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biopet.biopet
Commits
f74579d3
Commit
f74579d3
authored
Jul 13, 2017
by
Peter van 't Hof
Browse files
Fixed compile issues
parent
63547f9b
Changes
3
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
View file @
f74579d3
...
...
@@ -95,7 +95,7 @@ object SummaryToTsv extends ToolCommand {
def
fetchValues
(
summary
:
Summary
,
paths
:
Map
[
String
,
Array
[
String
]],
sample
:
Boolean
=
false
,
lib
:
Boolean
=
lib
=
false
)
:
Map
[
String
,
Map
[
String
,
Option
[
Any
]]]
=
{
lib
:
Boolean
=
false
)
:
Map
[
String
,
Map
[
String
,
Option
[
Any
]]]
=
{
for
((
name
,
path
)
<-
paths
)
yield
name
->
{
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
View file @
f74579d3
...
...
@@ -101,14 +101,14 @@ object VcfWithVcf extends ToolCommand {
val
header
=
reader
.
getFileHeader
val
vcfDict
=
header
.
getSequenceDictionary
match
{
case
r
if
r
!=
null
=>
r
.
assertSameDictionary
(
referenceDict
,
ignoreOrder
=
true
)
r
.
assertSameDictionary
(
referenceDict
,
true
)
r
case
_
=>
referenceDict
}
val
secondHeader
=
secondaryReader
.
getFileHeader
secondHeader
.
getSequenceDictionary
match
{
case
r
if
r
!=
null
=>
r
.
assertSameDictionary
(
referenceDict
,
ignoreOrder
=
true
)
case
r
if
r
!=
null
=>
r
.
assertSameDictionary
(
referenceDict
,
true
)
case
_
=>
}
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
View file @
f74579d3
...
...
@@ -95,7 +95,7 @@ object BamStats extends ToolCommand {
referenceFasta
.
map
{
f
=>
samHeader
.
getSequenceDictionary
.
assertSameDictionary
(
FastaUtils
.
getCachedDict
(
f
),
ignoreOrder
=
false
)
false
)
FastaUtils
.
getCachedDict
(
f
)
}
.
getOrElse
(
samHeader
.
getSequenceDictionary
)
...
...
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