Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
c58fbc6a
Commit
c58fbc6a
authored
Mar 05, 2015
by
Peter van 't Hof
Browse files
Added scala docs
parent
e3cf080d
Changes
7
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
View file @
c58fbc6a
...
...
@@ -25,6 +25,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import
scala.collection.mutable
import
scala.io.Source
/**
* Extension for sickle
* Based on version 1.33
*/
class
Sickle
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Summarizable
{
@Input
(
doc
=
"R1 input"
)
var
input_R1
:
File
=
_
...
...
@@ -57,10 +61,12 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
override
val
versionRegex
=
"""sickle version (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
/** Sets qualityType is still empty */
override
def
beforeGraph
{
if
(
qualityType
.
isEmpty
)
qualityType
=
Some
(
defaultQualityType
)
}
/** Return command to execute */
def
cmdLine
=
{
var
cmd
:
String
=
required
(
executable
)
if
(
input_R2
!=
null
)
{
...
...
@@ -81,6 +87,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
" > "
+
required
(
output_stats
)
}
/** returns stats map for summary */
def
summaryStats
:
Map
[
String
,
Any
]
=
{
val
pairKept
=
"""FastQ paired records kept: (\d*) \((\d*) pairs\)"""
.
r
val
singleKept
=
"""FastQ single records kept: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)"""
.
r
...
...
@@ -108,6 +115,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
stats
.
toMap
}
/** Merge stats incase of chunking */
override
def
resolveSummaryConflict
(
v1
:
Any
,
v2
:
Any
,
key
:
String
)
:
Any
=
{
(
v1
,
v2
)
match
{
case
(
v1
:
Int
,
v2
:
Int
)
=>
v1
+
v2
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
View file @
c58fbc6a
...
...
@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/** Extension for stampy */
class
Stampy
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"FastQ file R1"
,
shortName
=
"R1"
)
var
R1
:
File
=
_
...
...
@@ -68,12 +69,14 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
override
def
versionCommand
=
executable
+
" --help"
/** Sets readgroup when not set yet */
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
require
(
readgroup
!=
null
)
}
def
cmdLine
:
String
=
{
/** Returns command to execute */
def
cmdLine
=
{
var
cmd
:
String
=
required
(
executable
)
+
optional
(
"-t"
,
nCoresRequest
)
+
conditional
(
solexa
,
"--solexa"
)
+
...
...
@@ -99,6 +102,6 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
" -h "
+
required
(
hash
)
+
" -o "
+
required
(
output
)
+
" -M "
+
required
(
R1
)
+
optional
(
R2
)
return
cmd
cmd
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
View file @
c58fbc6a
...
...
@@ -21,6 +21,9 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Extension for STAR
*/
class
Star
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"The reference file for the bam files."
,
required
=
false
)
var
reference
:
File
=
new
File
(
config
(
"reference"
))
...
...
@@ -62,6 +65,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
override
val
defaultVmem
=
"6G"
override
val
defaultThreads
=
8
/** Sets output files for the graph */
override
def
beforeGraph
()
{
if
(
outFileNamePrefix
!=
null
&&
!
outFileNamePrefix
.
endsWith
(
"."
))
outFileNamePrefix
+=
"."
val
prefix
=
if
(
outFileNamePrefix
!=
null
)
outputDir
+
outFileNamePrefix
else
outputDir
...
...
@@ -77,7 +81,8 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
}
}
def
cmdLine
:
String
=
{
/** Returns command to execute */
def
cmdLine
=
{
var
cmd
:
String
=
required
(
"cd"
,
outputDir
)
+
"&&"
+
required
(
executable
)
if
(
runmode
!=
null
&&
runmode
==
"genomeGenerate"
)
{
// Create index
cmd
+=
required
(
"--runMode"
,
runmode
)
+
...
...
@@ -91,11 +96,22 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
optional
(
"--outFileNamePrefix"
,
outFileNamePrefix
)
if
(
sjdbOverhang
>
0
)
cmd
+=
optional
(
"--sjdbOverhang"
,
sjdbOverhang
)
return
cmd
cmd
}
}
object
Star
{
/**
* Create default star
* @param configurable root object
* @param R1 R1 fastq file
* @param R2 R2 fastq file
* @param outputDir Outputdir for Star
* @param isIntermediate
* @param deps Deps to add to wait on run
* @return Return Star
*
*/
def
apply
(
configurable
:
Configurable
,
R1
:
File
,
R2
:
File
,
outputDir
:
File
,
isIntermediate
:
Boolean
=
false
,
deps
:
List
[
File
]
=
Nil
)
:
Star
=
{
val
star
=
new
Star
(
configurable
)
star
.
R1
=
R1
...
...
@@ -107,7 +123,22 @@ object Star {
return
star
}
def
_2pass
(
configurable
:
Configurable
,
R1
:
File
,
R2
:
File
,
outputDir
:
File
,
isIntermediate
:
Boolean
=
false
,
deps
:
List
[
File
]
=
Nil
)
:
(
File
,
List
[
Star
])
=
{
/**
* returns Star with 2pass star method
* @param configurable root object
* @param R1 R1 fastq file
* @param R2 R2 fastq file
* @param outputDir Outputdir for Star
* @param isIntermediate
* @param deps Deps to add to wait on run
* @return Return Star
*/
def
_2pass
(
configurable
:
Configurable
,
R1
:
File
,
R2
:
File
,
outputDir
:
File
,
isIntermediate
:
Boolean
=
false
,
deps
:
List
[
File
]
=
Nil
)
:
(
File
,
List
[
Star
])
=
{
val
starCommand_pass1
=
Star
(
configurable
,
R1
,
if
(
R2
!=
null
)
R2
else
null
,
new
File
(
outputDir
,
"aln-pass1"
))
starCommand_pass1
.
isIntermediate
=
isIntermediate
starCommand_pass1
.
deps
=
deps
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
View file @
c58fbc6a
...
...
@@ -21,6 +21,9 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Extension for TopHad
*/
class
TopHat
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"FastQ file R1"
,
shortName
=
"R1"
)
var
R1
:
File
=
_
...
...
@@ -70,11 +73,10 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
}
def
cmdLine
:
String
=
{
var
cmd
:
String
=
required
(
executable
)
+
required
(
executable
)
+
optional
(
"-p"
,
nCoresRequest
)
+
"--no-convert-bam"
+
required
(
bowtie_index
)
+
required
(
R1
)
+
optional
(
R2
)
return
cmd
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
c58fbc6a
...
...
@@ -7,6 +7,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Extension for VariantEffectPredictor
* Created by ahbbollen on 15-1-15.
*/
class
VariantEffectPredictor
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
...
...
@@ -134,6 +135,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
}
}
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
vep_script
)
+
required
(
"-i"
,
input
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
View file @
c58fbc6a
...
...
@@ -27,6 +27,7 @@ class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction {
var
clip
:
Boolean
=
config
(
"clip"
,
default
=
false
)
var
unc
:
Boolean
=
config
(
"unc"
,
default
=
false
)
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
optional
(
"-blockSize="
,
blockSize
,
spaceSeparated
=
false
)
+
optional
(
"-itemsPerSlot="
,
itemsPerSlot
,
spaceSeparated
=
false
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
View file @
c58fbc6a
...
...
@@ -20,6 +20,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
/** Extension for zcat */
class
Zcat
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Zipped file"
)
var
input
:
File
=
_
...
...
@@ -29,10 +30,12 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
executable
=
config
(
"exe"
,
default
=
"zcat"
)
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
input
)
+
" > "
+
required
(
output
)
}
object
Zcat
{
/** Returns a default zcat */
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
Zcat
=
{
val
zcat
=
new
Zcat
(
root
)
zcat
.
input
=
input
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment