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Feature/parse large files low memory #33

Merged
merged 19 commits into from
Oct 30, 2019
Merged

Feature/parse large files low memory #33

merged 19 commits into from
Oct 30, 2019

Commits on Oct 22, 2019

  1. improve vcf parsing speed

    @willgdjones
    willgdjones committed Oct 22, 2019
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  2. add parse low memory functionality

    @willgdjones
    willgdjones committed Oct 22, 2019
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  3. add bytes parser for VCF files

    @willgdjones
    willgdjones committed Oct 22, 2019
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  4. parse large bytes files efficiently and allow functionality to retrie… 

    …ve selected rsids
    @willgdjones
    willgdjones committed Oct 22, 2019
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  5. add indicator that file is unannotated

    @willgdjones
    willgdjones committed Oct 22, 2019
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Commits on Oct 23, 2019

  1. Merge branch 'feature/improve-vcf-parsing-speed' into feature/parse-l… 

    …arge-files-low-memory

# Conflicts:
#	src/snps/io.py
#	tests/test_snps_collection.py
    @apriha
    apriha committed Oct 23, 2019
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  2. Black formatting

    @apriha
    apriha committed Oct 23, 2019
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  3. Merge branch 'develop' into feature/parse-large-files-low-memory

    @apriha
    apriha committed Oct 23, 2019
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  4. format black

    @willgdjones
    willgdjones committed Oct 23, 2019
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  5. Merge branch 'feature/parse-large-files-low-memory' of https://github… 

    ….com/willgdjones/snps into feature/parse-large-files-low-memory
    @willgdjones
    willgdjones committed Oct 23, 2019
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Commits on Oct 24, 2019

  1. Replace spaces with tabs

    @apriha
    apriha committed Oct 24, 2019
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  2. Update unannotated_vcf property

    @apriha
    apriha committed Oct 24, 2019
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  3. Update tests

    @apriha
    apriha committed Oct 24, 2019
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  4. Parse VCF with @willgdjones algorithm

    @apriha
    apriha committed Oct 24, 2019
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Commits on Oct 25, 2019

  1. Test extracting RSIDs from VCF file

    @apriha
    apriha committed Oct 25, 2019
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  2. Test phased genotype, no REF allele, no ALT allele, insertion, and de… 

    …letion
    @apriha
    apriha committed Oct 25, 2019
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  3. Handle cases when various alleles are not specified

    @apriha
    apriha committed Oct 25, 2019
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  4. Add documentation for loading SNPs and parsing VCF; fixes #18

    @apriha
    apriha committed Oct 25, 2019
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  5. Add rsids parameter to read_vcf

    @apriha
    apriha committed Oct 25, 2019
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