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
06cf90cb
Commit
06cf90cb
authored
Jun 22, 2015
by
Peter van 't Hof
Browse files
Change bwa to bwa-mem
parent
24837f5b
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
06cf90cb
...
...
@@ -40,7 +40,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
def
this
()
=
this
(
null
)
override
def
defaults
=
ConfigUtils
.
mergeMaps
(
Map
(
"mapping"
->
Map
(
"skip_markduplicates"
->
true
,
"aligner"
->
"bwa"
)
"mapping"
->
Map
(
"skip_markduplicates"
->
true
,
"aligner"
->
"bwa
-mem
"
)
),
super
.
defaults
)
def
summaryFile
=
new
File
(
outputDir
,
"Carp.summary.json"
)
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
06cf90cb
...
...
@@ -57,7 +57,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
protected
var
skipMetrics
:
Boolean
=
config
(
"skip_metrics"
,
default
=
false
)
/** Aligner */
protected
var
aligner
:
String
=
config
(
"aligner"
,
default
=
"bwa"
)
protected
var
aligner
:
String
=
config
(
"aligner"
,
default
=
"bwa
-mem
"
)
/** Number of chunks, when not defined pipeline will automatic calculate number of chunks */
protected
var
numberChunks
:
Option
[
Int
]
=
config
(
"number_chunks"
)
...
...
@@ -209,7 +209,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val
outputBam
=
new
File
(
chunkDir
,
outputName
+
".bam"
)
bamFiles
:+=
outputBam
aligner
match
{
case
"bwa
"
=>
addBwaMem
(
R1
,
R2
,
outputBam
,
deps
)
case
"bwa
-mem"
=>
addBwaMem
(
R1
,
R2
,
outputBam
,
deps
)
case
"bwa-aln"
=>
addBwaAln
(
R1
,
R2
,
outputBam
,
deps
)
case
"bowtie"
=>
addBowtie
(
R1
,
R2
,
outputBam
,
deps
)
case
"gsnap"
=>
addGsnap
(
R1
,
R2
,
outputBam
,
deps
)
...
...
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
06cf90cb
...
...
@@ -47,7 +47,7 @@ class MappingTest extends TestNGSuite with Matchers {
@DataProvider
(
name
=
"mappingOptions"
)
def
mappingOptions
=
{
val
aligners
=
Array
(
"bwa"
,
"bwa-aln"
,
"star"
,
"star-2pass"
,
"bowtie"
,
"stampy"
,
"gsnap"
,
"tophat"
)
val
aligners
=
Array
(
"bwa
-mem
"
,
"bwa-aln"
,
"star"
,
"star-2pass"
,
"bowtie"
,
"stampy"
,
"gsnap"
,
"tophat"
)
val
paired
=
Array
(
true
,
false
)
val
chunks
=
Array
(
1
,
5
,
10
,
100
)
val
skipMarkDuplicates
=
Array
(
true
,
false
)
...
...
@@ -99,7 +99,7 @@ class MappingTest extends TestNGSuite with Matchers {
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Gzip
])
shouldBe
(
if
(
skipFlexiprep
)
0
else
if
(
paired
)
2
else
1
)
//aligners
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaMem
])
shouldBe
((
if
(
aligner
==
"bwa"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaMem
])
shouldBe
((
if
(
aligner
==
"bwa
-mem
"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaAln
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
2
else
1
)
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaSampe
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
1
else
0
)
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaSamse
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
0
else
1
)
else
0
)
*
chunks
)
...
...
@@ -109,7 +109,7 @@ class MappingTest extends TestNGSuite with Matchers {
// Sort sam or replace readgroup
val
sort
=
aligner
match
{
case
"bwa"
|
"bwa-aln"
|
"stampy"
=>
"sortsam"
case
"bwa
-mem
"
|
"bwa-aln"
|
"stampy"
=>
"sortsam"
case
"star"
|
"star-2pass"
|
"bowtie"
|
"gsnap"
|
"tophat"
=>
"replacereadgroups"
case
_
=>
throw
new
IllegalArgumentException
(
"aligner: "
+
aligner
+
" does not exist"
)
}
...
...
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