- Mar 27, 2015
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Sander Bollen authored
Feature vcf with vcf peter Needed this tool for data that must be ready this Monday. While running this I found some issues that i fixed in this branch: - Type is kept from secondary vcf file, this makes filtering later much easier. - Field in secondary vcf can be different as in output vcf, otherwise records can overritten - raise errors when field already exist in input vcf or field are missing in secondary vcf - Style changes, lot of var names with '_', converted to camelCaps See merge request !138
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- Mar 20, 2015
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Peter van 't Hof authored
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Peter van 't Hof authored
Change setup so it can presume vcf types instead of forcing it to strings. Some style changes. Added support for different inputField and outputField
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- Mar 19, 2015
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Sander Bollen authored
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- Mar 16, 2015
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Sander Bollen authored
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Sander Bollen authored
Conflicts: public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
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- Mar 11, 2015
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bow authored
Patch toucan This enables to `--fork` command of the VEP to actually run with Biopet's `-qsub` command. See merge request !126
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Sander Bollen authored
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Sander Bollen authored
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Wai Yi Leung authored
Feature gentrap See merge request !111
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- Mar 10, 2015
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bow authored
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bow authored
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bow authored
Patch genotyper Fix a small bug on unified genotyper See merge request !125
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Peter van 't Hof authored
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bow authored
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bow authored
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bow authored
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Wai Yi Leung authored
Patch aln wrapper threads @p.j.van_t_hof, @wyleung, and @a.h.b.bollen ~ for the threads behavior that we saw earlier today See merge request !124
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bow authored
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bow authored
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bow authored
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bow authored
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bow authored
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bow authored
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bow authored
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bow authored
Feature test coverage Removed aggregated scoverage module, now not breaking packaging anymore. See merge request !117
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- Mar 09, 2015
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bow authored
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bow authored
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bow authored
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bow authored
Patch toucan Fix output directory path in Toucan See merge request !123
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bow authored
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bow authored
Conflicts: public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
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bow authored
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bow authored
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Sander Bollen authored
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bow authored
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bow authored
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bow authored
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bow authored
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bow authored
Feature shiva This will become a new version of the variantcalling pipeline. See also issue #116 and #119 See merge request !110
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