroup platform unit */
protected
var
p
latformUnit
:
Option
[
String
]
=
config
(
"platform_unit"
)
protected
var
readgroupP
latformUnit
:
Option
[
String
]
=
config
(
"
readgroup_
platform_unit"
)
/** Readgroup sequencing center */
protected
var
readgroupSequencingCenter
:
Option
[
String
]
=
config
(
"readgroup_sequencing_center"
)
...
...
@@ -387,8 +387,8 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
hisat2
.
R1
=
R1
hisat2
.
R2
=
R2
hisat2
.
rgId
=
Some
(
readgroupId
)
hisat2
.
rg
+:=
s
"PL:$
p
latform"
p
latformUnit
.
foreach
(
x
=>
hisat2
.
rg
+:=
s
"PU:$x"
)
hisat2
.
rg
+:=
s
"PL:$
readgroupP
latform"
readgroupP
latformUnit
.
foreach
(
x
=>
hisat2
.
rg
+:=
s
"PU:$x"
)
libId
match
{
case
Some
(
id
)
=>
hisat2
.
rg
+:=
s
"LB:$id"
case
otherwise
=>
;
...
...
@@ -461,11 +461,11 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
RG
+=
"SM:"
+
sampleId
.
get
+
","
RG
+=
"LB:"
+
libId
.
get
+
","
if
(
readgroupDescription
!=
null
)
RG
+=
"DS"
+
readgroupDescription
+
","
p
latformUnit
.
foreach
(
x
=>
RG
+=
"PU:"
+
x
+
","
)
readgroupP
latformUnit
.
foreach
(
x
=>
RG
+=
"PU:"
+
x
+
","
)
if
(
predictedInsertsize
.
getOrElse
(
0
)
>
0
)
RG
+=
"PI:"
+
predictedInsertsize
.
get
+
","
if
(
readgroupSequencingCenter
.
isDefined
)
RG
+=
"CN:"
+
readgroupSequencingCenter
.
get
+
","
if
(
readgroupDate
!=
null
)
RG
+=
"DT:"
+
readgroupDate
+
","
RG
+=
"PL:"
+
p
latform
RG
+=
"PL:"
+
readgroupP
latform
val
stampyCmd
=
new
Stampy
(
this
)
stampyCmd
.
R1
=
R1
...
...
@@ -505,8 +505,8 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
val
bowtie2
=
new
Bowtie2
(
this
)
bowtie2
.
rgId
=
Some
(
readgroupId
)
bowtie2
.
rg
+:=
(
"LB:"
+
libId
.
get
)
bowtie2
.
rg
+:=
(
"PL:"
+
p
latform
)
p
latformUnit
.
foreach
(
x
=>
bowtie2
.
rg
+:=
(
"PU:"
+
x
))
bowtie2
.
rg
+:=
(
"PL:"
+
readgroupP
latform
)
readgroupP
latformUnit
.
foreach
(
x
=>
bowtie2
.
rg
+:=
(
"PU:"
+
x
))
bowtie2
.
rg
+:=
(
"SM:"
+
sampleId
.
get
)
bowtie2
.
R1
=
R1
bowtie2
.
R2
=
R2
...
...
@@ -562,8 +562,8 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
addOrReplaceReadGroups
.
RGID
=
readgroupId
addOrReplaceReadGroups
.
RGLB
=
libId
.
get
addOrReplaceReadGroups
.
RGPL
=
p
latform
addOrReplaceReadGroups
.
RGPU
=
p
latformUnit
.
getOrElse
(
readgroupId
)
addOrReplaceReadGroups
.
RGPL
=
readgroupP
latform
addOrReplaceReadGroups
.
RGPU
=
readgroupP
latformUnit
.
getOrElse
(
readgroupId
)
addOrReplaceReadGroups
.
RGSM
=
sampleId
.
get
if
(
readgroupSequencingCenter
.
isDefined
)
addOrReplaceReadGroups
.
RGCN
=
readgroupSequencingCenter
.
get
if
(
readgroupDescription
.
isDefined
)
addOrReplaceReadGroups
.
RGDS
=
readgroupDescription
.
get
...
...
@@ -576,8 +576,8 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
def
getReadGroupBwa
:
String
=
{
var
RG
:
String
=
"@RG\\t"
+
"ID:"
+
readgroupId
+
"\\t"
readgroupLibrary
.
foreach
(
lb
=>
RG
+=
"LB:"
+
lb
+
"\\t"
)
RG
+=
"PL:"
+
p
latform
+
"\\t"
p
latformUnit
.
foreach
(
x
=>
RG
+=
"PU:"
+
x
+
"\\t"
)
RG
+=
"PL:"
+
readgroupP
latform
+
"\\t"
readgroupP
latformUnit
.
foreach
(
x
=>
RG
+=
"PU:"
+
x
+
"\\t"
)
RG
+=
"SM:"
+
sampleId
.
get
+
"\\t"
if
(
readgroupSequencingCenter
.
isDefined
)
RG
+=
"CN:"
+
readgroupSequencingCenter
.
get
+
"\\t"
if
(
readgroupDescription
.
isDefined
)
RG
+=
"DS:"
+
readgroupDescription
.
get
+
"\\t"
...
...
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