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biopet.biopet
Commits
c97f4ed7
Commit
c97f4ed7
authored
May 14, 2016
by
Peter van 't Hof
Browse files
Changes arg parser with getOrElse(throw new IllegalArgumentException)
parent
43253296
Changes
33
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
c97f4ed7
...
...
@@ -132,7 +132,7 @@ trait ReportBuilder extends ToolCommand {
logger
.
info
(
"Start"
)
val
argsParser
=
new
OptParser
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
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 @
c97f4ed7
...
...
@@ -80,7 +80,7 @@ object AnnotateVcfWithBed extends ToolCommand {
logger
.
info
(
"Start"
)
val
argsParser
=
new
OptParser
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
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 @
c97f4ed7
...
...
@@ -53,10 +53,7 @@ object BaseCounter extends ToolCommand {
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
match
{
case
Some
(
x
)
=>
x
case
_
=>
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 @
c97f4ed7
...
...
@@ -113,7 +113,7 @@ object BastyGenerateFasta extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
cmdArgs
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
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 @
c97f4ed7
...
...
@@ -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
sys
.
exit
(
1
)
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 @
c97f4ed7
...
...
@@ -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
sys
.
exit
(
1
)
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 @
c97f4ed7
...
...
@@ -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
sys
.
exit
(
1
)
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 @
c97f4ed7
...
...
@@ -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
sys
.
exit
(
1
)
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/ExtractAlignedFastq.scala
View file @
c97f4ed7
...
...
@@ -242,7 +242,7 @@ object ExtractAlignedFastq extends ToolCommand {
def
parseArgs
(
args
:
Array
[
String
])
:
Args
=
new
OptParser
()
.
parse
(
args
,
Args
())
.
getOrElse
(
sys
.
exit
(
1
)
)
.
getOrElse
(
throw
new
IllegalArgumentException
)
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
View file @
c97f4ed7
...
...
@@ -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
sys
.
exit
(
1
)
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/FastqSync.scala
View file @
c97f4ed7
...
...
@@ -151,7 +151,7 @@ object FastqSync extends ToolCommand {
*/
def
parseArgs
(
args
:
Array
[
String
])
:
Args
=
new
OptParser
()
.
parse
(
args
,
Args
())
.
getOrElse
(
sys
.
exit
(
1
)
)
.
getOrElse
(
throw
new
IllegalArgumentException
)
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
View file @
c97f4ed7
...
...
@@ -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
sys
.
exit
(
1
)
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 @
c97f4ed7
...
...
@@ -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
sys
.
exit
(
1
)
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/KrakenReportToJson.scala
View file @
c97f4ed7
...
...
@@ -90,7 +90,7 @@ object KrakenReportToJson extends ToolCommand {
*/
def
parseArgs
(
args
:
Array
[
String
])
:
Args
=
new
OptParser
()
.
parse
(
args
,
Args
())
.
getOrElse
(
sys
.
exit
(
1
)
)
.
getOrElse
(
throw
new
IllegalArgumentException
)
/**
* Takes a line from the kraken report, converts into Map with taxonID and
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
View file @
c97f4ed7
...
...
@@ -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
sys
.
exit
(
1
)
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 @
c97f4ed7
...
...
@@ -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
sys
.
exit
(
1
)
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/MergeTables.scala
View file @
c97f4ed7
...
...
@@ -188,7 +188,7 @@ object MergeTables extends ToolCommand {
/** Parses the command line argument */
def
parseArgs
(
args
:
Array
[
String
])
:
Args
=
new
OptParser
()
.
parse
(
args
,
Args
())
.
getOrElse
(
sys
.
exit
(
1
)
)
.
getOrElse
(
throw
new
IllegalArgumentException
)
/** Transforms the input file seq into a seq of [[InputTable]] objects */
def
prepInput
(
inFiles
:
Seq
[
File
],
ext
:
String
,
columnNames
:
Option
[
Seq
[
String
]])
:
Seq
[
InputTable
]
=
{
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
View file @
c97f4ed7
...
...
@@ -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
sys
.
exit
(
1
)
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 @
c97f4ed7
...
...
@@ -52,7 +52,7 @@ object PrefixFastq extends ToolCommand {
logger
.
info
(
"Start"
)
val
argsParser
=
new
OptParser
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
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 @
c97f4ed7
...
...
@@ -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
sys
.
exit
(
1
)
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
logger
.
info
(
"Start"
)
logger
.
info
(
"Reading bed file"
)
...
...
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