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biopet.biopet
Commits
92bdf700
Commit
92bdf700
authored
Nov 25, 2015
by
Wai Yi Leung
Browse files
Fix default values and conditionals instead of optionals
parent
cb684be5
Changes
1
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Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie2.scala
View file @
92bdf700
...
...
@@ -33,7 +33,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var
bowtieIndex
:
String
=
config
(
"bowtie_index"
)
/* Input options */
var
q
:
Boolean
=
config
(
"q"
,
default
=
tru
e
)
var
q
:
Boolean
=
config
(
"q"
,
default
=
fals
e
)
var
qseq
:
Boolean
=
config
(
"qseq"
,
default
=
false
)
var
f
:
Boolean
=
config
(
"f"
,
default
=
false
)
var
r
:
Boolean
=
config
(
"r"
,
default
=
false
)
...
...
@@ -106,7 +106,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var
un_conc_bz2
:
Option
[
String
]
=
config
(
"un_conc_bz2"
)
var
al_conc_bz2
:
Option
[
String
]
=
config
(
"al_conc_bz2"
)
var
quiet
:
Boolean
=
config
(
"quiet"
,
default
=
tru
e
)
var
quiet
:
Boolean
=
config
(
"quiet"
,
default
=
fals
e
)
var
met_file
:
Option
[
String
]
=
config
(
"met_file"
)
var
met_stderr
:
Boolean
=
config
(
"met_stderr"
,
default
=
false
)
var
met
:
Option
[
Int
]
=
config
(
"met"
)
...
...
@@ -122,7 +122,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
/* Performance */
var
reorder
:
Boolean
=
config
(
"reorder"
,
default
=
false
)
var
mm
:
Boolean
=
config
(
"mm"
,
default
=
tru
e
)
var
mm
:
Boolean
=
config
(
"mm"
,
default
=
fals
e
)
/* Other */
var
qc_filter
:
Boolean
=
config
(
"qc_filter"
,
default
=
false
)
...
...
@@ -150,7 +150,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
optional
(
"--n-ceil"
,
n_ceil
)
+
optional
(
"--dpad"
,
dpad
)
+
optional
(
"--gbar"
,
gbar
)
+
op
tional
(
"--
ignore
-
quals
"
,
ignore
_
quals
)
+
condi
tional
(
ignore
_
quals
,
"--
ignore
-
quals
"
)
+
conditional
(
nofw
,
"--nofw"
)
+
conditional
(
norc
,
"--norc"
)
+
conditional
(
no_1mm_upfront
,
"--no-1mm-upfront"
)
+
...
...
@@ -206,8 +206,8 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
conditional
(
omit_sec_seq
,
"--omit-sec-seq"
)
+
/* Performance */
optional
(
"--threads"
,
threads
)
+
op
tional
(
"--
reorder
"
,
reorder
)
+
op
tional
(
"--mm"
,
mm
)
+
condi
tional
(
reorder
,
"--
reorder
"
)
+
condi
tional
(
mm
,
"--mm"
)
+
/* Other */
conditional
(
qc_filter
,
"--qc-filter"
)
+
optional
(
"--seed"
,
seed
)
+
...
...
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