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Bugfix/sap 11534 handle clnhgvs using measure set name #58

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Bugfix/sap 11534 handle clnhgvs using measure set name #58

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Commits on May 10, 2018

  1. Added absolute paths for scripts so that pipeline can be run in a doc… 

    …ker container
    @jonkerry
    jonkerry committed May 10, 2018
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Commits on May 31, 2018

  1. Changes to column names and introduction of dbsnp by parsing of rsID … 

    …from XML file. SAP-4037
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    jonkerry committed May 31, 2018
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  2. Added "type" in merge and to the final list of headers. SAP-4037

    @jonkerry
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Commits on Jun 7, 2018

  1. Added function for translating clinical_significance terms to those r… 

    …equired for Sapientia. Stored in data-frame as clnsig. SAP-4037
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  2. Altered VCF output to not include a bunch of columns that we are not … 

    …using in our ClinVar VCFs. Set ID column to dbSNP/rsID
    @jonkerry
    jonkerry committed Jun 7, 2018
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Commits on Feb 5, 2019

  1. SAP-7990 : Modify XML parser to include variants with non-standard VC… 

    …F field names
    @jonkerry
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Commits on Feb 14, 2019

  1. Merge pull request #12 from Congenica/feature/SAP-7990_include_skippe… 

    …d_indels

SAP-7990 : Modify XML parser to include variants with non-standard VC…
    @jonkerry
    jonkerry committed Feb 14, 2019
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Commits on Feb 15, 2019

  1. SAP-6265 : Use most pathogenic submission for conflicted variants

    @jonkerry
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  2. Merge pull request #13 from Congenica/feature/SAP-6265_most_severe_pa… 

    …thogenicity

SAP-6265 : Show most severe pathogenicity for conflicted variants
    @jonkerry
    jonkerry committed Feb 15, 2019
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Commits on Feb 21, 2019

  1. SAP-8224 : Output expected variant numbers in ClinVar VCF header

    @jonkerry
    jonkerry committed Feb 21, 2019
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  2. Merge pull request #14 from Congenica/feature/SAP-8224_expected_varia… 

    …nt_numbers_in_vcf_header

SAP-8224 : Output expected variant numbers in ClinVar VCF header
    @jonkerry
    jonkerry committed Feb 21, 2019
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Commits on Feb 25, 2019

  1. SAP-8219 : Add "rs" the front of the rsID

    @jonkerry
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  2. Merge pull request #15 from Congenica/feature/SAP-8219_add_rs_to_vari… 

    …ant_name

SAP-8219 : Add "rs" the front of the rsID
    @jonkerry
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Commits on Feb 26, 2019

  1. SAP-8222 : Add "Haplotype;Phase unknown" to expected measureset types

    @jonkerry
    jonkerry committed Feb 26, 2019
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  2. Merge pull request #16 from Congenica/feature/SAP-8222_compatibility_… 

    …for_latest_clinvar

SAP-8222 : compatibility for latest clinvar
    @jonkerry
    jonkerry committed Feb 26, 2019
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Commits on Mar 5, 2019

  1. SAP-8433 : Add pathogenicity mapping for old terms

    @jonkerry
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Commits on Mar 6, 2019

  1. Merge pull request #17 from Congenica/feature/SAP-8433_use_refClinVar… 

    …Assertion_clnsig

SAP-8433 : Add pathogenicity mapping for old terms
    @jonkerry
    jonkerry committed Mar 6, 2019
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  2. SAP-8478 : Add human-readable descriptions for INFO fields in VCF header

    @jonkerry
    jonkerry committed Mar 6, 2019
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Commits on Mar 7, 2019

  1. Merge pull request #18 from Congenica/feature/SAP-8478_human_readable… 

    …_descriptions

SAP-8478 : Add human-readable descriptions for INFO fields in VCF header
    @jonkerry
    jonkerry committed Mar 7, 2019
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  2. SAP-8360 : Pass ClinVar version to VCF writer to add version and date… 

    … to VCF header
    @jonkerry
    jonkerry committed Mar 7, 2019
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Commits on Mar 11, 2019

  1. Merge pull request #19 from Congenica/feature/SAP-8360_cvl_descriptio… 

    …n_from_vcf_header

SAP-8360 : Pass ClinVar version to VCF writer to add version and date…
    @jonkerry
    jonkerry committed Mar 11, 2019
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Commits on Oct 28, 2019

  1. SAP-11534 : set CLNGHVS field to var_name as fallback

    @kevin-dunnicliffe
    kevin-dunnicliffe committed Oct 28, 2019
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Commits on Nov 1, 2019

  1. SAP-11534 : improve clnghvs handling by fallback to MeasureSet.name

    @kevin-dunnicliffe
    kevin-dunnicliffe committed Nov 1, 2019
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