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biopet.biopet
Commits
c7b0392c
Commit
c7b0392c
authored
Sep 17, 2015
by
Peter van 't Hof
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Fix plots for library level
parent
2d950663
Changes
3
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3 changed files
with
15 additions
and
11 deletions
+15
-11
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
...s/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
+1
-1
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
...nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
+1
-1
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+13
-9
No files found.
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @
c7b0392c
...
...
@@ -42,7 +42,7 @@
#end
#if (showPlot)
#{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId) }#
#{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId
, libId = libId
) }#
<div class="panel-body">
<img src="insertsize.png" class="img-responsive" />
...
...
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
View file @
c7b0392c
...
...
@@ -36,7 +36,7 @@
#end
#if (showPlot)
#{ BammetricsReport.wgsHistogramPlot(outputDir, "wgs", summary, !sampleLevel, sampleId = sampleId) }#
#{ BammetricsReport.wgsHistogramPlot(outputDir, "wgs", summary, !sampleLevel, sampleId = sampleId
, libId = libId
) }#
<div class="panel-body">
<img src="wgs.png" class="img-responsive" />
...
...
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
c7b0392c
...
...
@@ -156,14 +156,15 @@ object BammetricsReport extends ReportBuilder {
prefix
:
String
,
summary
:
Summary
,
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
String
]
=
None
)
:
Unit
=
{
sampleId
:
Option
[
String
]
=
None
,
libId
:
Option
[
String
]
=
None
)
:
Unit
=
{
val
tsvFile
=
new
File
(
outputDir
,
prefix
+
".tsv"
)
val
pngFile
=
new
File
(
outputDir
,
prefix
+
".png"
)
val
tsvWriter
=
new
PrintWriter
(
tsvFile
)
if
(
libraryLevel
)
{
tsvWriter
.
println
((
for
(
sample
<-
summary
.
samples
if
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
;
lib
<-
summary
.
libraries
(
sample
)
lib
<-
summary
.
libraries
(
sample
)
if
libId
.
isEmpty
||
libId
.
get
==
lib
)
yield
s
"$sample-$lib"
)
.
mkString
(
"library\t"
,
"\t"
,
""
))
}
else
{
...
...
@@ -198,7 +199,7 @@ object BammetricsReport extends ReportBuilder {
if
(
libraryLevel
)
{
for
(
sample
<-
summary
.
samples
if
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
;
lib
<-
summary
.
libraries
(
sample
)
lib
<-
summary
.
libraries
(
sample
)
if
libId
.
isEmpty
||
libId
.
get
==
lib
)
fill
(
sample
,
Some
(
lib
))
}
else
if
(
sampleId
.
isDefined
)
fill
(
sampleId
.
get
,
None
)
else
summary
.
samples
.
foreach
(
fill
(
_
,
None
))
...
...
@@ -208,7 +209,7 @@ object BammetricsReport extends ReportBuilder {
if
(
libraryLevel
)
{
for
(
sample
<-
summary
.
samples
if
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
;
lib
<-
summary
.
libraries
(
sample
)
lib
<-
summary
.
libraries
(
sample
)
if
libId
.
isEmpty
||
libId
.
get
==
lib
)
tsvWriter
.
print
(
"\t"
+
counts
.
getOrElse
(
s
"$sample-$lib"
,
"0"
))
}
else
{
for
(
sample
<-
summary
.
samples
if
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
)
{
...
...
@@ -243,14 +244,15 @@ object BammetricsReport extends ReportBuilder {
prefix
:
String
,
summary
:
Summary
,
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
String
]
=
None
)
:
Unit
=
{
sampleId
:
Option
[
String
]
=
None
,
libId
:
Option
[
String
]
=
None
)
:
Unit
=
{
val
tsvFile
=
new
File
(
outputDir
,
prefix
+
".tsv"
)
val
pngFile
=
new
File
(
outputDir
,
prefix
+
".png"
)
val
tsvWriter
=
new
PrintWriter
(
tsvFile
)
if
(
libraryLevel
)
{
tsvWriter
.
println
((
for
(
sample
<-
summary
.
samples
if
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
;
lib
<-
summary
.
libraries
(
sample
)
lib
<-
summary
.
libraries
(
sample
)
if
libId
.
isEmpty
||
libId
.
get
==
lib
)
yield
s
"$sample-$lib"
)
.
mkString
(
"library\t"
,
"\t"
,
""
))
}
else
{
...
...
@@ -285,7 +287,7 @@ object BammetricsReport extends ReportBuilder {
if
(
libraryLevel
)
{
for
(
sample
<-
summary
.
samples
if
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
;
lib
<-
summary
.
libraries
(
sample
)
lib
<-
summary
.
libraries
(
sample
)
if
libId
.
isEmpty
||
libId
.
get
==
lib
)
fill
(
sample
,
Some
(
lib
))
}
else
if
(
sampleId
.
isDefined
)
fill
(
sampleId
.
get
,
None
)
else
summary
.
samples
.
foreach
(
fill
(
_
,
None
))
...
...
@@ -295,8 +297,10 @@ object BammetricsReport extends ReportBuilder {
if
(
libraryLevel
)
{
for
(
sample
<-
summary
.
samples
if
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
;
lib
<-
summary
.
libraries
(
sample
)
)
tsvWriter
.
print
(
"\t"
+
counts
.
getOrElse
(
s
"$sample-$lib"
,
"0"
))
lib
<-
summary
.
libraries
(
sample
)
if
libId
.
isEmpty
||
libId
.
get
==
lib
)
{
tsvWriter
.
print
(
"\t"
+
counts
.
getOrElse
(
s
"$sample-$lib"
,
"0"
))
}
}
else
{
for
(
sample
<-
summary
.
samples
if
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
)
{
tsvWriter
.
print
(
"\t"
+
counts
.
getOrElse
(
sample
,
"0"
))
...
...
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