Commit e88b3068 authored 9 years ago by Wai Yi Leung

Merge branch 'fix-warns' into 'develop'

Fix warns

Going to try to fix most of the code warnings from the IDE
Also going to optimise imports for the whole repository

See merge request !187

parents 29a61dfe c1acac57

No related branches found

No related tags found

Hide whitespace changes

Inline Side-by-side

Showing

protected/biopet-gatk-extensions/pom.xml 0 additions, 1 deletion

protected/biopet-gatk-extensions/pom.xml
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala 2 additions, 1 deletion

...sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala 4 additions, 3 deletions

...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala 3 additions, 2 deletions

.../sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala 2 additions, 1 deletion

...lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala 2 additions, 1 deletion

...c/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala 4 additions, 4 deletions

.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala 2 additions, 1 deletion

...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala 2 additions, 2 deletions

...c/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala 2 additions, 1 deletion

...mc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala 2 additions, 1 deletion

...l/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala 2 additions, 1 deletion

...biopet/extensions/gatk/broad/RealignerTargetCreator.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala 2 additions, 1 deletion

...mc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala 2 additions, 2 deletions

.../sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala 2 additions, 1 deletion

.../sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala 7 additions, 6 deletions

.../lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala 2 additions, 1 deletion

...sc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
protected/biopet-gatk-pipelines/pom.xml 0 additions, 1 deletion

protected/biopet-gatk-pipelines/pom.xml
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala 2 additions, 0 deletions

...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala 5 additions, 5 deletions

.../sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

with 49 additions and 36 deletions

Please register or to comment