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Sshash module superkmer anno #497

Closed
wants to merge 56 commits into from
Closed

Sshash module superkmer anno #497

wants to merge 56 commits into from

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adamant-pwn
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Pull request to track merging of further changes from @mmarzett.

adamant-pwn and others added 30 commits November 6, 2023 15:19
@adamant-pwn
Initial DBGSSHash commit
eca1e79 
Add PTHash submodule, create boilerplate code for DBGSSHash class, add
it to test_dbg_helpers.
@adamant-pwn
Use SSHash submodule instead of PTHash
102bf31
@mmarzett
trying to use sshash as a submodule
5fbbc3a
@mmarzett
fixed index conversion between ssh and metagraph
7ff3382 
and list of contigs
@hmusta
some changes to sshash, first try at avoiding the compile error in ss…
52bb957 
…hash
@mmarzett
changes for unit_test usage
65c5d07
@mmarzett
new sshash version
e6800be
@mmarzett
ignore strict aliasing warning
885ccd3
@mmarzett
using sshash from cli
127ef00
@mmarzett
general path
f21eace
@mmarzett
fixed serialization and loading
49e68cd
@mmarzett
no longer need k.txt file + clean-up
f95b74c
@mmarzett
disabled tests that are incompatible with sshash
7b242cf
@mmarzett
stats changes
955129e
@mmarzett
stats file
d65be03
@mmarzett
added plotting scripts and improved input and output for stats
3245236
@mmarzett
annotate superkmers
6c3df19
@mmarzett
sshash with functions for superkmer mapping
49829df
@mmarzett
fixed minimizer bug
8ad8894
@mmarzett
fixed bug in skew index case
54a8a8e
@mmarzett
added superkmer mask for lossless annotation
2373fb8
@mmarzett
loading/serializing bit vector
88c9fc8
@mmarzett
small fixes
953e3f1
@mmarzett
mapping to kmers
4c9455e
@mmarzett
removed superkmer stats
b522bdc
@mmarzett
changes to decrease superkmer mask runtime
bf74651
@mmarzett
removed unnecessary line
05ff9ab
@mmarzett
getting superkmer label batches
7eec588
@mmarzett
sshash version
e205690
@mmarzett
tiny bug fix
d9b7f0b
mmarzett and others added 21 commits May 2, 2024 00:10
@mmarzett
removed 2 extra lookup calls added during debugging
361408e
@mmarzett
more efficient query for kmers in non-monochromatic superkmers
d6b40ae
@mmarzett
Merge branch 'sshash_module_superkmer_anno' of github.com:ratschlab/m…
69a408d 
…etagraph into sshash_module_superkmer_anno
@mmarzett
removed 2 extra lookup calls added during debugging
46e280d
@mmarzett
changed annotation type for superkmer mask construction
37fbec4
@mmarzett
fixed annotation type
5622357
@mmarzett
sshash both for superkmer bit vec construction and mapping
a2997de
@mmarzett
sshash both for superkmer bit vec construction and mapping
c97f396
@mmarzett
sshash both for superkmer bit vec construction and mapping
ce691b2
@mmarzett
reverse complement bug fix
3e3b885
@mmarzett
returning kmer index during superkmer lookup
e60ab9f
@mmarzett
use npos
6f39143
@mmarzett
Merge branch 'sshash_module_kmer_anno' into sshash_module_superkmer_anno
e399df9
@mmarzett
Merge branch 'sshash_module_lossy_superkmer_anno' into sshash_module_…
afca9e7 
…superkmer_anno
@mmarzett
annotation modus given by flag
3da03ad
@mmarzett
added stats
8a23844
@mmarzett
clean-up
7195300
@mmarzett
plotting and stats scripts updated
5b251ad
@adamant-pwn
Merge branch 'sshash_module_superkmer_anno'
c2c8030
@adamant-pwn
Don't disable tests for sshash
efce431
@adamant-pwn
Don't disable tests for sshash
4f86936
@adamant-pwn adamant-pwn requested a review from hmusta July 25, 2024 15:04
@adamant-pwn
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Also see ratschlab/sshash#10 for related changes in sshash repo.

@adamant-pwn adamant-pwn mentioned this pull request Jul 25, 2024
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@hmusta
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hmusta commented Oct 8, 2024 •
edited
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As mentioned during a previous meeting, I think annotating based on monotigs (monochromatic contigs) makes more sense. I've started an implementation at #500. Are there any fixes from the sshash library used here that we should port over there?

@adamant-pwn
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I'm not very familiar with this branch, and my fixes mostly were to properly merge changes from #481 into it and make sure it still compiles and passes current tests. Is #500 implemented fully from scratch without relying on the content of this branch? If so, we can drop this branch, I suppose.

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hmusta commented Oct 8, 2024

I'm not very familiar with this branch, and my fixes mostly were to properly merge changes from #481 into it and make sure it still compiles and passes current tests. Is #500 implemented fully from scratch without relying on the content of this branch? If so, we can drop this branch, I suppose.

Yes, it's implemented from scratch. So I'll close this.

@hmusta hmusta closed this Oct 8, 2024
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3 participants
@adamant-pwn @hmusta @mmarzett