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biopet.biopet
Commits
1a27786b
Commit
1a27786b
authored
Nov 25, 2015
by
Wai Yi Leung
Browse files
Set defaults for Boolean values
parent
6c3cd444
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 @
1a27786b
...
...
@@ -42,9 +42,9 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var
upto
:
Option
[
Int
]
=
config
(
"upto"
)
var
trim5
:
Option
[
Int
]
=
config
(
"trim5"
)
var
trim3
:
Option
[
Int
]
=
config
(
"trim3"
)
var
phred33
:
Boolean
=
config
(
"phred33"
)
var
phred64
:
Boolean
=
config
(
"phred64"
)
var
int_quals
:
Boolean
=
config
(
"int_quals"
)
var
phred33
:
Boolean
=
config
(
"phred33"
,
default
=
false
)
var
phred64
:
Boolean
=
config
(
"phred64"
,
default
=
false
)
var
int_quals
:
Boolean
=
config
(
"int_quals"
,
default
=
false
)
/* Alignment options */
var
N
:
Option
[
Int
]
=
config
(
"N"
)
...
...
@@ -54,11 +54,11 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var
dpad
:
Option
[
Int
]
=
config
(
"dpad"
)
var
gbar
:
Option
[
Int
]
=
config
(
"gbar"
)
var
ignore_quals
:
Boolean
=
config
(
"ignore_quals"
)
var
nofw
:
Boolean
=
config
(
"nofw"
)
var
norc
:
Boolean
=
config
(
"norc"
)
var
no_1mm_upfront
:
Boolean
=
config
(
"no_1mm_upfront"
)
var
end_to_end
:
Boolean
=
config
(
"end_to_end"
)
var
local
:
Boolean
=
config
(
"local"
)
var
nofw
:
Boolean
=
config
(
"nofw"
,
default
=
false
)
var
norc
:
Boolean
=
config
(
"norc"
,
default
=
false
)
var
no_1mm_upfront
:
Boolean
=
config
(
"no_1mm_upfront"
,
default
=
false
)
var
end_to_end
:
Boolean
=
config
(
"end_to_end"
,
default
=
false
)
var
local
:
Boolean
=
config
(
"local"
,
default
=
false
)
/* Scoring */
var
ma
:
Option
[
Int
]
=
config
(
"ma"
)
...
...
@@ -79,17 +79,17 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
/* Paired-end */
var
minins
:
Option
[
Int
]
=
config
(
"minins"
)
var
maxins
:
Option
[
Int
]
=
config
(
"maxins"
)
var
fr
:
Boolean
=
config
(
"fr"
)
var
rf
:
Boolean
=
config
(
"rf"
)
var
ff
:
Boolean
=
config
(
"ff"
)
var
no_mixed
:
Boolean
=
config
(
"no_mixed"
)
var
no_discordant
:
Boolean
=
config
(
"no_discordant"
)
var
no_dovetail
:
Boolean
=
config
(
"no_dovetail"
)
var
no_contain
:
Boolean
=
config
(
"no_contain"
)
var
no_overlap
:
Boolean
=
config
(
"no_overlap"
)
var
fr
:
Boolean
=
config
(
"fr"
,
default
=
false
)
var
rf
:
Boolean
=
config
(
"rf"
,
default
=
false
)
var
ff
:
Boolean
=
config
(
"ff"
,
default
=
false
)
var
no_mixed
:
Boolean
=
config
(
"no_mixed"
,
default
=
false
)
var
no_discordant
:
Boolean
=
config
(
"no_discordant"
,
default
=
false
)
var
no_dovetail
:
Boolean
=
config
(
"no_dovetail"
,
default
=
false
)
var
no_contain
:
Boolean
=
config
(
"no_contain"
,
default
=
false
)
var
no_overlap
:
Boolean
=
config
(
"no_overlap"
,
default
=
false
)
/* Output */
var
time
:
Boolean
=
config
(
"no_overlap"
)
var
time
:
Boolean
=
config
(
"no_overlap"
,
default
=
false
)
var
un
:
Option
[
String
]
=
config
(
"un"
)
var
al
:
Option
[
String
]
=
config
(
"al"
)
...
...
@@ -106,28 +106,28 @@ 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"
)
var
quiet
:
Boolean
=
config
(
"quiet"
,
default
=
true
)
var
met_file
:
Option
[
String
]
=
config
(
"met_file"
)
var
met_stderr
:
Boolean
=
config
(
"met_stderr"
)
var
met_stderr
:
Boolean
=
config
(
"met_stderr"
,
default
=
false
)
var
met
:
Option
[
Int
]
=
config
(
"met"
)
var
no_unal
:
Boolean
=
config
(
"no_unal"
)
var
no_head
:
Boolean
=
config
(
"no_head"
)
var
no_sq
:
Boolean
=
config
(
"no_sq"
)
var
no_unal
:
Boolean
=
config
(
"no_unal"
,
default
=
false
)
var
no_head
:
Boolean
=
config
(
"no_head"
,
default
=
false
)
var
no_sq
:
Boolean
=
config
(
"no_sq"
,
default
=
false
)
var
rg_id
:
Option
[
String
]
=
config
(
"rg_id"
)
var
rg
:
Option
[
String
]
=
config
(
"rg"
)
var
omit_sec_seq
:
Boolean
=
config
(
"omit_sec_seq"
)
var
omit_sec_seq
:
Boolean
=
config
(
"omit_sec_seq"
,
default
=
false
)
/* Performance */
var
reorder
:
Boolean
=
config
(
"reorder"
)
var
mm
:
Boolean
=
config
(
"mm"
)
var
reorder
:
Boolean
=
config
(
"reorder"
,
default
=
false
)
var
mm
:
Boolean
=
config
(
"mm"
,
default
=
true
)
/* Other */
var
qc_filter
:
Boolean
=
config
(
"qc_filter"
)
var
qc_filter
:
Boolean
=
config
(
"qc_filter"
,
default
=
false
)
var
seed
:
Option
[
Int
]
=
config
(
"seed"
)
var
non_deterministic
:
Boolean
=
config
(
"non_deterministic"
)
var
non_deterministic
:
Boolean
=
config
(
"non_deterministic"
,
default
=
false
)
/** return commandline to execute */
def
cmdLine
=
required
(
executable
)
+
...
...
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