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biopet.biopet
Commits
f418cc1a
Commit
f418cc1a
authored
Nov 19, 2016
by
Peter van 't Hof
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Moving flagstats from bamstats to summary
parent
a2d728c3
Changes
2
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2 changed files
with
21 additions
and
5 deletions
+21
-5
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+0
-4
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
...scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
+21
-1
No files found.
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
f418cc1a
...
...
@@ -82,10 +82,6 @@ class BamMetrics(val root: Configurable) extends QScript
def
biopetScript
()
{
add
(
SamtoolsFlagstat
(
this
,
inputBam
,
outputDir
))
val
biopetFlagstat
=
BiopetFlagstat
(
this
,
inputBam
,
outputDir
)
add
(
biopetFlagstat
)
addSummarizable
(
biopetFlagstat
,
"biopet_flagstat"
)
val
bamStats
=
new
BamStats
(
this
)
bamStats
.
bamFile
=
inputBam
bamStats
.
outputDir
=
new
File
(
outputDir
,
"bamstats"
)
...
...
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
View file @
f418cc1a
...
...
@@ -2,14 +2,18 @@ package nl.lumc.sasc.biopet.extensions.tools
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFunction
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
import
scala.collection.JavaConversions._
/**
* Created by pjvanthof on 18/11/2016.
*/
class
BamStats
(
val
root
:
Configurable
)
extends
ToolCommandFunction
with
Reference
{
class
BamStats
(
val
root
:
Configurable
)
extends
ToolCommandFunction
with
Reference
with
Summarizable
{
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
bamstats
.
BamStats
@Input
(
required
=
true
)
...
...
@@ -27,6 +31,13 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
override
def
defaultCoreMemory
=
5.0
override
def
dictRequired
=
true
def
flagstatSummaryFile
(
implicit
contig
:
Option
[
String
]
=
None
)
:
File
=
{
contig
match
{
case
Some
(
contig
)
=>
new
File
(
outputDir
,
"contigs"
+
File
.
separator
+
contig
+
File
.
separator
+
"flagstats.summary.json"
)
case
_
=>
new
File
(
outputDir
,
"flagstats.summary.json"
)
}
}
override
def
beforeGraph
()
{
super
.
beforeGraph
()
jobOutputFile
=
new
File
(
outputDir
,
".bamstats.out"
)
...
...
@@ -41,4 +52,13 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
optional
(
"--binSize"
,
binSize
)
+
optional
(
"--threadBinSize"
,
threadBinSize
)
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
(
"flagstats"
->
ConfigUtils
.
fileToConfigMap
(
flagstatSummaryFile
),
"flagstats_per_contig"
->
referenceDict
.
getSequences
.
map
{
c
=>
c
.
getSequenceName
->
ConfigUtils
.
fileToConfigMap
(
flagstatSummaryFile
(
Some
(
c
.
getSequenceName
)))
}.
toMap
)
}
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