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biopet.biopet
Commits
2139a95e
Commit
2139a95e
authored
Mar 13, 2015
by
bow
Browse files
Formatting updates
parent
0453d301
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
View file @
2139a95e
...
...
@@ -35,10 +35,10 @@ class ReorderSam(val root: Configurable) extends Picard {
var
output
:
File
=
null
@Argument
(
doc
=
"Allow incomplete dict concordance"
,
required
=
false
)
var
allowIncompleteDictConcordance
:
Boolean
=
config
(
"allow_incomplete_dict_concordance"
,
default
=
false
)
var
allowIncompleteDictConcordance
:
Boolean
=
config
(
"allow_incomplete_dict_concordance"
,
default
=
false
)
@Argument
(
doc
=
"Allow contig length discordance"
,
required
=
false
)
var
allowContigLengthDiscordance
:
Boolean
=
config
(
"allow_contig_length_discordance"
,
default
=
false
)
var
allowContigLengthDiscordance
:
Boolean
=
config
(
"allow_contig_length_discordance"
,
default
=
false
)
override
def
commandLine
=
super
.
commandLine
+
conditional
(
allowIncompleteDictConcordance
,
"ALLOW_INCOMPLETE_DICT_CONCORDANCE=TRUE"
)
+
...
...
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