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Normalize snarls #2336

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Commits on Jan 28, 2019

  1. Merge pull request #1 from vgteam/master 

    windows-friendly-filenames
    @Robin-Rounthwaite
    Robin-Rounthwaite authored Jan 28, 2019
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Commits on Feb 22, 2019

  1. partially implemented command-line interface

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    Robin-Rounthwaite committed Feb 22, 2019
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Commits on Mar 5, 2019

  1. added clean_all_snarls fxn to src/algorithms/0_demo_final_0 files.

    @Robin-Rounthwaite
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  2. Merge branch 'master' of https://github.com/Robin-Rounthwaite/vg

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Mar 5, 2019
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  3. updating src/subcommand/mod_main.cpp

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Mar 5, 2019
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  4. update msa_converter to have seqan format

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Mar 5, 2019
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Commits on Mar 6, 2019

  1. Changes to be committed: 

    	modified:   src/algorithms/0_demo_final_0.cpp
    @Robin-Rounthwaite
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Commits on Mar 7, 2019

  1. fixed bug in msa converter

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Mar 7, 2019
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  2. Merge branch 'master' of https://github.com/Robin-Rounthwaite/vg 

    Fixed bug in msa_converter
    @Robin-Rounthwaite
    Robin-Rounthwaite committed Mar 7, 2019
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Commits on Apr 3, 2019

  1. Changes to be committed: 

    	modified:   src/subcommand/mod_main.cpp
    @Robin-Rounthwaite
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  2. testing gbwt helper 

     Changes to be committed:
	modified:   src/algorithms/0_demo_final_0.cpp
	modified:   src/algorithms/0_demo_final_0.hpp
    @Robin-Rounthwaite
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  3. Merge remote-tracking branch 'upstream/master'

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Apr 3, 2019
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Commits on Apr 8, 2019

  1. updating haplotypes_to_strings

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  2. update haplotype_to_strings

    @Robin-Rounthwaite
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Commits on Jun 13, 2019

  1. new haplotype path oriented approach to aligning graphs, with old edg… 

    …e-oriented

approach tidied away.
 On branch normalize_snarls
 Changes to be committed:
	new file:   src/algorithms/0_draft_haplotype_realignment.cpp
	new file:   src/algorithms/0_draft_haplotype_realignment.hpp
	new file:   src/algorithms/0_old_drafts/0_demo_final_0_(before_code_clean_and_includes_non_path_oriented_approach).cpp
	new file:   src/algorithms/0_old_drafts/0_demo_final_old_0-diff_extension_for_not_at_source.cpp
	new file:   src/algorithms/0_old_drafts/0_demo_final_old_0-only_source_paths.cpp
	new file:   src/algorithms/0_old_drafts/0_demo_final_old_0-only_source_paths.hpp
	modified:   src/subcommand/mod_main.cpp
    @Robin-Rounthwaite
    Robin-Rounthwaite committed Jun 13, 2019
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  2. Merge remote-tracking branch 'upstream/master' into normalize_snarls

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Jun 13, 2019
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  3. Fixing makefile merge issue

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Jun 13, 2019
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  4. Makefile edits

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    Robin-Rounthwaite committed Jun 13, 2019
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Commits on Jul 1, 2019

  1. Added normalize snarl argument vg normalize. 

     On branch normalize_snarls
 Changes to be committed:
	modified:   src/algorithms/0_draft_haplotype_realignment.cpp
	modified:   src/algorithms/0_draft_haplotype_realignment.hpp
	deleted:    src/algorithms/0_old_drafts/0_demo_final_0_(before_code_clean_and_includes_non_path_oriented_approach).cpp
	deleted:    src/algorithms/0_old_drafts/0_demo_final_old_0-diff_extension_for_not_at_source.cpp
	deleted:    src/algorithms/0_old_drafts/0_demo_final_old_0-only_source_paths.cpp
	deleted:    src/algorithms/0_old_drafts/0_demo_final_old_0-only_source_paths.hpp
	new file:   src/subcommand/0_normalize_main.cpp
    @Robin-Rounthwaite
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  2. jemalloc compilation issue fixed. 

     Changes to be committed:
	modified:   Makefile
    @Robin-Rounthwaite
    Robin-Rounthwaite committed Jul 1, 2019
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  3. Merge remote-tracking branch 'upstream/master' into normalize_snarls to 

    get updated mod_main.cpp.
    @Robin-Rounthwaite
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  4. reverted mod_main.cpp (hackily) and continued to edit 0_draft_haploty… 

    …pe_realignment.cpp to debug move embedded paths.
    @Robin-Rounthwaite
    Robin-Rounthwaite committed Jul 1, 2019
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Commits on Jul 5, 2019

  1. embedded paths now move to new snarls successfully.

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Jul 5, 2019
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  2. Merge branch 'normalize_snarls' of https://github.com/Robin-Rounthwai… 

    …te/vg into normalize_snarls
    @Robin-Rounthwaite
    Robin-Rounthwaite committed Jul 5, 2019
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Commits on Jul 9, 2019

  1. Merge remote-tracking branch 'upstream/master' into normalize_snarls

    Robin Rounthwaite committed Jul 9, 2019
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  2. shell script update

    Robin Rounthwaite committed Jul 9, 2019
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  3. syncing updates

    Robin Rounthwaite committed Jul 9, 2019
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  4. update shell

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Jul 9, 2019
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  5. added normalize arguments -g and -s

    Robin Rounthwaite committed Jul 9, 2019
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Commits on Jul 10, 2019

  1. added arguments to normalize main, further updates

    Robin Rounthwaite committed Jul 10, 2019
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  2. checking code runs on local machine

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Jul 10, 2019
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  3. shell update

    Robin Rounthwaite committed Jul 10, 2019
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  4. fixing issues bash, also debugging arguments in normalize main

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Jul 10, 2019
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  5. bash commands for normalize smaller graph works

    Robin Rounthwaite committed Jul 10, 2019
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  6. made a subset of chromosome 10 for debugging

    Robin Rounthwaite committed Jul 10, 2019
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Commits on Jul 11, 2019

  1. local machine run subsetted chr10 commands added

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Jul 11, 2019
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  2. bash debug find command

    Robin Rounthwaite committed Jul 11, 2019
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  3. bash run on full chromosome on local machine

    Robin Rounthwaite committed Jul 11, 2019
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Commits on Jul 12, 2019

  1. bash update

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Commits on Aug 7, 2019

  1. normalize snarls now runs on full hg38 thousand genomes chr10 graph. … 

    …Evaluation pipeline started.
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Commits on Aug 9, 2019

  1. extract_gbwt_haplotypes now catches incorrect gbwt connections betwee… 

    …n handles within the snarl that have no connecting edge in the graph.
    @Robin-Rounthwaite
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  2. removed 200 thread limit (to see how long it takes to normalize all s… 

    …narls); also added timing to the main file.
    @Robin-Rounthwaite
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  3. debugged timing code

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Aug 9, 2019
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  4. added shebang

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    Robin-Rounthwaite committed Aug 9, 2019
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  5. Merge remote-tracking branch 'upstream/master' into normalize_snarls

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Aug 9, 2019
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Commits on Aug 12, 2019

  1. Merge remote-tracking branch 'upstream/master' into normalize_snarls

    @Robin-Rounthwaite
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Commits on Sep 27, 2019

  1. object-orientified the snarl normalizer, also renamed cpp/hpp files

    @Robin-Rounthwaite
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  2. regular update of vg 

    Merge remote-tracking branch 'upstream/master' into normalize_snarls
    @Robin-Rounthwaite
    Robin-Rounthwaite committed Sep 27, 2019
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Commits on Nov 4, 2019

  1. misc. updates while testing data for normalize. Fixed a bug with vpkg… 

    … dealing with hashgraphs
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  2. normalize update

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    Robin-Rounthwaite committed Nov 4, 2019
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  3. Merge remote-tracking branch 'upstream/master' into normalize_snarls

    @Robin-Rounthwaite
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Commits on Nov 5, 2019

  1. made a simple vpkg wrap function for old vg files.

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Commits on Nov 2, 2020

  1. old snarl normalizer updates

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Commits on Nov 3, 2020

  1. update from origin/master

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Commits on Nov 5, 2020

  1. resolving merge conflicts

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Commits on Nov 10, 2020

  1. resolve merge conflict

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Commits on Nov 24, 2020

  1. cleaned some comments

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    Robin-Rounthwaite committed Nov 24, 2020
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  2. made SnarlSequences class for gbwt sequences.

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Nov 24, 2020
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Commits on Nov 25, 2020

  1. exhaustive sequence finding moved to SnarlSequenceFinder

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  2. moved find_embedded_paths to snarl_sequence_finder

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Nov 25, 2020
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  3. deleted now-redundant fxns from SnarlNormalizer

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Nov 25, 2020
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  4. cleaned normalize_snarls hpp

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Nov 25, 2020
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Commits on Nov 26, 2020

  1. Merge branch 'clean_code'

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Commits on Dec 1, 2020

  1. resolved merge conflict

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Commits on Dec 4, 2020

  1. duplicate haplotypes removed before alignment

    @Robin-Rounthwaite
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Commits on Dec 17, 2020

  1. extraction of chosen subgraph, single snarl normalization.

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Commits on Jan 8, 2021

  1. added compatibility for snarls that are recorded 'backwards' in the g… 

    …raph
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Commits on Jan 28, 2021

  1. added debug prints, prep for fixing path moving between snarls

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    Robin-Rounthwaite committed Jan 28, 2021
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Commits on Feb 26, 2021

  1. right-to-left directed snarls are now supported.

    @Robin-Rounthwaite
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  2. right-to-left directed snarls are now supported in normalize_snarls.

    @Robin-Rounthwaite
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  3. subdivided part of integrate_snarl into new overwrite_node_id fxn.

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Commits on Mar 12, 2021

  1. added a few unit tests directly integrated with code; only prints if … 

    …failed.
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Commits on Mar 20, 2021

  1. commented out debug code

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Commits on Mar 21, 2021

  1. more informative debug info

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  2. Merge remote-tracking branch 'upstream/master'

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Mar 21, 2021
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Commits on Mar 24, 2021

  1. update to most recent vg

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Commits on Mar 25, 2021

  1. minor edits

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  2. Merge remote-tracking branch 'upstream/master'

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Commits on Mar 26, 2021

  1. fixed include error with seqan dependencies.

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Commits on Mar 30, 2021

  1. current draft of normalize snarls without debugging code

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Commits on Apr 2, 2021

  1. fixed bug with forcing end-character alignments

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    Robin-Rounthwaite committed Apr 2, 2021
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  2. removed debug prints

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Apr 2, 2021
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Commits on Apr 6, 2021

  1. fixed typo in comments

    @Robin-Rounthwaite
    Robin-Rounthwaite committed Apr 6, 2021
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