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Sfitz concat vcf #213

Merged
merged 18 commits into from
Aug 10, 2023
Merged

Sfitz concat vcf #213

merged 18 commits into from
Aug 10, 2023

Commits on Jul 26, 2023

  1. add concat VCF process. untested. need to add chksum

    @sorelfitzgibbon
    sorelfitzgibbon committed Jul 26, 2023
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Commits on Jul 27, 2023

  1. concat vcf works

    @sorelfitzgibbon
    sorelfitzgibbon committed Jul 27, 2023
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  2. update changelog

    @sorelfitzgibbon
    sorelfitzgibbon committed Jul 27, 2023
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Commits on Jul 28, 2023

  1. uncompressed concat vcf output and chksums

    @sorelfitzgibbon
    sorelfitzgibbon committed Jul 28, 2023
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Commits on Aug 2, 2023

  1. outfile: Intersect -> Consensus

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 2, 2023
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  2. merge in main

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 2, 2023
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  3. fix merge mistake and update resource allocation

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 2, 2023
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Commits on Aug 3, 2023

  1. use file.path() and update changelog

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 3, 2023
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  2. mv output of isec-1-or-more/*.txt and rm log task numbers

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 3, 2023
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  3. isec-1-or-more output fix and Consensus -> BCFtools filenames

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 3, 2023
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Commits on Aug 4, 2023

  1. minor edits

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 4, 2023
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Commits on Aug 7, 2023

  1. sort vcfs into isec and concat

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 7, 2023
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  2. standardize isec output filenames

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 7, 2023
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Commits on Aug 8, 2023

  1. fix standardized isec output and spacing in rscript

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 8, 2023
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  2. fix standard filename output

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 8, 2023
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Commits on Aug 9, 2023

  1. vcf sort fix in progress

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 9, 2023
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Commits on Aug 10, 2023

  1. vcf sort fixed

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 10, 2023
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  2. function for vcf sort

    @sorelfitzgibbon
    sorelfitzgibbon committed Aug 10, 2023
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