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Using SSHash submodule for graph representation #481

Merged
merged 130 commits into from
Jul 25, 2024
Merged

Using SSHash submodule for graph representation #481

merged 130 commits into from
Jul 25, 2024

Commits on May 2, 2024

  1. Fix CI failures for MacOS

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  2. update simde-no-tests

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Commits on May 22, 2024

  1. Switch to latest compiling simde-no-tests

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Commits on May 23, 2024

  1. replace restrict_to_mask_epi64 with fully scalar verison

    @hmusta
    hmusta authored May 23, 2024
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  2. Update CMakeLists.txt

    @hmusta
    hmusta authored May 23, 2024
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  3. Initial DBGSSHash commit 

    Add PTHash submodule, create boilerplate code for DBGSSHash class, add
it to test_dbg_helpers.
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  4. Use SSHash submodule instead of PTHash

    @adamant-pwn
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  5. trying to use sshash as a submodule

    @mmarzett @adamant-pwn
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  6. fixed index conversion between ssh and metagraph 

    and list of contigs
    @mmarzett @adamant-pwn
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  7. some changes to sshash, first try at avoiding the compile error in ss… 

    …hash
    @hmusta @adamant-pwn
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  8. changes for unit_test usage

    @mmarzett @adamant-pwn
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  9. new sshash version

    @mmarzett @adamant-pwn
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  10. ignore strict aliasing warning

    @mmarzett @adamant-pwn
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  11. using sshash from cli

    @mmarzett @adamant-pwn
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  12. general path

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  13. fixed serialization and loading

    @mmarzett @adamant-pwn
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  14. no longer need k.txt file + clean-up

    @mmarzett @adamant-pwn
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  15. disabled tests that are incompatible with sshash

    @mmarzett @adamant-pwn
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  16. fixes

    @hmusta @adamant-pwn
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  17. Update metagraph/src/graph/representation/hash/dbg_sshash.cpp

    @hmusta @adamant-pwn
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  18. update sshash

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  19. fix

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  20. gitignore

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  21. comments

    @hmusta @adamant-pwn
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  22. fix

    @hmusta @adamant-pwn
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  23. fixes

    @hmusta @adamant-pwn
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  24. remove temp files

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  25. cleanup

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  26. make sshash a system include

    @hmusta @adamant-pwn
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  27. for now, disable empty graph tests for SSHash

    @hmusta @adamant-pwn
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  28. no more unique_ptr

    @hmusta @adamant-pwn
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  29. remove redundant implementations

    @hmusta @adamant-pwn
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  30. cleanup

    @hmusta @adamant-pwn
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  31. use our impl of sshash, slight refactor

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  32. apply clang-format to dbg_sshash

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  33. fix compile errors in sshash

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  34. try to fix std::array compile error

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  35. add sshash_sequences empty folder to git for CI

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  36. wrap string_view, fix traverse_back bug

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  37. true skip for NonASCII SSHash

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  38. update sshash version

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  39. use kmer.data() instead of string(kmer).c_str()

    @adamant-pwn
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  40. pinpoint PuLP version for workflows

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  41. serialize k and mode with the graph

    @hmusta
    hmusta committed May 23, 2024
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  42. canonical tests for sshash

    @hmusta
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  43. Merge remote-tracking branch 'origin/master' into sshash_module

    @hmusta
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  44. remove data file

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Commits on May 27, 2024

  1. update sshash

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Commits on May 28, 2024

  1. update sshash

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  2. pass mode even for empty graphs

    @hmusta
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  3. fixes for empty graphs

    @hmusta
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  4. update sshash

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  5. more fixes

    @hmusta
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  6. fix graph construction for tests

    @hmusta
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  7. bug fix

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  8. silence sshash when not in verbose mode

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Commits on May 29, 2024

  1. fixes

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  2. fix traversal in canonical-mode sshash graphs

    @hmusta
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  3. minor

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  4. naive implementation of DBGSSHash::operator==

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  5. construct a DBGHashOrdered if DBGSSHash fails due to small input. ena… 

    …ble all unit tests for DBGSSHash
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  6. enable one more test

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  7. revert some test changes

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  8. use default call_kmers

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Commits on May 30, 2024

  1. update sshash and allow for setting number of threads in build config

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  2. for now, don't use streamer

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  3. minor cleanup

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  4. don't hard-code alphabet

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  5. incomplete: protein k-mer support

    @hmusta
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  6. more progress

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  7. t

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  8. update sshash

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  9. use aa_uint_kmer_t

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  10. Update sshash

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  11. Update sshash

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  12. Update sshash

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  13. Update sshash

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  14. Update sshash

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  15. Fix max_test_k for DBGSSHash

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Commits on Jun 1, 2024

  1. update sshash

    @hmusta
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  2. work with larger word types

    @hmusta
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  3. fully reset the dictionary when loading

    @hmusta
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  4. cleanup

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  5. k and m fixes

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Commits on Jun 2, 2024

  1. Simplify traverse

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Commits on Jun 3, 2024

  1. header cleanup

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Commits on Jun 6, 2024

  1. Update metagraph/tests/graph/all/test_dbg_helpers.cpp 

    Co-authored-by: Harun Mustafa <[email protected]>
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  2. Update metagraph/tests/graph/all/test_dbg_helpers.cpp 

    Co-authored-by: Harun Mustafa <[email protected]>
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  3. Update metagraph/CMakeLists.txt 

    Co-authored-by: Harun Mustafa <[email protected]>
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  4. Update metagraph/src/cli/build.cpp 

    Co-authored-by: Harun Mustafa <[email protected]>
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  5. Update metagraph/src/cli/build.cpp 

    Co-authored-by: Harun Mustafa <[email protected]>
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  6. Update metagraph/src/cli/config/config.cpp 

    Co-authored-by: Harun Mustafa <[email protected]>
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Commits on Jun 19, 2024

  1. Merge remote-tracking branch 'origin/master' into sshash_module

    @hmusta
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  2. minor, addressed reviewer comments

    @hmusta
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  3. minor

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  4. minor

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  5. clean

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  6. correct error

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  7. fix

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  8. reviewer comment

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  9. use std::variant for dictionary

    @hmusta
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  10. code simplification

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  11. reviewer comment

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  12. fix

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  13. move DeBruijnGraph::operator== to parent

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  14. allow the number of chars to be specified beforehand

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  15. this doesn't link, fix it

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Commits on Jun 20, 2024

  1. this works

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  2. minor

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  3. reviewer comment

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  4. Revert "this works" 

    This reverts commit 07b4653.
    @hmusta
    hmusta committed Jun 20, 2024
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  5. corner case

    @hmusta
    hmusta committed Jun 20, 2024
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  6. minor

    @hmusta
    hmusta committed Jun 20, 2024
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  7. added stop_early to call_kmers. replace bad_function_call throws with… 

    … a custom exception
    @hmusta
    hmusta committed Jun 20, 2024
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  8. addressed reviewer comment

    @hmusta
    hmusta committed Jun 20, 2024
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  9. minor

    @hmusta
    hmusta committed Jun 20, 2024
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  10. make sure to properly override

    @hmusta
    hmusta committed Jun 20, 2024
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  11. make load and serialize work for general istream and ostream

    @hmusta
    hmusta committed Jun 20, 2024
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  12. Add generic implementation of adjacent_*_nodes

    @hmusta
    hmusta committed Jun 20, 2024
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  13. fix

    @hmusta
    hmusta committed Jun 20, 2024
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  14. update sshash

    @hmusta
    hmusta committed Jun 20, 2024
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  15. num_nodes -> max_index, remove_const_ref -> decay_t

    @adamant-pwn
    adamant-pwn committed Jun 20, 2024
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  16. Update sshash, use essentials generic visitors

    @adamant-pwn
    adamant-pwn committed Jun 20, 2024
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Commits on Jul 1, 2024

  1. Update sshash

    @adamant-pwn
    adamant-pwn committed Jul 1, 2024
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  2. Update htslib (#490) (#491) 

    * install libdeflate-dev

* Link against libdeflate
    @adamant-pwn
    adamant-pwn authored Jul 1, 2024
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  3. Install libdeflate on clang

    @adamant-pwn
    adamant-pwn committed Jul 1, 2024
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Commits on Jul 2, 2024

  1. Merge branch 'master' into sshash_module

    @adamant-pwn
    adamant-pwn authored Jul 2, 2024
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  2. Put early_term in sequence_graph, silence sshash with rdbuf swap

    @adamant-pwn
    adamant-pwn committed Jul 2, 2024
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  3. Preserve failbit state

    @adamant-pwn
    adamant-pwn committed Jul 2, 2024
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Commits on Jul 15, 2024

  1. only use DBGSSHash in build_graph<DBGSSHash>

    @adamant-pwn
    adamant-pwn committed Jul 15, 2024
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