Draft: construct pangenome database from GFA

Related to !147, I would like to not only go from pantools_DB -> GFA but also vice versa. This merge request collects my tries of doing that. It's marked as draft for now because I'm not sure if I'll use this code in the end.

TODO:

• Fix kmer index
• Make working on cyclic graphs
• Find out what happens with degenerate nodes
• Don't require genome locations file if GFA is provided (if GFA contains sequences)
• Get it to run on any valid GFA
• Ensure neo4j -> GFA -> neo4j gives identical database
• Ensure GFA -> neo4j -> GFA gives identical GFA file
• Update documentation accordingly

assigned to @worku005

added 3 commits

• 54539b81 - add logging and make length calculation work
• 8c5ae7d7 - fix address and cigar for nucleotide nodes from GFA
• 296544bb - fix relationships in GFA to pangenome graph db

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• 840a99ef - remove sequence retrieval from GFA and add tag to pangenome node about type

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• cbf160e9 - add TODOs
• ab0e004c - fix ci/cd pipeline

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changed the description

added 447 commits

• ab0e004c...11c9c2e3 - 446 commits from branch add_gfa_export
• 926702fe - Merge branch 'add_gfa_export' into add_gfa_build_pangenome

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• 926702fe...a725713c - 35 commits from branch add_gfa_export
• c4323698 - Merge branch 'add_gfa_export' into add_gfa_build_pangenome

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added 1 commit

• 05140b51 - put graph reading back that went missing after merging in develop

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added 1 commit

• 724a27ec - start replacing duplicated graph classes by better ones

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added 2 commits

• df1027a2 - commented out old gfa reader code and start rewriting to common code with gfa writer
• a662b264 - document constructors of edges as they are important for graph conversion and...

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• 624cc62b - remove unused class

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marked the checklist item Make working on cyclic graphs as completed

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• 624cc62b...8bc7cd67 - 33 commits from branch add_gfa_export
• bf066516 - Merge branch 'add_gfa_export' into add_gfa_build_pangenome

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• bf066516...5292abba - 19 commits from branch add_gfa_export
• 36c14157 - Merge branch 'add_gfa_export' into add_gfa_build_pangenome

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mentioned in merge request !147

added 116 commits

• 36c14157...72deb51e - 114 commits from branch add_gfa_export
• 7ed7d2a0 - fix typo
• 8906de56 - Merge branch 'add_gfa_export' into add_gfa_build_pangenome

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added 1 commit

• 46dff639 - fix Vertex.java compilation error introduced in merge

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added 22 commits

• 46dff639...67d94b64 - 21 commits from branch add_gfa_export
• 68c98ae6 - Merge branch 'add_gfa_export' into add_gfa_build_pangenome

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added 33 commits

• 68c98ae6...be05107b - 2 commits from branch add_gfa_export
• be05107b...40d2f39f - 21 earlier commits
• d9b8f602 - Revert "updated changelog."
• 3d970397 - changed exception to runtimexception
• 400982fc - Merge branch 'develop' of https://git.wur.nl/bioinformatics/pantools into phased_pangenomics_bugfix
• 6234a12e - Merge branch 'bugfix_grouping' into 'develop'
• 776221c9 - Merge branch 'develop' of https://git.wur.nl/bioinformatics/pantools into phased_pangenomics_bugfix
• df0c998c - Merge branch 'phased_pangenomics_bugfix' into 'develop'
• 4a38b0ac - added exception with error message to transaction in alleleStatistics.
• 2655b1b2 - Merge branch 'gene_classification_error_message' into 'develop'
• 40096575 - Merge remote-tracking branch 'origin/develop' into add_gfa_export
• 42c12741 - Merge branch 'add_gfa_export' into add_gfa_build_pangenome

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added 23 commits

• 42c12741...3237ea61 - 21 commits from branch add_gfa_export
• 633a4dd4 - correct placement current changes in changelog
• 2d88eefb - Merge branch 'add_gfa_export' into add_gfa_build_pangenome

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added 52 commits

• 2d88eefb...5f80b023 - 51 commits from branch add_gfa_export
• 46f59af1 - Merge branch 'add_gfa_export' into add_gfa_build_pangenome

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• 56e18e0b - make GFA backbone build_pangenome work with localisation

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• b79cfe2f - implement first and last kmer for build_pangenome with gfa

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• c528caa1 - fix num_bases for pangenome from gfa

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• 619e3219 - add check for validity of GFA files to build_pangenome

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• ed781372 - correctly implement next_index property

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marked the checklist item Fix kmer index as completed

changed the description

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• 434ef60e - add more code to deal with degenerate nodes

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marked the checklist item Find out what happens with degenerate nodes as completed

added 12 commits

• 434ef60e...8aa7e189 - 2 earlier commits
• 6f4f343d - turning off trace logging in the code for build_pangenome to speed it up a bit
• cf15da6c - update changelog
• bc77b565 - fix build_pangenome for the last k-1 bases
• 282093c8 - implement more clever way of finding links in a GFA file
• 9021c920 - try implementing proper parsing of path names from both gfa to and from neo4j
• 738d1561 - let build_pangenome be able to deal with multiple sequences per genome
• 374c0433 - implement loosely matching the links in the GFAgit status
• 1947a48f - try improving speed a lot by disallowing double degenerate nodes
• 6377ba31 - implement cache for nodes when building graph from GFA
• a2580484 - Merge branch 'rewrite_legacy_code_node_localization_for_gfa_build_pangenome'...

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marked the checklist item Don't require genome locations file if GFA is provided (if GFA contains sequences) as completed

This merge request still needs the following fixed in order to be ready for merging back into add_gfa_export:

• Fix localization for generic graphs (see !239 (merged) for more information).
• Check for easy speed optimizations
• Add property to pangenome node with the type of pangenome and use this in if/else statements to not negatively impact cDBG creation (especially relevant for localization process)

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• bf3ab0fd - add some notes to the code so future me knows what went on

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added 56 commits

• bf3ab0fd...a60ef561 - 55 commits from branch add_gfa_export
• f4ea67d4 - Merge branch 'add_gfa_export' into add_gfa_build_pangenome

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added 1 commit

• 58710984 - build separate localization for build_pangenome from GFA

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added 2 commits

• 6355a5b2 - revert changes to localization since it was taken out
• 9c50b5ad - also enable parsing of weird panSN spec for GFA path names for compatibility with old MC

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added 7 commits

• 9c50b5ad...aa4366e0 - 5 commits from branch add_gfa_export
• f538e807 - removing temporary genomes fasta directory if it exists
• ea2936ff - Merge branch 'add_gfa_export' into add_gfa_build_pangenome

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• f2765635 - also update frequency property on nucleotide nodes

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