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biopet.biopet
Commits
dfed2154
Commit
dfed2154
authored
Aug 22, 2014
by
Peter van 't Hof
Browse files
convert MergeSamFiles to biopet function
parent
9b20e271
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
0 → 100644
View file @
dfed2154
package
nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
class
MergeSamFiles
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
"picard.sam.MergeSamFiles"
@Input
(
doc
=
"The input SAM or BAM files to analyze."
,
required
=
true
)
var
input
:
List
[
File
]
=
Nil
@Output
(
doc
=
"The output file to bam file to"
,
required
=
true
)
var
output
:
File
=
_
@Argument
(
doc
=
"Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} "
,
required
=
true
)
var
sortOrder
:
String
=
_
@Argument
(
doc
=
"ASSUME_SORTED"
,
required
=
false
)
var
assumeSorted
:
Boolean
=
config
(
"assumesorted"
,
default
=
false
)
@Argument
(
doc
=
"MERGE_SEQUENCE_DICTIONARIES"
,
required
=
false
)
var
mergeSequenceDictionaries
:
Boolean
=
config
(
"merge_sequence_dictionaries"
,
default
=
false
)
@Argument
(
doc
=
"USE_THREADING"
,
required
=
false
)
var
useThreading
:
Boolean
=
config
(
"use_threading"
,
default
=
false
)
@Argument
(
doc
=
"COMMENT"
,
required
=
false
)
var
comment
:
String
=
config
(
"comment"
)
override
def
commandLine
=
super
.
commandLine
+
required
(
"INPUT="
,
input
,
spaceSeparated
=
false
)
+
required
(
"OUTPUT="
,
output
,
spaceSeparated
=
false
)
+
required
(
"SORT_ORDER="
,
sortOrder
,
spaceSeparated
=
false
)
+
conditional
(
assumeSorted
,
"ASSUME_SORTED=TRUE"
)
+
conditional
(
mergeSequenceDictionaries
,
"MERGE_SEQUENCE_DICTIONARIES=TRUE"
)
+
optional
(
"COMMENT="
,
comment
,
spaceSeparated
=
false
)
}
object
MergeSamFiles
{
def
apply
(
root
:
Configurable
,
input
:
List
[
File
],
outputDir
:
String
,
sortOrder
:
String
=
null
)
:
MergeSamFiles
=
{
val
mergeSamFiles
=
new
MergeSamFiles
(
root
)
mergeSamFiles
.
input
=
input
mergeSamFiles
.
output
=
new
File
(
outputDir
,
input
.
head
.
getName
.
stripSuffix
(
".bam"
).
stripSuffix
(
".sam"
)
+
".merge.bam"
)
if
(
sortOrder
==
null
)
mergeSamFiles
.
sortOrder
=
"coordinate"
else
mergeSamFiles
.
sortOrder
=
sortOrder
return
mergeSamFiles
}
}
\ No newline at end of file
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
dfed2154
...
...
@@ -6,12 +6,12 @@ import java.util.Date
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.apps.FastqSplitter
import
nl.lumc.sasc.biopet.extensions.aligners.
{
Bwa
,
Star
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
SortSam
,
MergeSamFiles
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Argument
,
ClassType
}
import
org.broadinstitute.gatk.queue.extensions.picard.
{
MergeSamFiles
,
AddOrReplaceReadGroups
}
import
org.broadinstitute.gatk.queue.extensions.picard.
{
AddOrReplaceReadGroups
}
import
scala.math._
class
Mapping
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
...
...
@@ -218,7 +218,11 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
if
(!
skipMarkduplicates
)
{
bamFile
=
new
File
(
outputDir
+
outputName
+
".dedup.bam"
)
add
(
MarkDuplicates
(
this
,
bamFiles
,
bamFile
))
}
else
if
(
skipMarkduplicates
&&
chunking
)
bamFile
=
addMergeBam
(
bamFiles
,
new
File
(
outputDir
+
outputName
+
".bam"
),
outputDir
)
}
else
if
(
skipMarkduplicates
&&
chunking
)
{
val
mergeSamFile
=
MergeSamFiles
(
this
,
bamFiles
,
outputDir
)
add
(
mergeSamFile
)
bamFile
=
mergeSamFile
.
output
}
if
(!
skipMetrics
)
addAll
(
BamMetrics
.
apply
(
this
,
bamFile
,
outputDir
+
"metrics/"
).
functions
)
...
...
@@ -239,21 +243,21 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
// return sortSam.output
// }
def
addMergeBam
(
inputSam
:
List
[
File
],
outputFile
:
File
,
dir
:
String
)
:
File
=
{
val
mergeSam
=
new
MergeSamFiles
mergeSam
.
input
=
inputSam
mergeSam
.
createIndex
=
true
mergeSam
.
output
=
outputFile
mergeSam
.
memoryLimit
=
2
mergeSam
.
nCoresRequest
=
2
mergeSam
.
assumeSorted
=
true
mergeSam
.
USE_THREADING
=
true
mergeSam
.
jobResourceRequests
:+=
"h_vmem=4G"
if
(!
skipMarkduplicates
)
mergeSam
.
isIntermediate
=
true
add
(
mergeSam
)
return
mergeSam
.
output
}
//
def addMergeBam(inputSam: List[File], outputFile: File, dir: String): File = {
//
val mergeSam = new MergeSamFiles
//
mergeSam.input = inputSam
//
mergeSam.createIndex = true
//
mergeSam.output = outputFile
//
mergeSam.memoryLimit = 2
//
mergeSam.nCoresRequest = 2
//
mergeSam.assumeSorted = true
//
mergeSam.USE_THREADING = true
//
mergeSam.jobResourceRequests :+= "h_vmem=4G"
//
if (!skipMarkduplicates) mergeSam.isIntermediate = true
//
add(mergeSam)
//
//
return mergeSam.output
//
}
def
addAddOrReplaceReadGroups
(
inputSam
:
List
[
File
],
outputFile
:
File
,
dir
:
String
)
:
File
=
{
val
addOrReplaceReadGroups
=
new
AddOrReplaceReadGroups
...
...
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