Skip to content

Port row_diff_traverse from DBGSuccinct #512

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
Open
wants to merge 84 commits into
base: master
Choose a base branch
from
Open

Port row_diff_traverse from DBGSuccinct #512

wants to merge 84 commits into from

Conversation

hmusta
Copy link
Collaborator

@hmusta hmusta commented Mar 13, 2025

No description provided.

adamant-pwn and others added 30 commits August 9, 2024 04:38
@adamant-pwn
Add row_diff_traverse, row_diff_successor
f2e15e4
@adamant-pwn
Update, propagate to DBGSuccinct
f3fb0b0
@adamant-pwn
Use graph::DeBruijnGraph in build_pred_succ and assign_anchors
d7878bf
@adamant-pwn
Update download-artifact
3da66a9
@adamant-pwn @hmusta
Apply suggestions from code review
3a16332 
Co-authored-by: Harun Mustafa <[email protected]>
@adamant-pwn
Merge master to rowdiff (#504)
76b29b7 
* Update download-artifact

* Touch commit for workflows

* Update upload-artifact to @v4

* Own artifact name for _noAVX
@adamant-pwn
Try simplifying build_pred_succ, temporarily rollback to graph.get_la…
3a9f1c6 
…st()->size()
@adamant-pwn
Special handling of last.size()
b18d463
@adamant-pwn
Use last instead of rd_succ if it's empty
629cb09
@adamant-pwn
Add checks to fix integration tests
71c19a1
@adamant-pwn
Use BOSS index space in DBGSuccinct
90abc08
@adamant-pwn
override final for call_nodes + add select/rank node + some fixes
f019a05
@adamant-pwn
num_nodes() -> max_index() for dbg_succ_
358e445
@adamant-pwn
Add is_valid checks to nodes in DBGSuccinct
1068116
@adamant-pwn
Fix DBGSuccinct tests
42707ff
@adamant-pwn
Fix AnnotatedDBG test group
a49f07f
@adamant-pwn
Fix RowDiff tests
68dd5f5
@adamant-pwn
Return npos in certain callbacks for dummy nodes
ee0c4a8
@adamant-pwn
Validate edges on BOSS edge -> DBG node transition
a46f6a4
@adamant-pwn
More validate_edge checks
60851da
@adamant-pwn
Use is_valid in adjacent_outgoing_rc_strand
91ea56f
@adamant-pwn
Fix identation + annotations without succ
1976be1
@adamant-pwn
Fix RowDiff test
4e971da
@adamant-pwn
Move get_last, row_diff_traverse, row_diff_successor into row_diff_bu…
7737e26 
…ilder
@adamant-pwn
Preserve lifetime of get_last
04740f1
@adamant-pwn
Fix integration tests
e2347d6
@adamant-pwn
Fix integration tests + return dict in _get_stats
94e9f90
@adamant-pwn
Apply review suggestions
3bc714d
@adamant-pwn
Use valid_edges_->call_ones
3a87651
@adamant-pwn
Use RowDiff with DBGHashFast
9ed4bfd
hmusta added 24 commits February 10, 2025 22:40
@hmusta
multithreaded dbg succinct call_nodes
9b5c019
@hmusta
fix integration test
85750c3
@hmusta
fix
32849af
@hmusta
multithreaded call_nodes on masked graphs
798d0d2
@hmusta
compile on mac
9008f56
@hmusta
disable old DBGSuccinct check when loading rowdiff
58e28d5
@hmusta
Merge remote-tracking branch 'origin/master' into rowdiff
6807a50
@hmusta
Merge remote-tracking branch 'origin/rowdiff' into rowdiff-2
2b2518b
@hmusta
Merge remote-tracking branch 'origin/master' into rowdiff
99f726f
@hmusta
Merge branch 'rowdiff' into rowdiff-2
21864c4
@hmusta
Merge remote-tracking branch 'origin/master' into rowdiff
1e128a5
@hmusta
Merge branch 'rowdiff' into rowdiff-2
8cb9227
@hmusta
fix DBGSuccinct::call_nodes and RowDiff::get_columns
e57c4a5
@hmusta
fix bug where some dummy k-mers were marked as RowDiff termini
ee204b1
@hmusta
port row_diff_traverse from DBGSuccinct
fc1cf3c
@hmusta
DeBruijnGraph::in_graph
bd994d5
@hmusta
Merge branch 'rowdiff' into rowdiff-2
3cbfe34
@hmusta
revert
a0112be
@hmusta
extra check
f522249
@hmusta
don't set dummy k-mers as anchors
7f2d4bc
@hmusta
this works
b0e88fe
@hmusta
minor
c98716a
@hmusta
Merge remote-tracking branch 'origin/rowdiff' into rowdiff-2
c0730e0
@hmusta
fixes
6ecef56
@hmusta hmusta marked this pull request as draft March 14, 2025 20:35
@hmusta hmusta marked this pull request as ready for review March 16, 2025 13:00
Base automatically changed from rowdiff-2 to master March 21, 2025 07:24
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@hmusta @adamant-pwn