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biopet.biopet
Commits
10518502
Commit
10518502
authored
Dec 04, 2014
by
bow
Browse files
Documentation updates
parent
846acd6c
Changes
2
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
View file @
10518502
...
...
@@ -19,9 +19,10 @@ import nl.lumc.sasc.biopet.core.ToolCommand
object
ExtractAlignedFastq
extends
ToolCommand
{
/** type alias for Fastq input (may or may not be paired) */
type
FastqInput
=
(
FastqRecord
,
Option
[
FastqRecord
])
/**
function to get
FastqRecord ID */
/**
Get the
FastqRecord ID */
def
fastqId
(
rec
:
FastqRecord
)
=
rec
.
getReadHeader
.
split
(
" "
)(
0
)
/**
...
...
@@ -125,6 +126,13 @@ object ExtractAlignedFastq extends ToolCommand {
}
}
/**
* Extracts reads from the given input Fastq file and writes to a new output Fastq file
*
* @param memFunc Predicate for extracting reads. If evaluates to true, the read is extracted.
* @param inputFastq1 Input [[FastqReader]] object.
* @param outputFastq1 Output [[BasicFastqWriter]] object.
*/
def
extractReads
(
memFunc
:
FastqInput
=>
Boolean
,
inputFastq1
:
FastqReader
,
outputFastq1
:
BasicFastqWriter
)
:
Unit
=
inputFastq1
.
iterator
.
asScala
...
...
@@ -132,6 +140,15 @@ object ExtractAlignedFastq extends ToolCommand {
.
filter
(
rec
=>
memFunc
(
rec
.
_1
,
rec
.
_2
))
.
foreach
(
rec
=>
outputFastq1
.
write
(
rec
.
_1
))
/**
* Extracts reads from the given input Fastq pairs and writes to new output Fastq pair files
*
* @param memFunc Predicate for extracting reads. If evaluates to true, the read is extracted.
* @param inputFastq1 Input [[FastqReader]] object for pair 1.
* @param outputFastq1 Input [[FastqReader]] object for pair 2.
* @param inputFastq2 Output [[BasicFastqWriter]] object for pair 1.
* @param outputFastq2 Output [[BasicFastqWriter]] object for pair 2.
*/
def
extractReads
(
memFunc
:
FastqInput
=>
Boolean
,
inputFastq1
:
FastqReader
,
outputFastq1
:
BasicFastqWriter
,
inputFastq2
:
FastqReader
,
outputFastq2
:
BasicFastqWriter
)
:
Unit
=
...
...
@@ -143,6 +160,7 @@ object ExtractAlignedFastq extends ToolCommand {
outputFastq2
.
write
(
rec
.
_2
)
})
/** Default arguments */
case
class
Args
(
inputBam
:
File
=
new
File
(
""
),
intervals
:
List
[
String
]
=
List
.
empty
[
String
],
inputFastq1
:
File
=
new
File
(
""
),
...
...
@@ -152,6 +170,7 @@ object ExtractAlignedFastq extends ToolCommand {
minMapQ
:
Int
=
0
,
commonSuffixLength
:
Int
=
0
)
extends
AbstractArgs
/** Command line argument parser */
class
OptParser
extends
AbstractOptParser
{
head
(
...
...
@@ -213,6 +232,7 @@ object ExtractAlignedFastq extends ToolCommand {
}
}
/** Parses the command line argument */
def
parseArgs
(
args
:
Array
[
String
])
:
Args
=
new
OptParser
()
.
parse
(
args
,
Args
())
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
View file @
10518502
...
...
@@ -47,12 +47,7 @@ class WipeReads(val root: Configurable) extends BiopetJavaCommandLineFunction {
object
WipeReads
extends
ToolCommand
{
/**
* Creates a SamReader object from an input BAM file, ensuring it is indexed
*
* @param inBam input BAM file
* @return
*/
/** Creates a SamReader object from an input BAM file, ensuring it is indexed */
private
def
prepInBam
(
inBam
:
File
)
:
SamReader
=
{
val
bam
=
SamReaderFactory
.
make
()
...
...
@@ -62,6 +57,7 @@ object WipeReads extends ToolCommand {
bam
}
/** Creates a [[SAMFileWriter]] object for writing, indexed */
private
def
prepOutBam
(
outBam
:
File
,
templateBam
:
File
,
writeIndex
:
Boolean
=
true
,
async
:
Boolean
=
true
)
:
SAMFileWriter
=
new
SAMFileWriterFactory
()
...
...
@@ -336,6 +332,7 @@ object WipeReads extends ToolCommand {
}
}
/** Default arguments */
case
class
Args
(
inputBam
:
File
=
new
File
(
""
),
targetRegions
:
File
=
new
File
(
""
),
outputBam
:
File
=
new
File
(
""
),
...
...
@@ -348,6 +345,7 @@ object WipeReads extends ToolCommand {
bloomSize
:
Long
=
70000000
,
bloomFp
:
Double
=
4
e
-
7
)
extends
AbstractArgs
/** Command line argument parser */
class
OptParser
extends
AbstractOptParser
{
head
(
...
...
@@ -418,12 +416,7 @@ object WipeReads extends ToolCommand {
}
/**
* Parses the command line argument
*
* @param args Array of arguments
* @return
*/
/** Parses the command line argument */
def
parseArgs
(
args
:
Array
[
String
])
:
Args
=
new
OptParser
()
.
parse
(
args
,
Args
())
.
getOrElse
(
sys
.
exit
(
1
))
...
...
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