ksahlin strobealign issues

ksahlin / strobealign

Aligns short reads using dynamic seed size with strobemers

MIT License

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issues

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Switch to multi-context seeds hash function

#447 marcelm opened 1 hour ago
0
Rename Hit struct to Match

#446 marcelm opened 2 hours ago
0
Add make_randstrobe function

#445 marcelm closed 2 hours ago
0
Add operator<< for Cigar and Alignment

#444 marcelm closed 2 hours ago
0
Add samtools to conda install command

#443 marcelm closed 5 days ago
1
command line syntax

#442 jtamames closed 5 days ago
7
Explain that all best mapping locations are counted with --aemb, contrast to alignment mode

#441 marcelm closed 1 week ago
1
Missing alignment

#440 yazhinia closed 2 weeks ago
2
Do not compile unused.cpp

#439 marcelm closed 2 weeks ago
1
Add some diagnostics

#438 marcelm closed 4 hours ago
9
Reconsider the has_shared_substring heuristic

#437 marcelm opened 4 weeks ago
0
Start indexing while still reading the reference

#436 marcelm opened 1 month ago
0
vCPU Utilization ~33% ( and GIAB Concordance Work )

#435 iamh2o opened 1 month ago
8
Fix index construction statistics

#434 Itolstoganov closed 4 days ago
2
All secondary alignments lost

#433 tprodanov opened 2 months ago
7
Question about columns in PAF output

#432 W-L closed 2 months ago
1
Multiple mapping

#431 yazhinia opened 2 months ago
4
Mapping accuracy: --aemb vs -x vs base-level alignment

#430 jakobnissen closed 2 months ago
2
Closed syncmers with lower density

#429 Daniel-Liu-c0deb0t opened 3 months ago
1
Make Python bindings work with nanobind 2+

#428 marcelm closed 3 months ago
1
Add a debugging compilation option for showing list of NAMs

#427 marcelm closed 3 months ago
1
Multi-context seeds plus fixes and optimized parameters

#426 marcelm opened 4 months ago
15
Fix: Do not report failed alignments

#425 marcelm closed 4 months ago
2
Entries of the unaligned

#424 u-xixi closed 4 months ago
2
Optimized parameters for multi-context seeds

#423 marcelm opened 5 months ago
6
Test multi-block gzip files as input

#422 marcelm closed 5 months ago
0
strobealign: Too many reference sequences.

#421 lfdelzam opened 5 months ago
3
Explore using Block Aligner for extension and global DP alignment

#420 Daniel-Liu-c0deb0t opened 5 months ago
2
Do more hamming distance attempts?

#419 ksahlin opened 5 months ago
0
Decompress with ISA-L

#418 marcelm closed 4 weeks ago
19
Support for both open and closed syncmers

#417 ksahlin opened 5 months ago
0
Lower bounding w_min to 1 instead of 0?

#416 ksahlin opened 5 months ago
0
Joining nearby NAMs for combined score

#415 ksahlin opened 6 months ago
1
Skip to compute merge_hits_into_nams_forward_and_reverse if nonrepetitive_fraction above threshold

#414 ksahlin opened 6 months ago
0
Shuffle identical alignments pseudo-randomly on query name instead?

#413 ksahlin opened 6 months ago
0
Get rid of the last compiler warning

#412 marcelm closed 6 months ago
0
Better fix for #409

#411 drtconway closed 6 months ago
2
Add a fix for #409

#410 drtconway closed 6 months ago
0
Invalid @SQ header

#409 drtconway closed 6 months ago
2
end-to-end alignment with strobalign?

#408 fplazaonate closed 6 months ago
1
Optimize parameters (again)

#407 marcelm opened 6 months ago
4
Huge pages on Linux

#406 marcelm closed 6 months ago
0
Experiment: Asymmetric randstrobe hashes

#405 marcelm opened 6 months ago
6
Make --aemb work with -o

#404 marcelm closed 6 months ago
1
Set default number of threads to 1

#403 marcelm closed 6 months ago
3
Version 0.13.0

#402 marcelm closed 7 months ago
0
Change default number of threads

#401 marcelm closed 6 months ago
1
Fix StrobemerIndex.find() in Python bindings

#400 marcelm closed 7 months ago
0
Support end-to-end alignments?

#399 y9c opened 7 months ago
10
Make index creation deterministic

#398 marcelm closed 7 months ago
1