Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Less stringent alignment and seed filtering #453

Draft
wants to merge 205 commits into
base: master
Choose a base branch
from
Draft

Less stringent alignment and seed filtering #453

wants to merge 205 commits into from

Commits on Jun 5, 2023

  1. by default, don't put a limit on the number of alignments

    @hmusta
    hmusta committed Jun 5, 2023
    Configuration menu
    Copy the full SHA
    94658fa View commit details
    Browse the repository at this point in the history

Commits on Jun 6, 2023

  1. fix server errors

    @hmusta
    hmusta committed Jun 6, 2023
    Configuration menu
    Copy the full SHA
    764acc9 View commit details
    Browse the repository at this point in the history

  2. fix simple_align integration tests

    @hmusta
    hmusta committed Jun 6, 2023
    Configuration menu
    Copy the full SHA
    3ded0e8 View commit details
    Browse the repository at this point in the history

  3. cleanup

    @hmusta
    hmusta committed Jun 6, 2023
    Configuration menu
    Copy the full SHA
    76a9d4d View commit details
    Browse the repository at this point in the history

  4. minor

    @hmusta
    hmusta committed Jun 6, 2023
    Configuration menu
    Copy the full SHA
    98332f1 View commit details
    Browse the repository at this point in the history

  5. cleanup

    @hmusta
    hmusta committed Jun 6, 2023
    Configuration menu
    Copy the full SHA
    42b7dc2 View commit details
    Browse the repository at this point in the history

Commits on Jun 7, 2023

  1. Update config.cpp

    @hmusta
    hmusta authored Jun 7, 2023
    Configuration menu
    Copy the full SHA
    7115837 View commit details
    Browse the repository at this point in the history

  2. if a label is discarded, add the seed as an alignment without extension

    @hmusta
    hmusta committed Jun 7, 2023
    Configuration menu
    Copy the full SHA
    dbd28ee View commit details
    Browse the repository at this point in the history

Commits on Jun 9, 2023

  1. if a seed is filtered out, report the filtered out part as an alignment

    @hmusta
    hmusta committed Jun 9, 2023
    Configuration menu
    Copy the full SHA
    271fdba View commit details
    Browse the repository at this point in the history

Commits on Jun 12, 2023

  1. respect min_path_score

    @hmusta
    hmusta committed Jun 12, 2023
    Configuration menu
    Copy the full SHA
    6978902 View commit details
    Browse the repository at this point in the history

Commits on Jun 13, 2023

  1. Add pandas as a requirement

    @hmusta
    hmusta committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    4bbd320 View commit details
    Browse the repository at this point in the history

Commits on Jun 14, 2023

  1. test

    @hmusta
    hmusta committed Jun 14, 2023
    Configuration menu
    Copy the full SHA
    e8855ef View commit details
    Browse the repository at this point in the history

  2. handle annotations for dummy nodes:

    @hmusta
    hmusta committed Jun 14, 2023
    Configuration menu
    Copy the full SHA
    7323418 View commit details
    Browse the repository at this point in the history

Commits on Jun 15, 2023

  1. annotate dummy nodes during alignment

    @hmusta
    hmusta committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    2203f08 View commit details
    Browse the repository at this point in the history

  2. fixes

    @hmusta
    hmusta committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    b5cacd6 View commit details
    Browse the repository at this point in the history

  3. fix compilation issues on clang

    @hmusta
    hmusta committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    d9bf01c View commit details
    Browse the repository at this point in the history

  4. fixes

    @hmusta
    hmusta committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    e7c9921 View commit details
    Browse the repository at this point in the history

  5. minor

    @hmusta
    hmusta committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    92946b0 View commit details
    Browse the repository at this point in the history

  6. only BASIC graph for protein tests

    @hmusta
    hmusta committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    b222c78 View commit details
    Browse the repository at this point in the history

  7. avoid failing structural binding capture in lambda

    @hmusta
    hmusta committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    f404bb3 View commit details
    Browse the repository at this point in the history

  8. don't fetch annotations for dummy node neighbours if they've e alread… 

    …y been fetched
    @hmusta
    hmusta committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    b124536 View commit details
    Browse the repository at this point in the history

  9. fix unit test for proteins

    @hmusta
    hmusta committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    405472f View commit details
    Browse the repository at this point in the history

  10. helper function for merging seeds into maximal unique matches

    @hmusta
    hmusta committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    bf251be View commit details
    Browse the repository at this point in the history

  11. merge labeled seeds

    @hmusta
    hmusta committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    6394160 View commit details
    Browse the repository at this point in the history

Commits on Jun 16, 2023

  1. warn instead of assert failure when using masked DBGSuccinct

    @hmusta
    hmusta committed Jun 16, 2023
    Configuration menu
    Copy the full SHA
    40cd62e View commit details
    Browse the repository at this point in the history

  2. fix

    @hmusta
    hmusta committed Jun 16, 2023
    Configuration menu
    Copy the full SHA
    fabcc51 View commit details
    Browse the repository at this point in the history

  3. more reporting

    @hmusta
    hmusta committed Jun 16, 2023
    Configuration menu
    Copy the full SHA
    ebeacaf View commit details
    Browse the repository at this point in the history

  4. fix

    @hmusta
    hmusta committed Jun 16, 2023
    Configuration menu
    Copy the full SHA
    b336f1e View commit details
    Browse the repository at this point in the history

  5. fix unit test

    @hmusta
    hmusta committed Jun 16, 2023
    Configuration menu
    Copy the full SHA
    488a793 View commit details
    Browse the repository at this point in the history

  6. disable integration test

    @hmusta
    hmusta committed Jun 16, 2023
    Configuration menu
    Copy the full SHA
    7e1012f View commit details
    Browse the repository at this point in the history

  7. fix seed filtering after extension

    @hmusta
    hmusta committed Jun 16, 2023
    Configuration menu
    Copy the full SHA
    8ef3323 View commit details
    Browse the repository at this point in the history

  8. ensure seeds are correctly sorted after filtering

    @hmusta
    hmusta committed Jun 16, 2023
    Configuration menu
    Copy the full SHA
    d156dc2 View commit details
    Browse the repository at this point in the history

  9. simplify suffix seeding

    @hmusta
    hmusta committed Jun 16, 2023
    Configuration menu
    Copy the full SHA
    5dbacf2 View commit details
    Browse the repository at this point in the history

  10. fix

    @hmusta
    hmusta committed Jun 16, 2023
    Configuration menu
    Copy the full SHA
    c1bee7e View commit details
    Browse the repository at this point in the history

Commits on Jun 19, 2023

  1. cleanup

    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    45af9ae View commit details
    Browse the repository at this point in the history

  2. fixes

    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    f33f867 View commit details
    Browse the repository at this point in the history

  3. fix for canonical graphs

    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    2b94995 View commit details
    Browse the repository at this point in the history

  4. cleanup

    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    f591394 View commit details
    Browse the repository at this point in the history

  5. cleanup

    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    f5d3a2a View commit details
    Browse the repository at this point in the history

  6. redo suffix seeding on primary graphs

    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    15fb3ec View commit details
    Browse the repository at this point in the history

  7. fix computation of number of matching characters. include first k-len… 

    …gth seed if present
    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    9f00719 View commit details
    Browse the repository at this point in the history

  8. remove redundant seeds

    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    824484b View commit details
    Browse the repository at this point in the history

  9. find fewer seeds

    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    ab0f5f6 View commit details
    Browse the repository at this point in the history

  10. find fewer seeds

    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    2e8e49d View commit details
    Browse the repository at this point in the history

  11. add assertion

    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    beae397 View commit details
    Browse the repository at this point in the history

  12. fixed

    @hmusta
    hmusta committed Jun 19, 2023
    Configuration menu
    Copy the full SHA
    85e61cf View commit details
    Browse the repository at this point in the history

Commits on Jun 20, 2023

  1. fix

    @hmusta
    hmusta committed Jun 20, 2023
    Configuration menu
    Copy the full SHA
    d7eb8c9 View commit details
    Browse the repository at this point in the history

  2. avoid creating redundant suffix seeds

    @hmusta
    hmusta committed Jun 20, 2023
    Configuration menu
    Copy the full SHA
    4949bf4 View commit details
    Browse the repository at this point in the history

  3. more seed filtering

    @hmusta
    hmusta committed Jun 20, 2023
    Configuration menu
    Copy the full SHA
    1b6c572 View commit details
    Browse the repository at this point in the history

  4. cleanup

    @hmusta
    hmusta committed Jun 20, 2023
    Configuration menu
    Copy the full SHA
    c2b3e79 View commit details
    Browse the repository at this point in the history

  5. optim

    @hmusta
    hmusta committed Jun 20, 2023
    Configuration menu
    Copy the full SHA
    8aa04b9 View commit details
    Browse the repository at this point in the history

  6. fix

    @hmusta
    hmusta committed Jun 20, 2023
    Configuration menu
    Copy the full SHA
    c9fb9fb View commit details
    Browse the repository at this point in the history

  7. print errors when setUpClass happens

    @hmusta
    hmusta committed Jun 20, 2023
    Configuration menu
    Copy the full SHA
    d945eed View commit details
    Browse the repository at this point in the history

  8. fix

    @hmusta
    hmusta committed Jun 20, 2023
    Configuration menu
    Copy the full SHA
    e5af33a View commit details
    Browse the repository at this point in the history

Commits on Jun 21, 2023

  1. cleanup alignment aggregator

    @hmusta
    hmusta committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    5ab52be View commit details
    Browse the repository at this point in the history

  2. minor

    @hmusta
    hmusta committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    a1af22a View commit details
    Browse the repository at this point in the history

  3. fix

    @hmusta
    hmusta committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    bfa7015 View commit details
    Browse the repository at this point in the history

  4. fix seed filtering

    @hmusta
    hmusta committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    8d0afea View commit details
    Browse the repository at this point in the history

  5. fix

    @hmusta
    hmusta committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    00d52ce View commit details
    Browse the repository at this point in the history

  6. extra asserts. ensure that seeds are in correct order

    @hmusta
    hmusta committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    54ddb56 View commit details
    Browse the repository at this point in the history

  7. minor

    @hmusta
    hmusta committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    148d49e View commit details
    Browse the repository at this point in the history

  8. off by one

    @hmusta
    hmusta committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    79504fb View commit details
    Browse the repository at this point in the history

  9. test

    @hmusta
    hmusta committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    96c5b6c View commit details
    Browse the repository at this point in the history

Commits on Jun 22, 2023

  1. test

    @hmusta
    hmusta committed Jun 22, 2023
    Configuration menu
    Copy the full SHA
    9987a00 View commit details
    Browse the repository at this point in the history

Commits on Jun 23, 2023

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

    @hmusta
    hmusta committed Jun 23, 2023
    Configuration menu
    Copy the full SHA
    2bd0d00 View commit details
    Browse the repository at this point in the history

  2. rewrite fetching

    @hmusta
    hmusta committed Jun 23, 2023
    Configuration menu
    Copy the full SHA
    8ba12a4 View commit details
    Browse the repository at this point in the history

  3. cleanup

    @hmusta
    hmusta committed Jun 23, 2023
    Configuration menu
    Copy the full SHA
    ffa8ce7 View commit details
    Browse the repository at this point in the history

  4. cleanup

    @hmusta
    hmusta committed Jun 23, 2023
    Configuration menu
    Copy the full SHA
    a999508 View commit details
    Browse the repository at this point in the history

  5. more cleanup

    @hmusta
    hmusta committed Jun 23, 2023
    Configuration menu
    Copy the full SHA
    9258561 View commit details
    Browse the repository at this point in the history

  6. fix for coords in CANONICAL graphs

    @hmusta
    hmusta committed Jun 23, 2023
    Configuration menu
    Copy the full SHA
    3ee4efd View commit details
    Browse the repository at this point in the history

  7. minor

    @hmusta
    hmusta committed Jun 23, 2023
    Configuration menu
    Copy the full SHA
    044d6b7 View commit details
    Browse the repository at this point in the history

  8. minor

    @hmusta
    hmusta committed Jun 23, 2023
    Configuration menu
    Copy the full SHA
    d26221a View commit details
    Browse the repository at this point in the history

  9. minor

    @hmusta
    hmusta committed Jun 23, 2023
    Configuration menu
    Copy the full SHA
    e79f643 View commit details
    Browse the repository at this point in the history

  10. Add checks

    @hmusta
    hmusta committed Jun 23, 2023
    Configuration menu
    Copy the full SHA
    8b7d64b View commit details
    Browse the repository at this point in the history

  11. check coordinate consistency when merging seeds

    @hmusta
    hmusta committed Jun 23, 2023
    Configuration menu
    Copy the full SHA
    f2698fb View commit details
    Browse the repository at this point in the history

Commits on Jun 26, 2023

  1. don't seed both orientations in a CANONICAL graph

    @hmusta
    hmusta committed Jun 26, 2023
    Configuration menu
    Copy the full SHA
    0e874ec View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'origin/master' into hm/aln_alt

    @hmusta
    hmusta committed Jun 26, 2023
    Configuration menu
    Copy the full SHA
    9b8e7b7 View commit details
    Browse the repository at this point in the history

  3. filter out low-complexity sub-k seeds

    @hmusta
    hmusta committed Jun 26, 2023
    Configuration menu
    Copy the full SHA
    568ced2 View commit details
    Browse the repository at this point in the history

  4. move low complexity filter outside

    @hmusta
    hmusta committed Jun 26, 2023
    Configuration menu
    Copy the full SHA
    2286007 View commit details
    Browse the repository at this point in the history

  5. more messages

    @hmusta
    hmusta committed Jun 26, 2023
    Configuration menu
    Copy the full SHA
    65476f8 View commit details
    Browse the repository at this point in the history

  6. less verbose messages

    @hmusta
    hmusta committed Jun 26, 2023
    Configuration menu
    Copy the full SHA
    ad879da View commit details
    Browse the repository at this point in the history

Commits on Jun 27, 2023

  1. disable unit test

    @hmusta
    hmusta committed Jun 27, 2023
    Configuration menu
    Copy the full SHA
    d6a5eb7 View commit details
    Browse the repository at this point in the history

  2. extra checks

    @hmusta
    hmusta committed Jun 27, 2023
    Configuration menu
    Copy the full SHA
    d5c0b89 View commit details
    Browse the repository at this point in the history

  3. fix

    @hmusta
    hmusta committed Jun 27, 2023
    Configuration menu
    Copy the full SHA
    a6ecdd2 View commit details
    Browse the repository at this point in the history

  4. less backtracking for unannotated graphs

    @hmusta
    hmusta committed Jun 27, 2023
    Configuration menu
    Copy the full SHA
    714da0c View commit details
    Browse the repository at this point in the history

Commits on Jun 28, 2023

  1. don't fetch labels for low complexity seeds

    @hmusta
    hmusta committed Jun 28, 2023
    Configuration menu
    Copy the full SHA
    f0f73f1 View commit details
    Browse the repository at this point in the history

  2. less prefix seeding

    @hmusta
    hmusta committed Jun 28, 2023
    Configuration menu
    Copy the full SHA
    dc2de87 View commit details
    Browse the repository at this point in the history

Commits on Jun 29, 2023

  1. find fewer seeds

    @hmusta
    hmusta committed Jun 29, 2023
    Configuration menu
    Copy the full SHA
    aa999c9 View commit details
    Browse the repository at this point in the history

Commits on Jun 30, 2023

  1. merge annotations better when forming mums

    @hmusta
    hmusta committed Jun 30, 2023
    Configuration menu
    Copy the full SHA
    7f6ffb2 View commit details
    Browse the repository at this point in the history

Commits on Jul 1, 2023

  1. unneeded parameter

    @hmusta
    hmusta committed Jul 1, 2023
    Configuration menu
    Copy the full SHA
    c026a3e View commit details
    Browse the repository at this point in the history

  2. test

    @hmusta
    hmusta committed Jul 1, 2023
    Configuration menu
    Copy the full SHA
    bff8daf View commit details
    Browse the repository at this point in the history

Commits on Jul 3, 2023

  1. fix

    @hmusta
    hmusta committed Jul 3, 2023
    Configuration menu
    Copy the full SHA
    dcc6b3d View commit details
    Browse the repository at this point in the history

  2. minor, change default params

    @hmusta
    hmusta committed Jul 3, 2023
    Configuration menu
    Copy the full SHA
    8dc496c View commit details
    Browse the repository at this point in the history

  3. include more extensions if they add more labels

    @hmusta
    hmusta committed Jul 3, 2023
    Configuration menu
    Copy the full SHA
    35dad6b View commit details
    Browse the repository at this point in the history

Commits on Jul 4, 2023

  1. fixes

    @hmusta
    hmusta committed Jul 4, 2023
    Configuration menu
    Copy the full SHA
    45cdede View commit details
    Browse the repository at this point in the history

  2. fix

    @hmusta
    hmusta committed Jul 4, 2023
    Configuration menu
    Copy the full SHA
    d643222 View commit details
    Browse the repository at this point in the history

  3. don't report seeds filtered out after extensions

    @hmusta
    hmusta committed Jul 4, 2023
    Configuration menu
    Copy the full SHA
    493a78d View commit details
    Browse the repository at this point in the history

  4. fix unit test

    @hmusta
    hmusta committed Jul 4, 2023
    Configuration menu
    Copy the full SHA
    472cae3 View commit details
    Browse the repository at this point in the history

  5. fix labels

    @hmusta
    hmusta committed Jul 4, 2023
    Configuration menu
    Copy the full SHA
    63f20dd View commit details
    Browse the repository at this point in the history

  6. simplify suffix seeding

    @hmusta
    hmusta committed Jul 4, 2023
    Configuration menu
    Copy the full SHA
    86bbe7a View commit details
    Browse the repository at this point in the history

  7. path simplification

    @hmusta
    hmusta committed Jul 4, 2023
    Configuration menu
    Copy the full SHA
    441e4fd View commit details
    Browse the repository at this point in the history

  8. Revert "path simplification" 

    This reverts commit 441e4fd.
    @hmusta
    hmusta committed Jul 4, 2023
    Configuration menu
    Copy the full SHA
    f80cede View commit details
    Browse the repository at this point in the history

  9. Revert "simplify suffix seeding" 

    This reverts commit 86bbe7a.
    @hmusta
    hmusta committed Jul 4, 2023
    Configuration menu
    Copy the full SHA
    e473e44 View commit details
    Browse the repository at this point in the history

Commits on Jul 6, 2023

  1. cleanup suffix seeding

    @hmusta
    hmusta committed Jul 6, 2023
    Configuration menu
    Copy the full SHA
    50b39d2 View commit details
    Browse the repository at this point in the history

  2. more filtration

    @hmusta
    hmusta committed Jul 6, 2023
    Configuration menu
    Copy the full SHA
    cadb30f View commit details
    Browse the repository at this point in the history

  3. Revert "more filtration" 

    This reverts commit cadb30f.
    @hmusta
    hmusta committed Jul 6, 2023
    Configuration menu
    Copy the full SHA
    e3fe498 View commit details
    Browse the repository at this point in the history

Commits on Jul 7, 2023

  1. far fewer seeds

    @hmusta
    hmusta committed Jul 7, 2023
    Configuration menu
    Copy the full SHA
    e01668d View commit details
    Browse the repository at this point in the history

  2. fix

    @hmusta
    hmusta committed Jul 7, 2023
    Configuration menu
    Copy the full SHA
    8e55c6f View commit details
    Browse the repository at this point in the history

  3. fix

    @hmusta
    hmusta committed Jul 7, 2023
    Configuration menu
    Copy the full SHA
    41456d7 View commit details
    Browse the repository at this point in the history

  4. fewer seeds

    @hmusta
    hmusta committed Jul 7, 2023
    Configuration menu
    Copy the full SHA
    73c8185 View commit details
    Browse the repository at this point in the history

  5. fix

    @hmusta
    hmusta committed Jul 7, 2023
    Configuration menu
    Copy the full SHA
    0b1d054 View commit details
    Browse the repository at this point in the history

Commits on Jul 10, 2023

  1. cleanup. toggle shorter suffix seeds with a flag

    @hmusta
    hmusta committed Jul 10, 2023
    Configuration menu
    Copy the full SHA
    13ced4c View commit details
    Browse the repository at this point in the history

Commits on Jul 11, 2023

  1. Add in heuristic chainer

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    8b65639 View commit details
    Browse the repository at this point in the history

  2. t1

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    548aed6 View commit details
    Browse the repository at this point in the history

  3. t2

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    c2d7129 View commit details
    Browse the repository at this point in the history

  4. t3

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    aada964 View commit details
    Browse the repository at this point in the history

  5. t4

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    96f5918 View commit details
    Browse the repository at this point in the history

  6. t5

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    b2969d8 View commit details
    Browse the repository at this point in the history

  7. t6

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    f005460 View commit details
    Browse the repository at this point in the history

  8. t5

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    7b0e442 View commit details
    Browse the repository at this point in the history

  9. fix

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    b0fee9d View commit details
    Browse the repository at this point in the history

  10. fix compilation in clang

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    a35ebc2 View commit details
    Browse the repository at this point in the history

  11. find k-mer seeds if present

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    5f2c791 View commit details
    Browse the repository at this point in the history

  12. disable some tests for protein graphs

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    a38c13f View commit details
    Browse the repository at this point in the history

  13. minor

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    b1d3161 View commit details
    Browse the repository at this point in the history

  14. minor

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    fb65f9e View commit details
    Browse the repository at this point in the history

  15. fix

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    c67b38f View commit details
    Browse the repository at this point in the history

  16. allow splice if sharing at least one label

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    6b27a25 View commit details
    Browse the repository at this point in the history

  17. extra check

    @hmusta
    hmusta committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    30e376a View commit details
    Browse the repository at this point in the history

Commits on Jul 12, 2023

  1. t

    @hmusta
    hmusta committed Jul 12, 2023
    Configuration menu
    Copy the full SHA
    8819044 View commit details
    Browse the repository at this point in the history

  2. Revert "extra check" 

    This reverts commit 30e376a.
    @hmusta
    hmusta committed Jul 12, 2023
    Configuration menu
    Copy the full SHA
    872b769 View commit details
    Browse the repository at this point in the history

  3. fewer redundant alignments

    @hmusta
    hmusta committed Jul 12, 2023
    Configuration menu
    Copy the full SHA
    d4b3238 View commit details
    Browse the repository at this point in the history

  4. minor

    @hmusta
    hmusta committed Jul 12, 2023
    Configuration menu
    Copy the full SHA
    093f641 View commit details
    Browse the repository at this point in the history

Commits on Jul 13, 2023

  1. fixes

    @hmusta
    hmusta committed Jul 13, 2023
    Configuration menu
    Copy the full SHA
    e6dbd55 View commit details
    Browse the repository at this point in the history

  2. last try

    @hmusta
    hmusta committed Jul 13, 2023
    Configuration menu
    Copy the full SHA
    b2a3740 View commit details
    Browse the repository at this point in the history

  3. try this

    @hmusta
    hmusta committed Jul 13, 2023
    Configuration menu
    Copy the full SHA
    8771730 View commit details
    Browse the repository at this point in the history

Commits on Jul 14, 2023

  1. this works

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    9603009 View commit details
    Browse the repository at this point in the history

  2. cleanup

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    9222ca4 View commit details
    Browse the repository at this point in the history

  3. anchor filtering

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    768f283 View commit details
    Browse the repository at this point in the history

  4. fix

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    e931660 View commit details
    Browse the repository at this point in the history

  5. cleanup

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    87f7c8d View commit details
    Browse the repository at this point in the history

  6. cleanup

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    ba3467e View commit details
    Browse the repository at this point in the history

  7. cleanup

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    26ddc6f View commit details
    Browse the repository at this point in the history

  8. Added extra check

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    b400284 View commit details
    Browse the repository at this point in the history

  9. extra checks

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    f9c6936 View commit details
    Browse the repository at this point in the history

  10. minor

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    a22d910 View commit details
    Browse the repository at this point in the history

  11. fixes

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    7689276 View commit details
    Browse the repository at this point in the history

  12. fix

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    32fa3f4 View commit details
    Browse the repository at this point in the history

  13. discard chains all from the same alignment

    @hmusta
    hmusta committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    83d378b View commit details
    Browse the repository at this point in the history

Commits on Jul 15, 2023

  1. fix corner cases

    @hmusta
    hmusta committed Jul 15, 2023
    Configuration menu
    Copy the full SHA
    3bbbc5c View commit details
    Browse the repository at this point in the history

  2. minor

    @hmusta
    hmusta committed Jul 15, 2023
    Configuration menu
    Copy the full SHA
    3ba2a43 View commit details
    Browse the repository at this point in the history

  3. minor

    @hmusta
    hmusta committed Jul 15, 2023
    Configuration menu
    Copy the full SHA
    e5ec2a3 View commit details
    Browse the repository at this point in the history

  4. pass score so far

    @hmusta
    hmusta committed Jul 15, 2023
    Configuration menu
    Copy the full SHA
    337684a View commit details
    Browse the repository at this point in the history

  5. test

    @hmusta
    hmusta committed Jul 15, 2023
    Configuration menu
    Copy the full SHA
    feb72db View commit details
    Browse the repository at this point in the history

  6. fix

    @hmusta
    hmusta committed Jul 15, 2023
    Configuration menu
    Copy the full SHA
    ad16920 View commit details
    Browse the repository at this point in the history

  7. fixes

    @hmusta
    hmusta committed Jul 15, 2023
    Configuration menu
    Copy the full SHA
    1d39d29 View commit details
    Browse the repository at this point in the history

  8. callback full alignments

    @hmusta
    hmusta committed Jul 15, 2023
    Configuration menu
    Copy the full SHA
    b0f463d View commit details
    Browse the repository at this point in the history

  9. fix scoring

    @hmusta
    hmusta committed Jul 15, 2023
    Configuration menu
    Copy the full SHA
    ea16efb View commit details
    Browse the repository at this point in the history

  10. discard chains with short front

    @hmusta
    hmusta committed Jul 15, 2023
    Configuration menu
    Copy the full SHA
    793f5d1 View commit details
    Browse the repository at this point in the history

  11. only consider chains if they're better than input alignments

    @hmusta
    hmusta committed Jul 15, 2023
    Configuration menu
    Copy the full SHA
    4943979 View commit details
    Browse the repository at this point in the history

Commits on Jul 16, 2023

  1. fewer suffix ranges

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    f39e03f View commit details
    Browse the repository at this point in the history

  2. fixes

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    a186a3d View commit details
    Browse the repository at this point in the history

  3. lots of fixes

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    41279d0 View commit details
    Browse the repository at this point in the history

  4. fixes

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    51ef02c View commit details
    Browse the repository at this point in the history

  5. better filtering

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    f2e5b74 View commit details
    Browse the repository at this point in the history

  6. more filtering

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    2d2400b View commit details
    Browse the repository at this point in the history

  7. update repos before starting CI workflow

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    00e6615 View commit details
    Browse the repository at this point in the history

  8. remove redundant checks

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    54b76ef View commit details
    Browse the repository at this point in the history

  9. only connect chains with subsets of labels

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    e238a24 View commit details
    Browse the repository at this point in the history

  10. remove redundant

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    1d493d7 View commit details
    Browse the repository at this point in the history

  11. fix another corner case

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    678469c View commit details
    Browse the repository at this point in the history

  12. put chains at the front

    @hmusta
    hmusta committed Jul 16, 2023
    Configuration menu
    Copy the full SHA
    c64bfc4 View commit details
    Browse the repository at this point in the history

Commits on Jul 17, 2023

  1. keep adding chains as long as a label is extended

    @hmusta
    hmusta committed Jul 17, 2023
    Configuration menu
    Copy the full SHA
    d4b5535 View commit details
    Browse the repository at this point in the history

  2. fix corner case

    @hmusta
    hmusta committed Jul 17, 2023
    Configuration menu
    Copy the full SHA
    89b37b8 View commit details
    Browse the repository at this point in the history

  3. Merge remote-tracking branch 'origin/master' into hm/aln_alt

    @hmusta
    hmusta committed Jul 17, 2023
    Configuration menu
    Copy the full SHA
    cbe9410 View commit details
    Browse the repository at this point in the history

Commits on Jul 18, 2023

  1. fixes for handling label diffs

    @hmusta
    hmusta committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    93dc25c View commit details
    Browse the repository at this point in the history

  2. chain one label at a time

    @hmusta
    hmusta committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    bd675cd View commit details
    Browse the repository at this point in the history

  3. filter chains before constructing them

    @hmusta
    hmusta committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    32b2949 View commit details
    Browse the repository at this point in the history

  4. cleanup

    @hmusta
    hmusta committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    65b691d View commit details
    Browse the repository at this point in the history

  5. chain per label

    @hmusta
    hmusta committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    ee5f386 View commit details
    Browse the repository at this point in the history

  6. better seed merging

    @hmusta
    hmusta committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    12065ec View commit details
    Browse the repository at this point in the history

  7. fix compilation error

    @hmusta
    hmusta committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    df970ae View commit details
    Browse the repository at this point in the history

  8. merge identical chains, fold in their labels

    @hmusta
    hmusta committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    5a43e58 View commit details
    Browse the repository at this point in the history

Commits on Jul 19, 2023

  1. merge identical chains if they have no labels

    @hmusta
    hmusta committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    d11da11 View commit details
    Browse the repository at this point in the history

  2. don't apply the seed complexity filter to k-length seeds

    @hmusta
    hmusta committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    b2d36e6 View commit details
    Browse the repository at this point in the history

  3. don't prematurely discard seeds if low coverage

    @hmusta
    hmusta committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    7ec7a30 View commit details
    Browse the repository at this point in the history

  4. clean up suffix seeding

    @hmusta
    hmusta committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    f5b6f09 View commit details
    Browse the repository at this point in the history

  5. cleaned up suffix seeding

    @hmusta
    hmusta committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    59fa85a View commit details
    Browse the repository at this point in the history

  6. extra check

    @hmusta
    hmusta committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    0ca80c7 View commit details
    Browse the repository at this point in the history

  7. fix test

    @hmusta
    hmusta committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    2816905 View commit details
    Browse the repository at this point in the history

  8. fix seed complexity check

    @hmusta
    hmusta committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    e69d7d3 View commit details
    Browse the repository at this point in the history

  9. fix complexity checking on rc strand

    @hmusta
    hmusta committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    1381823 View commit details
    Browse the repository at this point in the history

  10. fix annotation fetching on CANONICAL mode graphs

    @hmusta
    hmusta committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    72ab02f View commit details
    Browse the repository at this point in the history

Commits on Jul 24, 2023

  1. change default seed length back to 19

    @hmusta
    hmusta committed Jul 24, 2023
    Configuration menu
    Copy the full SHA
    eb0b609 View commit details
    Browse the repository at this point in the history

Commits on Jul 28, 2023

  1. Merge branch 'master' into hm/aln_alt

    @hmusta
    hmusta committed Jul 28, 2023
    Configuration menu
    Copy the full SHA
    2b3a748 View commit details
    Browse the repository at this point in the history

  2. fix

    @hmusta
    hmusta committed Jul 28, 2023
    Configuration menu
    Copy the full SHA
    a0d4281 View commit details
    Browse the repository at this point in the history

Commits on Aug 24, 2023

  1. fix

    @hmusta
    hmusta committed Aug 24, 2023
    Configuration menu
    Copy the full SHA
    220e388 View commit details
    Browse the repository at this point in the history

Commits on Sep 7, 2023

  1. minor

    @hmusta
    hmusta committed Sep 7, 2023
    Configuration menu
    Copy the full SHA
    1c070d1 View commit details
    Browse the repository at this point in the history

  2. fix for coordinates

    @hmusta
    hmusta committed Sep 7, 2023
    Configuration menu
    Copy the full SHA
    d5f4026 View commit details
    Browse the repository at this point in the history

  3. for now, disable some checks

    @hmusta
    hmusta committed Sep 7, 2023
    Configuration menu
    Copy the full SHA
    0e934a8 View commit details
    Browse the repository at this point in the history

  4. put vscode in gitignore

    @hmusta
    hmusta committed Sep 7, 2023
    Configuration menu
    Copy the full SHA
    d1fc8c4 View commit details
    Browse the repository at this point in the history

  5. minor cleanup

    @hmusta
    hmusta committed Sep 7, 2023
    Configuration menu
    Copy the full SHA
    96a875c View commit details
    Browse the repository at this point in the history

  6. minor

    @hmusta
    hmusta committed Sep 7, 2023
    Configuration menu
    Copy the full SHA
    2684005 View commit details
    Browse the repository at this point in the history

  7. fewer checks in debug mode

    @hmusta
    hmusta committed Sep 7, 2023
    Configuration menu
    Copy the full SHA
    5bb30fd View commit details
    Browse the repository at this point in the history

Commits on Sep 8, 2023

  1. remove superfluous asserts

    @hmusta
    hmusta committed Sep 8, 2023
    Configuration menu
    Copy the full SHA
    5705309 View commit details
    Browse the repository at this point in the history