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More complete rGFA support (experimental) #4113

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More complete rGFA support (experimental) #4113

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Commits on Mar 25, 2024

  1. start wiring in new rgfa interface

    @glennhickey
    glennhickey committed Mar 25, 2024
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  2. start wiring in cli interface

    @glennhickey
    glennhickey committed Mar 25, 2024
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  3. add rgfa options to save_graph interface

    @glennhickey
    glennhickey committed Mar 25, 2024
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  4. open intervals

    @glennhickey
    glennhickey committed Mar 25, 2024
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  5. clean a few cases

    @glennhickey
    glennhickey committed Mar 25, 2024
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  6. rgfa tests

    @glennhickey
    glennhickey committed Mar 25, 2024
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  7. Add tag test

    @glennhickey
    glennhickey committed Mar 25, 2024
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  8. add rgfa support to deconstruct

    @glennhickey
    glennhickey committed Mar 25, 2024
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  9. fix up some edge cases

    @glennhickey
    glennhickey committed Mar 25, 2024
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  10. allow multiple -S in call

    @glennhickey
    glennhickey committed Mar 25, 2024
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  11. rgfa call test

    @glennhickey
    glennhickey committed Mar 25, 2024
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  12. speed up rgfa path application

    @glennhickey
    glennhickey committed Mar 25, 2024
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  13. sample option for surject path selection, some rgfa support

    @glennhickey
    glennhickey committed Mar 25, 2024
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  14. fix bugs in load() and get_rank()

    @glennhickey
    glennhickey committed Mar 25, 2024
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  15. ignore rgfa path fragments in depth and clip coverage calcs

    @glennhickey
    glennhickey committed Mar 25, 2024
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  16. use (by default) fragment not original paths in rgfa index

    @glennhickey
    glennhickey committed Mar 25, 2024
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  17. break ties with name when choosing cover

    @glennhickey
    glennhickey committed Mar 25, 2024
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  18. work around step iterator issue in gbz

    @glennhickey
    glennhickey committed Mar 25, 2024
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  19. get rgfa tests passing; add back end range where possible

    @glennhickey
    glennhickey committed Mar 25, 2024
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  20. fix option collision from last merge

    @glennhickey
    glennhickey committed Mar 25, 2024
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  21. rGFA selection option

    @glennhickey
    glennhickey committed Mar 25, 2024
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  22. leave subrange in surjected-to rgfa fragments

    @glennhickey
    glennhickey committed Mar 25, 2024
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  23. keep rgfa subpaths in surject

    @glennhickey
    glennhickey committed Mar 25, 2024
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  24. revert rgfa name processing in paths listing -- too confusing for now

    @glennhickey
    glennhickey committed Mar 25, 2024
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  25. clean rgfa names in fasta output

    @glennhickey
    glennhickey committed Mar 25, 2024
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  26. fair enough, clang

    @glennhickey
    glennhickey committed Mar 25, 2024
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  27. fix rgfa tests post merge

    @glennhickey
    glennhickey committed Mar 25, 2024
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  28. start rgfa VCF annotator

    @glennhickey
    glennhickey committed Mar 25, 2024
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  29. Fix assertion bug

    @glennhickey
    glennhickey committed Mar 25, 2024
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  30. better rgfa support in call

    @glennhickey
    glennhickey committed Mar 25, 2024
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  31. fix merge re -S option

    @glennhickey
    glennhickey committed Mar 25, 2024
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Commits on Mar 27, 2024

  1. merge contiguous rgfa fragments

    @glennhickey
    glennhickey committed Mar 27, 2024
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Commits on Mar 28, 2024

  1. disable rank check

    @glennhickey
    glennhickey committed Mar 28, 2024
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Commits on Apr 5, 2024

  1. auto-add rgfa prefix during rgfa conversion

    @glennhickey
    glennhickey committed Apr 5, 2024
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  2. merge adjacent intervals from different threads

    @glennhickey
    glennhickey committed Apr 5, 2024
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Commits on Apr 10, 2024

  1. Merge remote-tracking branch 'origin/master' into rgfa2

    @glennhickey
    glennhickey committed Apr 10, 2024
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  2. fix merge

    @glennhickey
    glennhickey committed Apr 10, 2024
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Commits on Apr 11, 2024

  1. fix bug where cyclic paths mishandled during interval merging

    @glennhickey
    glennhickey committed Apr 11, 2024
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Commits on Apr 12, 2024

  1. Revert "auto-add rgfa prefix during rgfa conversion" 

    This reverts commit 89af9b6.
    @glennhickey
    glennhickey committed Apr 12, 2024
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  2. fix debug message

    @glennhickey
    glennhickey committed Apr 12, 2024
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  3. fix debug msg

    @glennhickey
    glennhickey committed Apr 12, 2024
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Commits on Apr 13, 2024

  1. fix bug where double-ended merge would lead to invalid overlap

    @glennhickey
    glennhickey committed Apr 13, 2024
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  2. fix bug in last commit

    @glennhickey
    glennhickey committed Apr 13, 2024
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Commits on Apr 21, 2024

  1. treat phase block as subrange to hand converted gbz

    @glennhickey
    glennhickey committed Apr 21, 2024
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Commits on May 1, 2024

  1. opt to print rgfa stats table

    @glennhickey
    glennhickey committed May 1, 2024
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  2. can use previous step from path end on gbz

    @glennhickey
    glennhickey committed May 1, 2024
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  3. dont crash with multiple references

    @glennhickey
    glennhickey committed May 1, 2024
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  4. dont crash with multiple references

    @glennhickey
    glennhickey committed May 1, 2024
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