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Port row_diff_traverse from DBGSuccinct #512

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Port row_diff_traverse from DBGSuccinct #512

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@hmusta hmusta commented Mar 13, 2025

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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
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3 participants

@hmusta @adamant-pwn