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biopet.biopet
Commits
d4aba683
Commit
d4aba683
authored
Nov 22, 2016
by
Peter van 't Hof
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Fixed bug
parent
682d5937
Changes
1
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12 additions
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12 deletions
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-12
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+12
-12
No files found.
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
d4aba683
...
...
@@ -199,11 +199,11 @@ object BammetricsReport extends ReportBuilder {
}
def
mappingQualityPlot
(
outputDir
:
File
,
prefix
:
String
,
summary
:
Summary
,
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
String
]
=
None
,
libId
:
Option
[
String
]
=
None
)
:
Unit
=
{
prefix
:
String
,
summary
:
Summary
,
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
String
]
=
None
,
libId
:
Option
[
String
]
=
None
)
:
Unit
=
{
val
tsvFile
=
new
File
(
outputDir
,
prefix
+
".tsv"
)
val
pngFile
=
new
File
(
outputDir
,
prefix
+
".png"
)
...
...
@@ -227,11 +227,11 @@ object BammetricsReport extends ReportBuilder {
}
def
clippingPlot
(
outputDir
:
File
,
prefix
:
String
,
summary
:
Summary
,
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
String
]
=
None
,
libId
:
Option
[
String
]
=
None
)
:
Unit
=
{
prefix
:
String
,
summary
:
Summary
,
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
String
]
=
None
,
libId
:
Option
[
String
]
=
None
)
:
Unit
=
{
val
tsvFile
=
new
File
(
outputDir
,
prefix
+
".tsv"
)
val
pngFile
=
new
File
(
outputDir
,
prefix
+
".png"
)
...
...
@@ -348,7 +348,7 @@ object BammetricsReport extends ReportBuilder {
require
(
value
.
isDefined
,
s
"Sample: $sampleId, library: $libId on path: '${path.mkString("
,
")}' does not exist in summary"
)
key
->
value
.
get
}
require
(
pathValues
.
map
(
_
.
_2
.
size
).
toList
.
distinct
==
1
,
s
"Arrays in summary does not have the same number of values, $paths"
)
require
(
pathValues
.
map
(
_
.
_2
.
size
).
toList
.
distinct
.
size
==
1
,
s
"Arrays in summary does not have the same number of values, $paths"
)
pathValues
}
...
...
@@ -361,7 +361,7 @@ object BammetricsReport extends ReportBuilder {
}
def
writeTableToTsv
(
tsvFile
:
File
,
table
:
Map
[
String
,
Array
[
Any
]],
firstColumn
:
String
)
:
Unit
=
{
require
(
table
.
map
(
_
.
_2
.
size
).
toList
.
distinct
==
1
,
"Not all values has the same number or rows"
)
require
(
table
.
map
(
_
.
_2
.
size
).
toList
.
distinct
.
size
==
1
,
"Not all values has the same number or rows"
)
val
keys
=
table
.
keys
.
filterNot
(
_
==
firstColumn
).
toList
.
sorted
val
writer
=
new
PrintWriter
(
tsvFile
)
writer
.
println
((
firstColumn
::
keys
).
mkString
(
"\t"
))
...
...
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