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biopet.biopet
Commits
29bf997a
Commit
29bf997a
authored
Jun 10, 2014
by
Peter van 't Hof
Browse files
Changed filenames of bam files at star
parent
65a485aa
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
29bf997a
...
...
@@ -90,7 +90,7 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri
}
else
if
(
aligner
==
"star"
)
{
val
starCommand
=
new
Star
(
config
)
{
R1
=
fastq_R1
;
if
(
paired
)
R2
=
fastq_R2
;
this
.
outputDir
=
qscript
.
outputDir
+
"star/"
;
init
}
add
(
starCommand
)
bamFile
=
addAddOrReplaceReadGroups
(
List
(
starCommand
.
outputSam
),
swapExt
(
outputDir
,
starCommand
.
output
S
am
,
".sam"
,
".bam"
),
outputDir
)
bamFile
=
addAddOrReplaceReadGroups
(
List
(
starCommand
.
outputSam
),
new
File
(
outputDir
+
output
N
am
e
+
".bam"
),
outputDir
)
}
else
if
(
aligner
==
"star-2pass"
)
{
val
starCommand_pass1
=
new
Star
(
config
)
{
R1
=
fastq_R1
;
if
(
paired
)
R2
=
fastq_R2
;
this
.
outputDir
=
qscript
.
outputDir
+
"star-2pass/aln-pass1/"
;
init
}
...
...
@@ -103,7 +103,7 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri
val
starCommand_pass2
=
new
Star
(
config
)
{
R1
=
fastq_R1
;
if
(
paired
)
R2
=
fastq_R2
;
this
.
deps
++=
starCommand_reindex
.
outputs
;
this
.
outputDir
=
qscript
.
outputDir
+
"star-2pass/aln-pass2/"
;
this
.
genomeDir
=
starCommand_reindex
.
outputDir
;
init
}
add
(
starCommand_pass2
)
bamFile
=
addAddOrReplaceReadGroups
(
List
(
starCommand_pass2
.
outputSam
),
swapExt
(
outputDir
,
starCommand_pass2
.
outputSam
,
".sam"
,
".bam"
),
outputDir
)
bamFile
=
addAddOrReplaceReadGroups
(
List
(
starCommand_pass2
.
outputSam
),
new
File
(
outputDir
+
outputName
+
".bam"
),
outputDir
)
}
else
throw
new
IllegalStateException
(
"Option Alginer: '"
+
aligner
+
"' is not valid"
)
if
(!
skipMarkduplicates
)
bamFile
=
addMarkDuplicates
(
List
(
bamFile
),
swapExt
(
outputDir
,
bamFile
,
".bam"
,
".dedup.bam"
),
outputDir
)
...
...
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