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biopet.biopet
Commits
8a9ad332
Commit
8a9ad332
authored
Feb 10, 2015
by
Peter van 't Hof
Browse files
Fix format
parent
26bc48af
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
8a9ad332
...
...
@@ -68,7 +68,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
f
.
checkExecutable
f
.
afterGraph
}
case
_
=>
case
_
=>
}
if
(
new
File
(
outputDir
).
canWrite
)
Config
.
global
.
writeReport
(
qSettings
.
runName
,
outputDir
+
".log/"
+
qSettings
.
runName
)
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
View file @
8a9ad332
...
...
@@ -53,15 +53,15 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
* @throws IllegalStateException if the module lines have no content or mapping is empty.
*/
def
qcModules
:
Map
[
String
,
FastQCModule
]
=
{
val
fqModules
=
Source
.
fromFile
(
dataFile
)
// drop all the characters before the first module delimiter (i.e. '>>')
.
dropWhile
(
_
!=
'>'
)
// pull everything into a string
.
mkString
// split into modules
.
split
(
">>END_MODULE\n"
)
// make map of module name -> module lines
.
map
{
val
fqModules
=
Source
.
fromFile
(
dataFile
)
// drop all the characters before the first module delimiter (i.e. '>>')
.
dropWhile
(
_
!=
'>'
)
// pull everything into a string
.
mkString
// split into modules
.
split
(
">>END_MODULE\n"
)
// make map of module name -> module lines
.
map
{
case
(
modString
)
=>
// module name is in the first line, without '>>' and before the tab character
val
Array
(
firstLine
,
otherLines
)
=
modString
...
...
@@ -77,10 +77,10 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
.
slice
(
0
,
2
)
modName
->
FastQCModule
(
modName
,
modStatus
,
otherLines
.
split
(
"\n"
).
toSeq
)
}
.
toMap
.
toMap
if
(
fqModules
.
isEmpty
)
throw
new
IllegalStateException
(
"Empty FastQC data file "
+
dataFile
.
toString
)
else
fqModules
if
(
fqModules
.
isEmpty
)
throw
new
IllegalStateException
(
"Empty FastQC data file "
+
dataFile
.
toString
)
else
fqModules
}
/**
...
...
@@ -93,11 +93,11 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
def
encoding
:
String
=
{
if
(
dataFile
.
exists
())
qcModules
(
"Basic Statistics"
)
//FIXME: not save
.
lines
.
dropWhile
(!
_
.
startsWith
(
"Encoding"
))
.
head
.
stripPrefix
(
"Encoding\t"
)
.
stripSuffix
(
"\t"
)
.
lines
.
dropWhile
(!
_
.
startsWith
(
"Encoding"
))
.
head
.
stripPrefix
(
"Encoding\t"
)
.
stripSuffix
(
"\t"
)
else
""
}
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
View file @
8a9ad332
...
...
@@ -27,11 +27,11 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
if
(
fastqc
!=
null
&&
Q
==
None
)
{
val
encoding
=
fastqc
.
encoding
Q
=
encoding
match
{
case
null
=>
None
case
null
=>
None
case
s
if
(
s
.
contains
(
"Sanger / Illumina 1.9"
))
=>
None
case
s
if
(
s
.
contains
(
"Illumina <1.3"
))
=>
Option
(
64
)
case
s
if
(
s
.
contains
(
"Illumina 1.3"
))
=>
Option
(
64
)
case
s
if
(
s
.
contains
(
"Illumina 1.5"
))
=>
Option
(
64
)
case
s
if
(
s
.
contains
(
"Illumina <1.3"
))
=>
Option
(
64
)
case
s
if
(
s
.
contains
(
"Illumina 1.3"
))
=>
Option
(
64
)
case
s
if
(
s
.
contains
(
"Illumina 1.5"
))
=>
Option
(
64
)
case
_
=>
None
}
if
(
Q
!=
None
)
V
=
true
...
...
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