- 28 Apr, 2015 2 commits
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Peter van 't Hof authored
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Peter van 't Hof authored
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- 14 Apr, 2015 2 commits
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Peter van 't Hof authored
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Peter van 't Hof authored
Conflicts: public/biopet-framework/pom.xml
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- 13 Apr, 2015 12 commits
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Wai Yi Leung authored
Tsv mod This fixes/closes #73 Changes: * Use VCF naming conventions for default fields * Spelling/typos * Adding the option to change the separator * Adding option to change amount of decimals for numeric values * Fixes sorting function * adding tests See merge request !153
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Sander Bollen authored
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Sander Bollen authored
Quality scores based on formatter max nr of decimals can be set by flag separators can be changed by flag
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Wai Yi Leung authored
Fixed parsing of empty values See merge request !152
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Peter van 't Hof authored
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Peter van 't Hof authored
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Peter van 't Hof authored
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Wai Yi Leung authored
Fix vcfwriters This branch fixes issues #152 and #153, and it includes test cases for #152. See merge request !151
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Sander Bollen authored
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Sander Bollen authored
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Sander Bollen authored
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Sander Bollen authored
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- 12 Apr, 2015 1 commit
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Wai Yi Leung authored
added extra options to bowtie See merge request !150
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- 10 Apr, 2015 7 commits
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Peter van 't Hof authored
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Sander Bollen authored
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Sander Bollen authored
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Sander Bollen authored
adding checkAllelesVcfInBamTest stub and adding bgzipped and tabixed VCF files for tools that need indexed files
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Sander Bollen authored
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Sander Bollen authored
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Sander Bollen authored
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- 09 Apr, 2015 11 commits
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Sander Bollen authored
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Sander Bollen authored
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Peter van 't Hof authored
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Peter van 't Hof authored
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Sander Bollen authored
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Peter van 't Hof authored
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Peter van 't Hof authored
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Sander van der Zeeuw authored
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Sander Bollen authored
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Peter van 't Hof authored
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Sander Bollen authored
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- 08 Apr, 2015 5 commits
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Sander Bollen authored
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Sander Bollen authored
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Wai Yi Leung authored
Patch meta in summary This pull request adds a `meta` entry to the root of each summary JSON file. The contents of the meta is: `last_commit_hash`: the commit hash of the repository when the JAR was built. If the repository has uncommitted changes, `-dirty` is appended to the commit hash. `pipeline_version`: the version of the pipeline (the one we put in the `pom.xml` file). This information is static across all modules and subpipelines to any given pipeline run, so I decided to put this in the root. See merge request !144
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Wai Yi Leung authored
Patch extractalignedfastq The changeset + commit message should be clear enough :). This was caused by a passing a wrong variable to the `BasicFastqWriter` constructor. See merge request !142
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Wai Yi Leung authored
Fix intervals Fix for #128 See merge request !145
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