Skip to content
Projects
Groups
Snippets
Help
Loading...
Help
Support
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Cycle Analytics
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Charts
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Charts
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Charts
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
273091b4
Commit
273091b4
authored
Apr 20, 2017
by
akaljuvee
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
filling the samples table
parent
7d179c4e
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
15 additions
and
1 deletion
+15
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
+15
-1
No files found.
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
View file @
273091b4
...
...
@@ -20,9 +20,14 @@ import nl.lumc.sasc.biopet.extensions.Pysvtools
import
nl.lumc.sasc.biopet.extensions.tools.VcfStatsForSv
import
nl.lumc.sasc.biopet.pipelines.shiva.svcallers._
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
Logging
}
import
org.broadinstitute.gatk.queue.QScript
import
scala.concurrent.Await
import
scala.concurrent.duration.Duration
import
scala.concurrent.ExecutionContext.Implicits.global
/**
* Common trait for ShivaVariantcalling
*
...
...
@@ -43,7 +48,16 @@ class ShivaSvCalling(val parent: Configurable) extends QScript with SummaryQScri
/** Executed before script */
def
init
()
:
Unit
=
{
if
(
inputBamsArg
.
nonEmpty
)
inputBams
=
BamUtils
.
sampleBamMap
(
inputBamsArg
)
if
(
inputBamsArg
.
nonEmpty
)
{
inputBams
=
BamUtils
.
sampleBamMap
(
inputBamsArg
)
val
db
=
SummaryDb
.
openSqliteSummary
(
summaryDbFile
)
for
(
sampleName
<-
inputBams
.
keys
)
{
if
(
Await
.
result
(
db
.
getSampleId
(
summaryRunId
,
sampleName
),
Duration
.
Inf
).
isEmpty
)
{
db
.
createSample
(
sampleName
,
summaryRunId
)
}
}
}
outputMergedVCF
=
new
File
(
outputDir
,
"allsamples.merged.vcf"
)
}
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
Attach a 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