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biopet.biopet
Commits
7a8ef0e4
Commit
7a8ef0e4
authored
Nov 19, 2015
by
Peter van 't Hof
Browse files
Fixed bowtie index
parent
19a93bbb
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
View file @
7a8ef0e4
...
...
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
,
Reference
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
@@ -33,9 +34,6 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
@Input
(
doc
=
"Fastq file R2"
,
shortName
=
"R2"
,
required
=
false
)
var
R2
:
Option
[
File
]
=
None
@Input
(
doc
=
"The reference file for the bam files."
,
shortName
=
"R"
,
required
=
true
)
var
reference
:
File
=
null
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
,
required
=
true
)
var
output
:
File
=
null
...
...
@@ -59,13 +57,20 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
var
maqerr
:
Option
[
Int
]
=
config
(
"maqerr"
)
var
maxins
:
Option
[
Int
]
=
config
(
"maxins"
)
var
largeIndex
:
Boolean
=
config
(
"large-index"
,
default
=
false
)
var
bowtieIndex
:
String
=
config
(
"bowtie_index"
)
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
val
basename
=
reference
.
getName
.
stripSuffix
(
".fasta"
).
stripSuffix
(
".fa"
)
if
(
reference
.
getParentFile
.
list
().
toList
.
filter
(
_
.
startsWith
(
basename
)).
exists
(
_
.
endsWith
(
".ebwtl"
)))
largeIndex
=
config
(
"large-index"
,
default
=
true
)
val
indexDir
=
new
File
(
bowtieIndex
).
getParentFile
val
basename
=
bowtieIndex
.
stripPrefix
(
indexDir
.
getPath
+
File
.
separator
)
if
(
indexDir
.
exists
())
{
if
(
indexDir
.
list
().
toList
.
filter
(
_
.
startsWith
(
basename
)).
exists
(
_
.
endsWith
(
".ebwtl"
)))
largeIndex
=
config
(
"large-index"
,
default
=
true
)
else
{
if
(!
indexDir
.
list
().
toList
.
filter
(
_
.
startsWith
(
basename
)).
exists
(
_
.
endsWith
(
".ebwt"
)))
Logging
.
addError
(
s
"No index files found for bowtie in: $indexDir with basename: $basename"
)
}
}
}
/** return commandline to execute */
...
...
@@ -83,7 +88,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
optional
(
"--maxbts"
,
maxbts
)
+
optional
(
"--maqerr"
,
maqerr
)
+
optional
(
"--maxins"
,
maxins
)
+
required
(
reference
.
getAbsolutePath
.
stripSuffix
(
".fa"
).
stripSuffix
(
".fasta"
)
)
+
required
(
bowtieIndex
)
+
(
R2
match
{
case
Some
(
r2
)
=>
required
(
"-1"
,
R1
)
+
...
...
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