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Disconnect connection to hive database if not used. This is to avoid … #60

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wants to merge 29 commits into from
Closed

Disconnect connection to hive database if not used. This is to avoid … #60

wants to merge 29 commits into from

Commits on Jul 24, 2017

  1. multiple_ok flag also fetches all transcripts for gene

    William McLaren committed Jul 24, 2017
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  2. replace exac with gnomad, add uk10k and topmed

    William McLaren committed Jul 24, 2017
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  3. Plugged a (super massive) memory leak in the results cache of BaseVep… 

    …TabixPlugin
    @mkschuster
    mkschuster authored and William McLaren committed Jul 24, 2017
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  4. HGVS fix for reverse strand long deletions over intron+exon

    @sarahhunt
    sarahhunt committed Jul 24, 2017
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Commits on Jul 25, 2017

  1. remove trailing spaces on phenotype_feature_attrib value

    @sarahhunt
    sarahhunt committed Jul 25, 2017
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Commits on Jul 26, 2017

  1. Disconnect connection to hive database if not used. This is to avoid … 

    …getting a failed job if it has been running for more than 8h
    Thomas Maurel committed Jul 26, 2017
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  2. Update SubmitJob.pm 

    Fixed previous commit to allow this runnable to be run as a standalone.
    @thomasmaurel
    thomasmaurel committed Jul 26, 2017
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  3. fix vcf config paths

    William McLaren committed Jul 26, 2017
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  4. add gnomAD to favoured list of pops for max AF

    William McLaren committed Jul 26, 2017
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Commits on Jul 28, 2017

  1. add get_matched_variant_alleles util method

    William McLaren committed Jul 28, 2017
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  2. use get_matched_variant_alleles to compare VF to VCF

    William McLaren committed Jul 28, 2017
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Commits on Aug 2, 2017

  1. fix for ref copying bug

    William McLaren committed Aug 2, 2017
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Commits on Aug 3, 2017

  1. HGVS fix for long subs

    @sarahhunt
    sarahhunt committed Aug 3, 2017
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Commits on Aug 4, 2017

  1. create MTMP_transcript_variation table from scratch on init

    William McLaren committed Aug 4, 2017
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Commits on Aug 7, 2017

  1. patch test DBs to e90

    William McLaren committed Aug 7, 2017
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  2. FastaSequence.pm now also overrides Slice::subseq

    William McLaren committed Aug 7, 2017
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Commits on Aug 8, 2017

  1. reverting d896527 as it is causing REST to fail

    William McLaren committed Aug 8, 2017
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  2. reverting d896527 as it is causing REST to fail

    William McLaren committed Aug 8, 2017
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  3. reimplement fixed subseq override in FastaSequence

    William McLaren committed Aug 8, 2017
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Commits on Aug 9, 2017

  1. properly map VCF->VF alleles; add code to catch alleles found in VCF … 

    …but not in VF
    William McLaren committed Aug 9, 2017
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Commits on Aug 11, 2017

  1. Fix external link

    Laurent Gil committed Aug 11, 2017
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  2. Actually there is no need to have extra link parameters

    Laurent Gil committed Aug 11, 2017
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  3. Remove the import of the allele data into the 'allele' table for HGMD… 

    … and COSMIC
    Laurent Gil committed Aug 11, 2017
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Commits on Aug 16, 2017

  1. Use the vcf_config.json file to get the population list for some proj… 

    …ects instead of listing them directly into the script
    Laurent Gil committed Aug 16, 2017
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Commits on Aug 21, 2017

  1. only add synonyms if vf has attached variation object

    @at7
    at7 committed Aug 21, 2017
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  2. update values

    @at7
    at7 committed Aug 21, 2017
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  3. update dump split slice

    @at7
    at7 committed Aug 21, 2017
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  4. compute base before insertion

    @at7
    at7 committed Aug 21, 2017
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  5. Merge branch 'master' of https://github.com/Ensembl/ensembl-variation … 

    …into registry_and_divisions_support_release_90
    Thomas Maurel committed Aug 21, 2017
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