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biopet.biopet
Commits
eceac8c1
Commit
eceac8c1
authored
Sep 13, 2015
by
Peter van 't Hof
Browse files
Move scripts to bammetrics
parent
d0f1cdd7
Changes
4
Hide whitespace changes
Inline
Side-by-side
public/b
iopet-core
/src/main/resources/nl/lumc/sasc/biopet/scripts/bedtools_cov_stats.py
→
public/b
ammetrics
/src/main/resources/nl/lumc/sasc/biopet/
pipelines/bammetrics/
scripts/bedtools_cov_stats.py
View file @
eceac8c1
File moved
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
eceac8c1
...
...
@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
}
import
nl.lumc.sasc.biopet.extensions.picard._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import
nl.lumc.sasc.biopet.scripts.CoverageStats
import
nl.lumc.sasc.biopet.
pipelines.bammetrics.
scripts.CoverageStats
import
nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import
org.broadinstitute.gatk.queue.QScript
...
...
public/b
iopet-core
/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
→
public/b
ammetrics
/src/main/scala/nl/lumc/sasc/biopet/
pipelines/bammetrics/
scripts/CoverageStats.scala
View file @
eceac8c1
...
...
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.scripts
package
nl.lumc.sasc.biopet.
pipelines.bammetrics.
scripts
import
java.io.File
...
...
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @
eceac8c1
...
...
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
}
import
nl.lumc.sasc.biopet.extensions.picard._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import
nl.lumc.sasc.biopet.scripts.CoverageStats
import
nl.lumc.sasc.biopet.
pipelines.bammetrics.
scripts.CoverageStats
import
nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.apache.commons.io.FileUtils
...
...
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