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biopet.biopet
Commits
bb12d6db
Commit
bb12d6db
authored
Mar 07, 2016
by
Peter van 't Hof
Browse files
Fixed layout
parent
42ebd301
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
View file @
bb12d6db
...
...
@@ -19,8 +19,8 @@ import java.io.File
import
htsjdk.samtools.reference.IndexedFastaSequenceFile
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryQScript
,
Summarizable
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
scala.collection.JavaConversions._
...
...
@@ -77,14 +77,16 @@ trait Reference extends Configurable {
this
match
{
case
c
:
BiopetCommandLineFunction
=>
c
.
deps
:::=
dict
::
fai
::
Nil
case
_
=>
case
_
=>
}
}
else
{
val
defaults
=
ConfigUtils
.
mergeMaps
(
this
.
defaults
,
this
.
internalDefaults
)
def
getReferences
(
map
:
Map
[
String
,
Any
])
:
Set
[(
String
,
String
)]
=
(
for
(
(
species
,
species_content
:
Map
[
String
,
Any
])
<-
map
.
getOrElse
(
"references"
,
Map
[
String
,
Any
]()).
asInstanceOf
[
Map
[
String
,
Any
]].
toList
;
(
reference_name
,
_
)
<-
species_content
.
toList
)
yield
(
species
,
reference_name
)).
toSet
val
references
=
getReferences
(
defaults
)
++
getReferences
(
Config
.
global
.
map
)
if
(!
references
.
contains
((
referenceSpecies
,
referenceName
)))
{
val
buffer
=
new
StringBuilder
()
...
...
@@ -139,8 +141,8 @@ object Reference {
/**
* Raise an exception when given fasta file has no fai file
*
* @param fastaFile Fasta file
*
* @param fastaFile Fasta file
*/
def
requireFai
(
fastaFile
:
File
)
:
Unit
=
{
val
fai
=
new
File
(
fastaFile
.
getAbsolutePath
+
".fai"
)
...
...
@@ -155,8 +157,8 @@ object Reference {
/**
* Raise an exception when given fasta file has no dict file
*
* @param fastaFile Fasta file
*
* @param fastaFile Fasta file
*/
def
requireDict
(
fastaFile
:
File
)
:
Unit
=
{
val
dict
=
new
File
(
fastaFile
.
getAbsolutePath
...
...
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