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Merge tip-clipping from GSoC into GenomeGraphs framework #15

Merged
merged 28 commits into from
Nov 27, 2019
Merged

Merge tip-clipping from GSoC into GenomeGraphs framework #15

merged 28 commits into from
Nov 27, 2019

Commits on Jul 12, 2019

  1. Draft clip_tips method

    Ben J. Ward committed Jul 12, 2019
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Commits on Jul 13, 2019

  1. error

    @ardakdemir
    ardakdemir committed Jul 13, 2019
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  2. tip removal added

    @ardakdemir
    ardakdemir committed Jul 13, 2019
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Commits on Jul 14, 2019

  1. error correction fixed

    @ardakdemir
    ardakdemir committed Jul 14, 2019
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Commits on Jul 21, 2019

  1. bubble popping implemented

    @ardakdemir
    ardakdemir committed Jul 21, 2019
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Commits on Jul 30, 2019

  1. revised bubble popping

    @ardakdemir
    ardakdemir committed Jul 30, 2019
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Commits on Aug 1, 2019

  1. sorting and canonical conversion added into the builder

    @ardakdemir
    ardakdemir committed Aug 1, 2019
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Commits on Aug 2, 2019

  1. arapan way of bubble popping initialized

    @ardakdemir
    ardakdemir committed Aug 2, 2019
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Commits on Aug 3, 2019

  1. bubble popping/unitig extension from graph implemented!

    @ardakdemir
    ardakdemir committed Aug 3, 2019
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Commits on Aug 6, 2019

  1. building from fastq

    @ardakdemir
    ardakdemir committed Aug 6, 2019
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Commits on Aug 7, 2019

  1. kmer coverage using mean

    @ardakdemir
    ardakdemir committed Aug 7, 2019
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Commits on Aug 12, 2019

  1. tip deletion from graph

    @ardakdemir
    ardakdemir committed Aug 12, 2019
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Commits on Aug 15, 2019

  1. neighbor finding for sequences is updated but still looks very messy.

    @ardakdemir
    ardakdemir committed Aug 15, 2019
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Commits on Aug 24, 2019

  1. error correction updates

    @ardakdemir
    ardakdemir committed Aug 24, 2019
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Commits on Sep 26, 2019

  1. Merge branch 'gsoc/error-correction2' into benjward/gsocmerge

    Ben J. Ward committed Sep 26, 2019
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  2. Move Arda's tip deletion func to its own file in processes directory.

    Ben J. Ward committed Sep 26, 2019
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  3. Merge branch 'benjward/tip-clipping' into benjward/gsocmerge

    Ben J. Ward committed Sep 26, 2019
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  4. Use links & graph topology instead of prefixes and suffixes to find tips

    Ben J. Ward committed Sep 26, 2019
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Commits on Sep 27, 2019

  1. Fix GFAv1 writing & node deletion & add unitig finding method

    Ben J. Ward committed Sep 27, 2019
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Commits on Sep 29, 2019

  1. Add ability to search for a link in the graph

    Ben J. Ward committed Sep 29, 2019
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  2. Allow sequence creation from a path, and joining paths to make a node

    Ben J. Ward committed Sep 29, 2019
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Commits on Oct 9, 2019

  1. Fix the unitig finder

    Ben J. Ward committed Oct 9, 2019
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Commits on Oct 31, 2019

  1. Add logo to the getting started guide

    Ben J. Ward committed Oct 31, 2019
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  2. Update manual again

    Ben J. Ward committed Oct 31, 2019
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Commits on Nov 4, 2019

  1. Add very basic NodeView interface

    Ben J. Ward committed Nov 4, 2019
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Commits on Nov 22, 2019

  1. Add Windows testing, and adjust behaviour of the sequence method

    Ben J. Ward committed Nov 22, 2019
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Commits on Nov 25, 2019

  1. Use updated documenter

    Ben J. Ward committed Nov 25, 2019
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  2. Fix a typo

    Ben J. Ward committed Nov 25, 2019
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