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Mirrors
biopet.biopet
Commits
856f286b
Commit
856f286b
authored
Apr 16, 2015
by
Peter van 't Hof
Browse files
Added stats from bam metrics to summary
parent
553a7538
Changes
13
Hide whitespace changes
Inline
Side-by-side
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
856f286b
...
...
@@ -51,7 +51,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
def
summaryFiles
=
Map
(
"input_bam"
->
inputBam
)
/** return settings */
def
summarySettings
=
Map
()
def
summarySettings
=
Map
(
"ampliconBedFile"
->
ampliconBedFile
,
"roiBedFiles"
->
roiBedFiles
)
/** executed before script */
def
init
()
{
...
...
@@ -69,13 +69,17 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
multiMetrics
.
input
=
inputBam
multiMetrics
.
outputName
=
new
File
(
outputDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
))
add
(
multiMetrics
)
addSummarizable
(
multiMetrics
,
"multi_metrics"
)
add
(
CollectGcBiasMetrics
(
this
,
inputBam
,
outputDir
))
val
gcBiasMetrics
=
CollectGcBiasMetrics
(
this
,
inputBam
,
outputDir
)
add
(
gcBiasMetrics
)
addSummarizable
(
gcBiasMetrics
,
"gc_bias"
)
val
wgsMetrics
=
new
CollectWgsMetrics
(
this
)
wgsMetrics
.
input
=
inputBam
wgsMetrics
.
output
=
swapExt
(
outputDir
,
inputBam
,
".bam"
,
".rna.metrics"
)
add
(
wgsMetrics
)
addSummarizable
(
wgsMetrics
,
"wgs"
)
if
(
rnaMetrics
)
{
val
rnaMetrics
=
new
CollectRnaSeqMetrics
(
this
)
...
...
@@ -83,6 +87,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
rnaMetrics
.
output
=
swapExt
(
outputDir
,
inputBam
,
".bam"
,
".rna.metrics"
)
rnaMetrics
.
chartOutput
=
Some
(
swapExt
(
outputDir
,
inputBam
,
".bam"
,
".rna.metrics.pdf"
))
add
(
rnaMetrics
)
addSummarizable
(
rnaMetrics
,
"rna"
)
}
case
class
Intervals
(
bed
:
File
,
intervals
:
File
)
...
...
@@ -107,10 +112,12 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
val
chsMetrics
=
CalculateHsMetrics
(
this
,
inputBam
,
List
(
ampIntervals
),
ampIntervals
::
roiIntervals
.
map
(
_
.
intervals
),
outputDir
)
add
(
chsMetrics
)
addSummarizable
(
chsMetrics
,
"hs_metrics"
)
val
pcrMetrics
=
CollectTargetedPcrMetrics
(
this
,
inputBam
,
ampIntervals
,
ampIntervals
::
roiIntervals
.
map
(
_
.
intervals
),
outputDir
)
add
(
pcrMetrics
)
addSummarizable
(
chsMetrics
,
"targeted_pcr_metrics"
)
Intervals
(
ampliconBedFile
,
ampIntervals
)
}
...
...
@@ -118,8 +125,8 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
// Create stats and coverage plot for each bed/interval file
for
(
intervals
<-
roiIntervals
++
ampIntervals
)
{
//TODO: Add target jobs to summary
val
targetDir
=
new
File
(
outputDir
,
intervals
.
bed
.
getName
.
stripSuffix
(
".bed"
)
)
val
targetName
=
intervals
.
bed
.
getName
.
stripSuffix
(
".bed"
)
val
targetDir
=
new
File
(
outputDir
,
targetName
)
val
biStrict
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
output
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.strict.bam"
),
...
...
@@ -127,7 +134,9 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
biStrict
.
isIntermediate
=
true
add
(
biStrict
)
add
(
SamtoolsFlagstat
(
this
,
biStrict
.
output
,
targetDir
))
add
(
BiopetFlagstat
(
this
,
biStrict
.
output
,
targetDir
))
val
biopetFlagstatStrict
=
BiopetFlagstat
(
this
,
biStrict
.
output
,
targetDir
)
add
(
biopetFlagstatStrict
)
addSummarizable
(
biopetFlagstatStrict
,
targetName
+
"_biopet_flagstat_strict"
)
val
biLoose
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
output
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.loose.bam"
),
...
...
@@ -135,13 +144,17 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
biLoose
.
isIntermediate
=
true
add
(
biLoose
)
add
(
SamtoolsFlagstat
(
this
,
biLoose
.
output
,
targetDir
))
add
(
BiopetFlagstat
(
this
,
biLoose
.
output
,
targetDir
))
val
biopetFlagstatLoose
=
BiopetFlagstat
(
this
,
biLoose
.
output
,
targetDir
)
add
(
biopetFlagstatLoose
)
addSummarizable
(
biopetFlagstatLoose
,
targetName
+
"_biopet_flagstat_loose"
)
val
coverageFile
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".coverage"
)
//FIXME:should use piping
add
(
BedtoolsCoverage
(
this
,
inputBam
,
intervals
.
bed
,
coverageFile
,
depth
=
true
),
true
)
add
(
CoverageStats
(
this
,
coverageFile
,
targetDir
))
val
covStats
=
CoverageStats
(
this
,
coverageFile
,
targetDir
)
add
(
covStats
)
addSummarizable
(
covStats
,
"cov_stats"
)
}
addSummaryJobs
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
View file @
856f286b
...
...
@@ -17,10 +17,11 @@ package nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
/** Extension for picard CalculateHsMetrics */
class
CalculateHsMetrics
(
val
root
:
Configurable
)
extends
Picard
{
class
CalculateHsMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
{
javaMainClass
=
new
picard
.
analysis
.
directed
.
CalculateHsMetrics
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze. Must be coordinate sorted."
,
required
=
true
)
...
...
@@ -57,6 +58,12 @@ class CalculateHsMetrics(val root: Configurable) extends Picard {
repeat
(
"TARGET_INTERVALS="
,
targetIntervals
,
spaceSeparated
=
false
)
+
optional
(
"PER_TARGET_COVERAGE="
,
perTargetCoverage
,
spaceSeparated
=
false
)
+
optional
(
"BAIT_SET_NAME="
,
baitSetName
,
spaceSeparated
=
false
)
/** Returns files for summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
object
CalculateHsMetrics
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
View file @
856f286b
...
...
@@ -66,19 +66,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
)
match
{
case
None
=>
Map
()
case
Some
((
header
,
content
))
=>
(
for
(
category
<-
0
until
content
.
size
)
yield
{
content
(
category
)(
0
).
toString
->
(
for
(
i
<-
1
until
header
.
size
if
i
<
content
(
category
).
size
)
yield
{
header
(
i
).
toLowerCase
->
content
(
category
)(
i
)
}).
toMap
}
).
toMap
}
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
object
CollectAlignmentSummaryMetrics
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
View file @
856f286b
...
...
@@ -17,10 +17,11 @@ package nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
/** Extension for picard CollectGcBiasMetrics */
class
CollectGcBiasMetrics
(
val
root
:
Configurable
)
extends
Picard
{
class
CollectGcBiasMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
{
javaMainClass
=
new
picard
.
analysis
.
CollectGcBiasMetrics
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze. Must be coordinate sorted."
,
required
=
true
)
...
...
@@ -65,6 +66,12 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
optional
(
"MINIMUM_GENOME_FRACTION="
,
minGenomeFraction
,
spaceSeparated
=
false
)
+
conditional
(
assumeSorted
,
"ASSUME_SORTED=TRUE"
)
+
conditional
(
isBisulfiteSequinced
.
getOrElse
(
false
),
"IS_BISULFITE_SEQUENCED=TRUE"
)
/** Returns files for summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
object
CollectGcBiasMetrics
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
View file @
856f286b
...
...
@@ -75,13 +75,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
/** Returns files for summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"output_histogram"
->
outputHistogram
)
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
)
match
{
case
None
=>
Map
()
case
Some
((
header
,
content
))
=>
(
for
(
i
<-
0
to
header
.
size
if
i
<
content
.
head
.
size
)
yield
header
(
i
).
toLowerCase
->
content
.
head
(
i
)).
toMap
}
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
object
CollectInsertSizeMetrics
{
...
...
@@ -90,6 +84,6 @@ object CollectInsertSizeMetrics {
val
collectInsertSizeMetrics
=
new
CollectInsertSizeMetrics
(
root
)
collectInsertSizeMetrics
.
input
=
input
collectInsertSizeMetrics
.
output
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".insertsizemetrics"
)
return
collectInsertSizeMetrics
collectInsertSizeMetrics
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
View file @
856f286b
...
...
@@ -4,12 +4,13 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.BiopetQScript
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Argument
,
Input
}
/**
* Created by pjvan_thof on 4/16/15.
*/
class
CollectMultipleMetrics
(
val
root
:
Configurable
)
extends
Picard
{
class
CollectMultipleMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
{
import
CollectMultipleMetrics._
javaMainClass
=
new
picard
.
analysis
.
CollectMultipleMetrics
().
getClass
.
getName
...
...
@@ -64,6 +65,38 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard {
conditional
(
assumeSorted
,
"ASSUME_SORTED=true"
)
+
optional
(
"STOP_AFTER="
,
stopAfter
,
spaceSeparated
=
false
)
+
repeat
(
"PROGRAM="
,
program
,
spaceSeparated
=
false
)
override
def
addToQscriptSummary
(
qscript
:
SummaryQScript
,
name
:
String
)
:
Unit
=
{
program
.
foreach
(
p
=>
{
val
stats
:
Map
[
String
,
Any
]
=
p
match
{
case
_
if
p
==
Programs
.
CollectAlignmentSummaryMetrics
.
toString
=>
Picard
.
getMetrics
(
new
File
(
outputName
+
".alignment_summary_metrics"
)).
getOrElse
(
Map
())
case
_
if
p
==
Programs
.
CollectInsertSizeMetrics
.
toString
=>
Map
()
Picard
.
getMetrics
(
new
File
(
outputName
+
".insert_size_metrics"
)).
getOrElse
(
Map
())
case
_
if
p
==
Programs
.
QualityScoreDistribution
.
toString
=>
Map
()
Picard
.
getMetrics
(
new
File
(
outputName
+
".quality_distribution_metrics"
)).
getOrElse
(
Map
())
case
_
if
p
==
Programs
.
MeanQualityByCycle
.
toString
=>
Map
()
Picard
.
getMetrics
(
new
File
(
outputName
+
".quality_by_cycle_metrics"
)).
getOrElse
(
Map
())
case
_
if
p
==
Programs
.
CollectBaseDistributionByCycle
.
toString
=>
Map
()
Picard
.
getMetrics
(
new
File
(
outputName
+
".base_distribution_by_cycle_metrics"
)).
getOrElse
(
Map
())
case
_
=>
Map
()
}
val
sum
=
new
Summarizable
{
override
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
override
def
summaryStats
:
Map
[
String
,
Any
]
=
stats
}
qscript
.
addSummarizable
(
sum
,
p
)
})
}
def
summaryFiles
=
Map
()
def
summaryStats
=
Map
()
}
object
CollectMultipleMetrics
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
View file @
856f286b
...
...
@@ -84,12 +84,7 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
"output_chart"
->
chartOutput
).
collect
{
case
(
key
,
Some
(
value
))
=>
key
->
value
}
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
)
match
{
case
None
=>
Map
()
case
Some
((
header
,
content
))
=>
(
for
(
i
<-
0
to
header
.
size
if
i
<
content
.
head
.
size
)
yield
header
(
i
).
toLowerCase
->
content
.
head
(
i
)).
toMap
}
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
override
def
commandLine
=
super
.
commandLine
+
required
(
"INPUT="
,
input
,
spaceSeparated
=
false
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
View file @
856f286b
...
...
@@ -3,12 +3,13 @@ package nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Output
,
Input
}
/**
* Created by pjvan_thof on 4/16/15.
*/
class
CollectTargetedPcrMetrics
(
val
root
:
Configurable
)
extends
Picard
{
class
CollectTargetedPcrMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
{
javaMainClass
=
new
picard
.
analysis
.
directed
.
CollectTargetedPcrMetrics
().
getClass
.
getName
...
...
@@ -41,6 +42,12 @@ class CollectTargetedPcrMetrics(val root: Configurable) extends Picard {
repeat
(
"TARGET_INTERVALS="
,
targetIntervals
,
spaceSeparated
=
false
)
+
optional
(
"PER_TARGET_COVERAGE="
,
perTargetCoverage
,
spaceSeparated
=
false
)
+
optional
(
"CUSTOM_AMPLICON_SET_NAME="
,
customAmpliconSetName
,
spaceSeparated
=
false
)
/** Returns files for summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
object
CollectTargetedPcrMetrics
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
View file @
856f286b
...
...
@@ -3,12 +3,13 @@ package nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Output
,
Input
}
/**
* Created by pjvan_thof on 4/16/15.
*/
class
CollectWgsMetrics
(
val
root
:
Configurable
)
extends
Picard
{
class
CollectWgsMetrics
(
val
root
:
Configurable
)
extends
Picard
with
Summarizable
{
javaMainClass
=
new
picard
.
analysis
.
CollectWgsMetrics
().
getClass
.
getName
...
...
@@ -45,4 +46,10 @@ class CollectWgsMetrics(val root: Configurable) extends Picard {
optional
(
"COVERAGE_CAP="
,
covCap
,
spaceSeparated
=
false
)
+
optional
(
"STOP_AFTER="
,
stopAfter
,
spaceSeparated
=
false
)
+
conditional
(
includeBqHistogram
,
"INCLUDE_BQ_HISTOGRAM=true"
)
/** Returns files for summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
View file @
856f286b
...
...
@@ -100,19 +100,7 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
outputMetrics
)
match
{
case
None
=>
Map
()
case
Some
((
header
,
content
))
=>
(
for
(
category
<-
0
until
content
.
size
)
yield
{
content
(
category
)(
0
).
toString
->
(
for
(
i
<-
1
until
header
.
size
if
i
<
content
(
category
).
size
)
yield
{
header
(
i
).
toLowerCase
->
content
(
category
)(
i
)
}).
toMap
}
).
toMap
}
def
summaryStats
:
Map
[
String
,
Any
]
=
Picard
.
getMetrics
(
outputMetrics
).
getOrElse
(
Map
())
}
object
MarkDuplicates
{
/** Returns default MarkDuplicates */
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
View file @
856f286b
...
...
@@ -81,20 +81,18 @@ object Picard {
* @param file input metrics file
* @return (header, content)
*/
def
getMetrics
(
file
:
File
)
:
Option
[(
Array
[
String
]
,
List
[
Array
[
Any
]])]
=
if
(
file
.
exists
)
{
def
getMetrics
(
file
:
File
,
tag
:
String
=
"METRICS CLASS"
)
:
Option
[
Map
[
String
,
Any
]]
=
if
(!
file
.
exists
)
None
else
{
val
lines
=
Source
.
fromFile
(
file
).
getLines
().
toArray
val
start
=
lines
.
indexWhere
(
_
.
startsWith
(
"##
METRICS CLASS"
))
+
1
val
start
=
lines
.
indexWhere
(
_
.
startsWith
(
"##
"
+
tag
))
+
1
val
end
=
lines
.
indexOf
(
""
,
start
)
val
header
=
lines
(
start
).
split
(
"\t"
)
val
content
=
(
for
(
i
<-
(
start
+
1
)
until
end
)
yield
lines
(
i
).
split
(
"\t"
))
.
map
(
row
=>
row
.
map
(
col
=>
tryToParseNumber
(
col
,
true
).
getOrElse
(
col
)))
Option
((
header
,
content
.
toList
))
}
else
{
None
Some
(
Map
(
"header"
->
header
,
"content"
->
content
))
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
View file @
856f286b
...
...
@@ -16,11 +16,12 @@
package
nl.lumc.sasc.biopet.scripts
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
class
CoverageStats
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
class
CoverageStats
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
with
Summarizable
{
setPythonScript
(
"bedtools_cov_stats.py"
)
@Input
(
doc
=
"Input file"
)
...
...
@@ -36,6 +37,10 @@ class CoverageStats(val root: Configurable) extends PythonCommandLineFunction {
def
cmdLine
=
getPythonCommand
+
required
(
input
)
+
required
(
"--plot"
,
plot
)
+
" > "
+
required
(
output
)
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"output"
->
output
,
"plot"
->
plot
)
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
()
}
object
CoverageStats
{
...
...
@@ -44,6 +49,6 @@ object CoverageStats {
coverageStats
.
input
=
input
coverageStats
.
output
=
new
File
(
outputDir
,
input
.
getName
+
".stats"
)
coverageStats
.
plot
=
new
File
(
outputDir
,
input
.
getName
+
".stats.png"
)
return
coverageStats
coverageStats
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
856f286b
...
...
@@ -109,7 +109,6 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction wit
val
sum
=
new
Summarizable
{
override
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
override
def
summaryStats
:
Map
[
String
,
Any
]
=
stats
}
...
...
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