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biopet.biopet
Commits
4df69c64
Commit
4df69c64
authored
May 18, 2016
by
bow
Browse files
Merge branch 'feature-singletons_flagstat' into 'develop'
Added singletons to summary See merge request !404
parents
e11ff161
e37fd3ac
Changes
2
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
View file @
4df69c64
...
...
@@ -211,7 +211,8 @@ object BiopetFlagstat extends ToolCommand {
def
summary
:
String
=
{
val
map
=
(
for
(
t
<-
0
until
names
.
size
)
yield
{
names
(
t
)
->
totalCounts
(
t
)
}).
toMap
}).
toMap
++
Map
(
"Singletons"
->
crossCounts
(
names
.
find
(
_
.
_2
==
"Mapped"
).
map
(
_
.
_1
).
getOrElse
(-
1
))(
names
.
find
(
_
.
_2
==
"MateUnmapped"
).
map
(
_
.
_1
).
getOrElse
(-
1
))
)
ConfigUtils
.
mapToJson
(
map
).
spaces4
}
...
...
biopet-tools/src/test/resources/flagstat_summary.txt
View file @
4df69c64
...
...
@@ -11,6 +11,7 @@
"MateNegativeStrand" : 1,
"FirstOfPair" : 1,
"ReadPaired" : 1,
"Singletons" : 0,
"SecondaryOrSupplementary" : 0,
"SecondOfPair" : 0
}
\ No newline at end of file
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