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

Support for flow based sequencing #7876

Merged
merged 46 commits into from
Jul 26, 2022
Merged

Support for flow based sequencing #7876

merged 46 commits into from
Jul 26, 2022

Commits on Jul 22, 2022

  1. Squashed changes brought in by flow based support

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    3bc069d View commit details
    Browse the repository at this point in the history

  2. MERGE fixes WIP

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    cd53841 View commit details
    Browse the repository at this point in the history

  3. Merge fixes

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    0ab1477 View commit details
    Browse the repository at this point in the history

  4. Fixed ClipAdapters test that was broken during code refactor

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    1ab0d75 View commit details
    Browse the repository at this point in the history

  5. Output for cram splitter fixed

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    a148f47 View commit details
    Browse the repository at this point in the history

  6. Fixed what seems to be a bug in adding allele to the last base

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    33f7577 View commit details
    Browse the repository at this point in the history

  7. Chances that the Assembly bug is solved

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    82bab71 View commit details
    Browse the repository at this point in the history

  8. Ramp test upated

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    46ec62e View commit details
    Browse the repository at this point in the history

  9. fixed a rebase issue for loop in the readThradingAssembler

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    f821535 View commit details
    Browse the repository at this point in the history

  10. cleaning up mistaken gga code in assembly from rebase

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    5ddb833 View commit details
    Browse the repository at this point in the history

  11. removing failed documenation line from WellbasedFlowBasedReadFilter

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    ce8d3b1 View commit details
    Browse the repository at this point in the history

  12. removing failed documenation line from WellbasedFlowBasedReadFilter

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    e2be5d6 View commit details
    Browse the repository at this point in the history

  13. Fixed an edge case in insertAllele when deleting the edge bases

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    5d705d2 View commit details
    Browse the repository at this point in the history

  14. fixed a very rare edge case in the adaptive chain pruner where the ja… 

    …va priority queue is non-determinsitic (#120)
    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    8cce72c View commit details
    Browse the repository at this point in the history

  15. re-creation of #113 to the correct branch (#122) 

    * Adding tree score threshold to remove low quality sites in reblockGVCF


Co-authored-by: Megan Shand <mshand@broadinstitute.org>
    @ilyasoifer @meganshand @jamesemery
    2 people authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    1e913cf View commit details
    Browse the repository at this point in the history

  16. fixing rebase issue

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    f85c60a View commit details
    Browse the repository at this point in the history

  17. Fixing a bug in allele filtering (#7877) 

    * [BIOIN-519] Looks like the alleles that were worse than the reference were not ordered correctly

* Tests updated
    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    e433e15 View commit details
    Browse the repository at this point in the history

  18. Test fix

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    ddfa3f5 View commit details
    Browse the repository at this point in the history

  19. Ramped tests updated

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    de2035f View commit details
    Browse the repository at this point in the history

  20. temporary fix

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    6fc79b9 View commit details
    Browse the repository at this point in the history

  21. Reverted test

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    c65b47a View commit details
    Browse the repository at this point in the history

  22. Fixed data files

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    1737bba View commit details
    Browse the repository at this point in the history

  23. slightly improving the error message for this zip utility

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    b3e418a View commit details
    Browse the repository at this point in the history

  24. Fixed the Zip comaprison to hopefully be agnostic to filecompression

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    5459af0 View commit details
    Browse the repository at this point in the history

  25. updating the test hopefully one last time

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    9253917 View commit details
    Browse the repository at this point in the history

  26. i have no idea why the index bytes mismatch inside of the zip file so… 

    …metimes...
    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    6a19613 View commit details
    Browse the repository at this point in the history

  27. Lookahead Covariates moved to UG_feature_branch

    @dror27 @jamesemery
    dror27 authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    3ce718d View commit details
    Browse the repository at this point in the history

  28. (post filter) read transformers can be added on command line

    @dror27 @jamesemery
    dror27 authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    64990d2 View commit details
    Browse the repository at this point in the history

  29. Quality and attribute mappers

    @dror27 @jamesemery
    dror27 authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    4a990c0 View commit details
    Browse the repository at this point in the history

  30. Revert "Quality and attribute mappers" 

    This reverts commit afc11d7.
    @dror27 @jamesemery
    dror27 authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    a285cee View commit details
    Browse the repository at this point in the history

  31. Revert "(post filter) read transformers can be added on command line" 

    This reverts commit 386e1e6.
    @dror27 @jamesemery
    dror27 authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    0038bb2 View commit details
    Browse the repository at this point in the history

  32. throwing in the towel

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    efe28a3 View commit details
    Browse the repository at this point in the history

  33. more random bits

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    8df983e View commit details
    Browse the repository at this point in the history

  34. a cudgle to fix the memory

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    cf5c0ce View commit details
    Browse the repository at this point in the history

  35. fixed the zip test and added a utility to unzip archives to files

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    3135494 View commit details
    Browse the repository at this point in the history

  36. annoying test

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    8baee5c View commit details
    Browse the repository at this point in the history

  37. SplitCRAM: limit number of output shards

    @dror27 @jamesemery
    dror27 authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    a6f439f View commit details
    Browse the repository at this point in the history

  38. PR fixes

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    70463ba View commit details
    Browse the repository at this point in the history

  39. DK PR Changes 

    NonRandomReplacementMode test added

nonRandomDownsamplingMode turned into override method

PartialReadWalker example and test added

FlowBasedTPAttributeSymetricReadFilter unit test

CalculateAverageCombinedAnnotations included in command line

FlowBasedAlignmentArgumentCollection moved

getFlowMatrixModsInstructions moved to utils class

remove use of explicit string

FlowAnnotatorUnitTest extends GATKBaseTest

new flow annotation doc

dragen and flow mode are mutually exclusive

string literal removed
    @dror27 @jamesemery
    dror27 authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    4b29a5f View commit details
    Browse the repository at this point in the history

  40. PR comments

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    862bbe7 View commit details
    Browse the repository at this point in the history

  41. PR comments

    @ilyasoifer @jamesemery
    ilyasoifer authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    d3c7cf4 View commit details
    Browse the repository at this point in the history

  42. adding documentation for RawGtCount

    @meganshand @jamesemery
    meganshand authored and jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    e8926ea View commit details
    Browse the repository at this point in the history

  43. removed cloudbuild.yml

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    cc670d2 View commit details
    Browse the repository at this point in the history

  44. resolving various issues from the code review comments

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    1c8d481 View commit details
    Browse the repository at this point in the history

  45. added documented feature to the new flow based read filters

    @jamesemery
    jamesemery committed Jul 22, 2022
    Configuration menu
    Copy the full SHA
    cd5bd81 View commit details
    Browse the repository at this point in the history

Commits on Jul 23, 2022

  1. Revert "Lookahead Covariates moved to UG_feature_branch" 

    This reverts commit 3ce718d.
    @dror27
    dror27 committed Jul 23, 2022
    Configuration menu
    Copy the full SHA
    825a63f View commit details
    Browse the repository at this point in the history