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biopet.biopet
Commits
7b78d005
Commit
7b78d005
authored
Oct 02, 2014
by
bow
Browse files
Update access modifiers for WipeReads functions
parent
9cd1b9d7
Changes
1
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Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/WipeReads.scala
View file @
7b78d005
...
...
@@ -35,7 +35,7 @@ object WipeReads {
type
OptionMap
=
Map
[
String
,
Any
]
case
class
RawInterval
(
chrom
:
String
,
start
:
Int
,
end
:
Int
,
strand
:
String
)
object
Strand
extends
Enumeration
{
private
object
Strand
extends
Enumeration
{
type
Strand
=
Value
val
Identical
,
Opposite
,
Both
=
Value
}
...
...
@@ -103,7 +103,7 @@ object WipeReads {
else
throw
new
IOException
(
"Input file "
+
inFile
.
getPath
+
" not found"
)
def
checkInputBAM
(
inBAM
:
File
)
:
File
=
{
private
def
checkInputBAM
(
inBAM
:
File
)
:
File
=
{
// input BAM must have a .bam.bai index
if
(
new
File
(
inBAM
.
getPath
+
".bai"
).
exists
)
checkInputFile
(
inBAM
)
...
...
@@ -141,7 +141,7 @@ object WipeReads {
=>
throw
new
IllegalArgumentException
(
"Unexpected or duplicate option flag: "
+
option
)
}
def
validateOption
(
opts
:
OptionMap
)
:
Unit
=
{
private
def
validateOption
(
opts
:
OptionMap
)
:
Unit
=
{
// TODO: better way to check for required arguments ~ use scalaz.Validation?
if
(
opts
.
get
(
"inputBAM"
)
==
None
)
throw
new
IllegalArgumentException
(
"Input BAM not supplied"
)
...
...
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