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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added 1 commit

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

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added 2 commits

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

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changed the description

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

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added 36 commits

• 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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added 1 commit

• 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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added 20 commits

• 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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