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biopet.biopet
Commits
18cee8f8
Commit
18cee8f8
authored
Nov 30, 2016
by
Sander Bollen
Browse files
Merge branch 'fix-BIOPET-481' into 'develop'
Fixing BIOPET-481 See merge request !486
parents
057f8873
2373dae2
Changes
3
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biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
View file @
18cee8f8
...
...
@@ -14,7 +14,7 @@
*/
package
nl.lumc.sasc.biopet.utils
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
java.util
import
argonaut.Argonaut._
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
View file @
18cee8f8
...
...
@@ -15,6 +15,7 @@
package
nl.lumc.sasc.biopet
import
scala.util.
{
Failure
,
Success
,
Try
}
import
scala.math._
/**
* General utility functions.
...
...
@@ -29,6 +30,15 @@ package object utils {
/** Regular expression for matching entire decimal numbers (compatible with the scientific notation) */
val
isDecimal
=
"""^([-+]?\d*\.?\d+(?:[eE][-+]?[0-9]+)?)$"""
.
r
def
textToSize
(
text
:
String
)
:
Long
=
{
text
.
last
match
{
case
'g'
|
'G'
=>
((
1L
<<
30
)
*
text
.
stripSuffix
(
"g"
).
stripSuffix
(
"G"
).
toDouble
).
toLong
case
'm'
|
'M'
=>
((
1L
<<
20
)
*
text
.
stripSuffix
(
"g"
).
stripSuffix
(
"G"
).
toDouble
).
toLong
case
'k'
|
'K'
=>
((
1L
<<
10
)
*
text
.
stripSuffix
(
"g"
).
stripSuffix
(
"G"
).
toDouble
).
toLong
case
_
=>
text
.
toLong
}
}
/**
* Tries to convert the given string with the given conversion functions recursively.
*
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
18cee8f8
...
...
@@ -19,11 +19,11 @@ import java.util.Date
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie
2
,
Bowtie
}
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie
,
Bowtie
2
}
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
import
nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import
nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
...
...
@@ -31,6 +31,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
import
nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
import
nl.lumc.sasc.biopet.utils.textToSize
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -163,10 +164,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if
(
numberChunks
.
isEmpty
)
{
if
(
config
.
contains
(
"numberchunks"
))
numberChunks
=
config
(
"numberchunks"
,
default
=
None
)
else
{
val
chunkSize
:
Int
=
config
(
"chunksize"
,
1
<<
30
)
val
chunkSize
:
String
=
config
(
"chunksize"
,
default
=
"5G"
)
val
filesize
=
if
(
inputR1
.
getName
.
endsWith
(
".gz"
)
||
inputR1
.
getName
.
endsWith
(
".gzip"
))
inputR1
.
length
*
3
else
inputR1
.
length
numberChunks
=
Option
(
ceil
(
filesize
.
toDouble
/
chunkSize
).
toInt
)
numberChunks
=
Option
(
ceil
(
filesize
.
toDouble
/
textToSize
(
chunkSize
)
)
.
toInt
)
}
}
logger
.
debug
(
"Chunks: "
+
numberChunks
.
getOrElse
(
1
))
...
...
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