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biopet.biopet
Commits
6a83d167
Commit
6a83d167
authored
Sep 09, 2015
by
Peter van 't Hof
Browse files
Add output arg to biopet flagstat
parent
f2d40822
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
View file @
6a83d167
...
...
@@ -61,12 +61,18 @@ object BiopetFlagstat extends ToolCommand {
flagstat
}
case
class
Args
(
inputFile
:
File
=
null
,
summaryFile
:
Option
[
File
]
=
None
,
region
:
Option
[
String
]
=
None
)
extends
AbstractArgs
case
class
Args
(
inputFile
:
File
=
null
,
outputFile
:
Option
[
File
]
=
None
,
summaryFile
:
Option
[
File
]
=
None
,
region
:
Option
[
String
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
opt
[
File
](
'I'
,
"inputFile"
)
required
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFile
=
x
)
}
text
"input bam file"
opt
[
File
](
'o'
,
"outputFile"
)
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
outputFile
=
Some
(
x
))
}
text
"output file"
opt
[
File
](
's'
,
"summaryFile"
)
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
summaryFile
=
Some
(
x
))
}
text
"summary output file"
...
...
@@ -151,7 +157,14 @@ object BiopetFlagstat extends ToolCommand {
writer
.
close
()
}
println
(
flagstatCollector
.
report
)
commandArgs
.
outputFile
match
{
case
Some
(
file
)
=>
{
val
writer
=
new
PrintWriter
(
file
)
writer
.
println
(
flagstatCollector
.
report
)
writer
.
close
()
}
case
_
=>
println
(
flagstatCollector
.
report
)
}
}
class
FlagstatCollector
{
...
...
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