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biopet.biopet
Commits
04e8b466
Commit
04e8b466
authored
Dec 12, 2016
by
Peter van 't Hof
Browse files
Fixing BIOPET-496
parent
0b4c76c5
Changes
1
Hide whitespace changes
Inline
Side-by-side
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
04e8b466
...
...
@@ -118,13 +118,13 @@ object BammetricsReport extends ReportBuilder {
tsvWriter
.
println
(
"\tMapped\tDuplicates\tUnmapped\tSecondary"
)
def
getLine
(
summary
:
Summary
,
sample
:
String
,
lib
:
Option
[
String
]
=
None
)
:
String
=
{
val
mapped
=
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"b
iopet_
flagstat"
,
"Mapped"
),
val
mapped
=
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"b
amstats"
,
"
flagstat
s
"
,
"Mapped"
),
summary
,
Some
(
sample
),
lib
).
value
.
getOrElse
(
0
).
toString
.
toLong
val
duplicates
=
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"b
iopet_
flagstat"
,
"Duplicates"
),
val
duplicates
=
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"b
amstats"
,
"
flagstat
s
"
,
"Duplicates"
),
summary
,
Some
(
sample
),
lib
).
value
.
getOrElse
(
0
).
toString
.
toLong
val
total
=
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"b
iopet_
flagstat"
,
"All"
),
val
total
=
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"b
amstats"
,
"
flagstat
s
"
,
"All"
),
summary
,
Some
(
sample
),
lib
).
value
.
getOrElse
(
0
).
toString
.
toLong
val
secondary
=
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"b
iopet_
flagstat"
,
"NotPrimaryAlignment"
),
val
secondary
=
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"b
amstats"
,
"
flagstat
s
"
,
"NotPrimaryAlignment"
),
summary
,
Some
(
sample
),
lib
).
value
.
getOrElse
(
0
).
toString
.
toLong
val
sb
=
new
StringBuffer
()
if
(
lib
.
isDefined
)
sb
.
append
(
sample
+
"-"
+
lib
.
get
+
"\t"
)
else
sb
.
append
(
sample
+
"\t"
)
...
...
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