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Commits on Mar 23, 2018

• Merge branch 'hotfix-4.5.x' into develop

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Commits on Mar 21, 2018

• hotfix-4.5.x: new CLI parameter enables avoiding decomposition of MNVs/block substitutions

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Commits on Mar 19, 2018

• hotfix-4.5.x: Update version to 4.5.5-SNAPSHOT

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Commits on Feb 8, 2018

• Update version to 4.5.4

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Commits on Feb 7, 2018

• Merge branch 'hotfix-4.5.x' into develop

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• hotfix-4.5.x: minor bug fixed. If no path at all was provided for the variant-annotation output, i.e. -o test.json.gz rather than -o ./test.json.gz, an error was raised. This is now checked and err…

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Commits on Feb 1, 2018

• Merge branch 'hotfix-4.5.x' into develop

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• hotfix-4.5.x: bug fixed. Transcripts for which there is no xrefs at all will now always include geneName, geneId, transcriptName and transcriptId

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• Merge branch 'hotfix-4.5.x' into develop

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• hotfix-4.5.x: bugfix. Thread safe issue fixed at CellBaseClient. See https://en.wikipedia.org/wiki/Double-checked_locking

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Commits on Dec 19, 2017

• Merge branch 'develop' into feature-vep-comparison

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Commits on Dec 12, 2017

• feature-vep-comparison: attempt to refine start_lost annotation for SNVs

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Commits on Dec 6, 2017

• feature-vep-comparison: several minor adjustments done to start_lost annotation

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Commits on Dec 1, 2017

• feature-vep-comparison: bug fixed when checking start codon for MT

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Commits on Nov 30, 2017

• Merge branch 'hotfix-4.5.x' into develop

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• hotfix-4.5.x: minor bug fixed at VariantAnnotationCommandExecutor. completeInputPopulation variable is only checked if external pop freqs files are provided

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• Merge branch 'hotfix-4.5.x' of https://github.com/opencb/cellbase into hotfix-4.5.x

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Commits on Nov 29, 2017

• feature-vep-comparison: start_lost refined for SNVs. All tests working

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• Merge branch 'develop' into feature-vep-comparison

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Commits on Nov 28, 2017

• feature-improve-tests: all tests fixed

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• Merge branch 'hotfix-4.5.x' into develop

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• hotfix-4.5.x: bugfix at REST client. When multiple ids were used as an input each of them returning more than 1000 results, could potentially happen that these result lists were not appropriately p…

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• hotfix-4.5.x: upgrade version to 4.5.4-SNAPSHOT

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Commits on Nov 24, 2017

• feature-vep-comparison: start_lost refinement for insertions finished. Tests added

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• feature-improve-tests: adding population frequencies tests to Fitnesse

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Commits on Nov 22, 2017

• Merge branch 'develop' into feature-improve-tests

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• develop: bugfix at VariantClient; it can happen that no annotation is returned for variants raising problems such as 1:645710:A:<INS:ME:ALU>

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• Merge branch 'develop' into feature-improve-tests

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Commits on Nov 21, 2017

• feature-vep-comparison: start_lost refined for Insertions in negative transcripts. Corresponding test needs to be fixed. start_lost annotation to be refined for remaining cases

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• Merge branch 'develop' into feature-vep-comparison

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• Merge branch 'hotfix-4.5.x' into develop

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• hotfix-4.5.x: heritableTraitList and genomicFeatureList are no longer initialised to null when parsing ClinVar variant summary txt

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• hotfix-4.5.x: upgrade version to 4.5.4-SNAPSHOT

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• develop: upgraded biodata and java-common-libs dependencies

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Commits on Nov 20, 2017

• Prepare bugfix release 4.5.3

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