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biopet.biopet
Commits
afbc3f9b
Commit
afbc3f9b
authored
Jun 08, 2015
by
Peter van 't Hof
Browse files
Fixed insertsize plot
parent
780cfddc
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
afbc3f9b
...
...
@@ -112,18 +112,20 @@ object BammetricsReport extends ReportBuilder {
var
map
:
Map
[
Int
,
Map
[
String
,
Int
]]
=
Map
()
def
fill
(
sample
:
String
,
lib
:
Option
[
String
])
:
Unit
=
{
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"CollectInsertSizeMetrics"
,
"histogram"
,
"content"
),
summary
,
Some
(
sample
),
lib
).
value
.
getOrElse
(
List
(
List
(
"insert_size"
,
"All_Reads.fr_count"
)))
match
{
case
l
:
List
[
_
]
=>
{
l
.
tail
.
foreach
(
_
match
{
case
l
:
List
[
_
]
=>
{
val
insertSize
=
l
.
head
.
toString
.
toInt
val
count
=
l
.
tail
.
head
.
toString
.
toInt
val
old
=
map
.
getOrElse
(
insertSize
,
Map
())
if
(
libraryLevel
)
map
+=
insertSize
->
(
old
+
((
s
"$sample-"
+
lib
.
get
)
->
count
))
else
map
+=
insertSize
->
(
old
+
(
sample
->
count
))
}
case
_
=>
throw
new
IllegalStateException
(
"Must be a list"
)
val
insertSize
=
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"CollectInsertSizeMetrics"
,
"histogram"
,
"insert_size"
),
summary
,
Some
(
sample
),
lib
).
value
.
getOrElse
(
List
())
val
counts
=
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"CollectInsertSizeMetrics"
,
"histogram"
,
"All_Reads.fr_count"
),
summary
,
Some
(
sample
),
lib
).
value
.
getOrElse
(
List
())
(
insertSize
,
counts
)
match
{
case
(
l
:
List
[
_
],
l2
:
List
[
_
])
=>
{
l
.
zip
(
l2
).
foreach
(
i
=>
{
val
insertSize
=
i
.
_1
.
toString
.
toInt
val
count
=
i
.
_2
.
toString
.
toInt
val
old
=
map
.
getOrElse
(
insertSize
,
Map
())
if
(
libraryLevel
)
map
+=
insertSize
->
(
old
+
((
s
"$sample-"
+
lib
.
get
)
->
count
))
else
map
+=
insertSize
->
(
old
+
(
sample
->
count
))
})
}
case
_
=>
throw
new
IllegalStateException
(
"Must be a list"
)
...
...
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