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Mirrors
biopet.biopet
Commits
26a7681c
Commit
26a7681c
authored
May 17, 2016
by
Peter van 't Hof
Browse files
Style fixes
parent
10bbbbda
Changes
26
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
26a7681c
...
...
@@ -132,7 +132,7 @@ trait ReportBuilder extends ToolCommand {
logger
.
info
(
"Start"
)
val
argsParser
=
new
OptParser
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
require
(
cmdArgs
.
outputDir
.
exists
(),
"Output dir does not exist"
)
require
(
cmdArgs
.
outputDir
.
isDirectory
,
"Output dir is not a directory"
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
View file @
26a7681c
...
...
@@ -80,7 +80,7 @@ object AnnotateVcfWithBed extends ToolCommand {
logger
.
info
(
"Start"
)
val
argsParser
=
new
OptParser
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
fieldType
=
cmdArgs
.
fieldType
match
{
case
"Integer"
=>
VCFHeaderLineType
.
Integer
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
View file @
26a7681c
...
...
@@ -53,7 +53,7 @@ object BaseCounter extends ToolCommand {
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
//Sets picard logging level
htsjdk
.
samtools
.
util
.
Log
.
setGlobalLogLevel
(
htsjdk
.
samtools
.
util
.
Log
.
LogLevel
.
valueOf
(
logger
.
getLevel
.
toString
))
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
View file @
26a7681c
...
...
@@ -113,7 +113,7 @@ object BastyGenerateFasta extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
cmdArgs
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
cmdArgs
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
if
(
cmdArgs
.
outputVariants
!=
null
)
{
writeVariantsOnly
()
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
View file @
26a7681c
...
...
@@ -47,7 +47,7 @@ object BedToInterval extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
writer
=
new
PrintWriter
(
commandArgs
.
outputFile
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
View file @
26a7681c
...
...
@@ -39,7 +39,7 @@ object BedtoolsCoverageToCounts extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
if
(!
commandArgs
.
input
.
exists
)
throw
new
IllegalStateException
(
"Input file not found, file: "
+
commandArgs
.
input
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
View file @
26a7681c
...
...
@@ -50,7 +50,7 @@ object BiopetFlagstat extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
inputSam
=
SamReaderFactory
.
makeDefault
.
open
(
commandArgs
.
inputFile
)
val
iterSam
=
if
(
commandArgs
.
region
.
isEmpty
)
inputSam
.
iterator
else
{
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
View file @
26a7681c
...
...
@@ -71,7 +71,7 @@ object CheckAllelesVcfInBam extends ToolCommand {
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
if
(
commandArgs
.
bamFiles
.
size
!=
commandArgs
.
samples
.
size
)
logger
.
warn
(
"Number of samples is different from number of bam files: additional samples or bam files will not be used"
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
View file @
26a7681c
...
...
@@ -45,7 +45,7 @@ object FastqSplitter extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
groupSize
=
100
val
output
=
for
(
file
<-
commandArgs
.
outputFile
)
yield
new
AsyncFastqWriter
(
new
BasicFastqWriter
(
file
),
groupSize
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
View file @
26a7681c
...
...
@@ -46,7 +46,7 @@ object FindRepeatsPacBio extends ToolCommand {
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
bamReader
=
SamReaderFactory
.
makeDefault
.
validationStringency
(
ValidationStringency
.
SILENT
)
.
open
(
commandArgs
.
inputBam
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala
View file @
26a7681c
...
...
@@ -57,7 +57,7 @@ object GvcfToBed extends ToolCommand {
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
cmdArgs
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
cmdArgs
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
logger
.
debug
(
"Opening reader"
)
val
reader
=
new
VCFFileReader
(
cmdArgs
.
inputVcf
,
false
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
View file @
26a7681c
...
...
@@ -50,7 +50,7 @@ object MergeAlleles extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
readers
=
commandArgs
.
inputFiles
.
map
(
new
VCFFileReader
(
_
,
true
))
val
referenceFile
=
new
FastaSequenceFile
(
commandArgs
.
reference
,
true
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala
View file @
26a7681c
...
...
@@ -41,7 +41,7 @@ object MergeOtuMaps extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
var
map
:
Map
[
Long
,
String
]
=
Map
()
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
View file @
26a7681c
...
...
@@ -62,7 +62,7 @@ object MpileupToVcf extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
if
(
commandArgs
.
input
!=
null
&&
!
commandArgs
.
input
.
exists
)
throw
new
IllegalStateException
(
"Input file does not exist"
)
val
writer
=
new
PrintWriter
(
commandArgs
.
output
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
View file @
26a7681c
...
...
@@ -52,7 +52,7 @@ object PrefixFastq extends ToolCommand {
logger
.
info
(
"Start"
)
val
argsParser
=
new
OptParser
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
writer
=
new
AsyncFastqWriter
(
new
BasicFastqWriter
(
cmdArgs
.
output
),
3000
)
val
reader
=
new
FastqReader
(
cmdArgs
.
input
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
View file @
26a7681c
...
...
@@ -49,7 +49,7 @@ object RegionAfCount extends ToolCommand {
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
logger
.
info
(
"Start"
)
logger
.
info
(
"Reading bed file"
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
View file @
26a7681c
...
...
@@ -41,7 +41,7 @@ object SageCountFastq extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
if
(!
commandArgs
.
input
.
exists
)
throw
new
IllegalStateException
(
"Input file not found, file: "
+
commandArgs
.
input
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
View file @
26a7681c
...
...
@@ -74,7 +74,7 @@ object SageCreateLibrary extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
if
(!
commandArgs
.
input
.
exists
)
throw
new
IllegalStateException
(
"Input file not found, file: "
+
commandArgs
.
input
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
View file @
26a7681c
...
...
@@ -52,7 +52,7 @@ object SageCreateTagCounts extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
if
(!
commandArgs
.
input
.
exists
)
throw
new
IllegalStateException
(
"Input file not found, file: "
+
commandArgs
.
input
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
View file @
26a7681c
...
...
@@ -46,7 +46,7 @@ object SamplesTsvToJson extends ToolCommand {
/** Executes SamplesTsvToJson */
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
jsonString
=
stringFromInputs
(
cmdArgs
.
inputFiles
,
cmdArgs
.
tagFiles
)
cmdArgs
.
outputFile
match
{
...
...
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