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biopet.biopet
Commits
159c6184
Commit
159c6184
authored
Feb 28, 2017
by
Peter van 't Hof
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Adding lost modules
parent
8314da08
Changes
4
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4 changed files
with
18 additions
and
15 deletions
+18
-15
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
...scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+2
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
...asc/biopet/extensions/picard/CollectMultipleMetrics.scala
+14
-13
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
+1
-1
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
View file @
159c6184
...
...
@@ -30,7 +30,7 @@ trait Summarizable {
def
summaryStats
:
Any
/** Can be used to add additional Summarizable, this is executed at the start of WriteSummary*/
def
addToQscriptSummary
(
qscript
:
SummaryQScript
,
name
:
String
)
{}
def
addToQscriptSummary
(
qscript
:
SummaryQScript
)
{}
/**
* This function is used to merge value that are found at the same path in the map. Default there will throw a exception at conflicting values.
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
159c6184
...
...
@@ -53,6 +53,8 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
}
def
init
()
:
Unit
=
{
qscript
.
summarizables
.
foreach
(
_
.
_2
.
foreach
(
_
.
addToQscriptSummary
(
qscript
)))
val
db
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
if
(
qscript
==
root
)
{
// This initialize the database
qscript
match
{
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
View file @
159c6184
...
...
@@ -86,31 +86,32 @@ class CollectMultipleMetrics(val parent: Configurable) extends Picard with Summa
optional
(
"REFERENCE_SEQUENCE="
,
reference
,
spaceSeparated
=
false
)
+
repeat
(
"PROGRAM="
,
program
,
spaceSeparated
=
false
)
override
def
addToQscriptSummary
(
qscript
:
SummaryQScript
,
name
:
String
)
:
Unit
=
{
override
def
addToQscriptSummary
(
qscript
:
SummaryQScript
)
:
Unit
=
{
def
summarizable
(
stats
:
()
=>
Any
)
:
Summarizable
=
new
Summarizable
{
def
summaryStats
=
stats
()
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
}
program
.
filterNot
(
_
==
Programs
.
CollectInsertSizeMetrics
.
toString
&&
!
new
File
(
outputName
+
".insert_size_metrics"
).
exists
())
.
foreach
{
p
=>
val
stats
:
Any
=
p
match
{
p
match
{
case
_
if
p
==
Programs
.
CollectAlignmentSummaryMetrics
.
toString
=>
Picard
.
getMetrics
(
new
File
(
outputName
+
".alignment_summary_metrics"
),
groupBy
=
Some
(
"CATEGORY"
))
qscript
.
addSummarizable
(
summarizable
(()
=>
Picard
.
getMetrics
(
new
File
(
outputName
+
".alignment_summary_metrics"
),
groupBy
=
Some
(
"CATEGORY"
))
),
p
)
case
_
if
p
==
Programs
.
CollectInsertSizeMetrics
.
toString
=>
Map
(
qscript
.
addSummarizable
(
summarizable
(()
=>
Map
(
"metrics"
->
Picard
.
getMetrics
(
new
File
(
outputName
+
".insert_size_metrics"
)),
"histogram"
->
Picard
.
getHistogram
(
new
File
(
outputName
+
".insert_size_metrics"
))
)
)
),
p
)
case
_
if
p
==
Programs
.
QualityScoreDistribution
.
toString
=>
Picard
.
getHistogram
(
new
File
(
outputName
+
".quality_distribution_metrics"
))
qscript
.
addSummarizable
(
summarizable
(()
=>
Picard
.
getHistogram
(
new
File
(
outputName
+
".quality_distribution_metrics"
))
),
p
)
case
_
if
p
==
Programs
.
MeanQualityByCycle
.
toString
=>
Picard
.
getHistogram
(
new
File
(
outputName
+
".quality_by_cycle_metrics"
))
qscript
.
addSummarizable
(
summarizable
(()
=>
Picard
.
getHistogram
(
new
File
(
outputName
+
".quality_by_cycle_metrics"
))
),
p
)
case
_
if
p
==
Programs
.
CollectBaseDistributionByCycle
.
toString
=>
Picard
.
getHistogram
(
new
File
(
outputName
+
".base_distribution_by_cycle_metrics"
),
tag
=
"METRICS CLASS"
)
qscript
.
addSummarizable
(
summarizable
(()
=>
Picard
.
getHistogram
(
new
File
(
outputName
+
".base_distribution_by_cycle_metrics"
),
tag
=
"METRICS CLASS"
)
),
p
)
case
_
=>
None
}
val
sum
=
new
Summarizable
{
override
def
summaryStats
=
stats
override
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
}
qscript
.
addSummarizable
(
sum
,
p
)
}
}
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
159c6184
...
...
@@ -70,7 +70,7 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
override
def
summaryDeps
=
trim
.
map
(
_
.
summaryDeps
).
toList
.
flatten
:::
super
.
summaryDeps
override
def
addToQscriptSummary
(
qscript
:
SummaryQScript
,
name
:
String
)
:
Unit
=
{
override
def
addToQscriptSummary
(
qscript
:
SummaryQScript
)
:
Unit
=
{
clip
match
{
case
Some
(
job
)
=>
qscript
.
addSummarizable
(
job
,
s
"clipping_$read"
)
case
_
=>
...
...
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