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Merge branch 'fix-reference_dict_check' into 'develop'
Extract checkDict and checkFai in a public method Fix for #173 Still needs testing. See merge request !190
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- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala 1 addition, 1 deletion...rc/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala 1 addition, 1 deletion...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala 1 addition, 1 deletion...rc/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala 1 addition, 1 deletion...main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala 1 addition, 1 deletion...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala 1 addition, 1 deletion...scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala 1 addition, 1 deletion...rk/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala 1 addition, 1 deletion.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala 2 additions, 2 deletions...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala 1 addition, 1 deletion.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala 1 addition, 0 deletions...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
- public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp 2 additions, 2 deletions.../sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
- public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp 3 additions, 3 deletions.../sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
- public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala 9 additions, 0 deletions...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
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