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First public release #34

Merged
merged 44 commits into from
Nov 18, 2024
Merged

First public release #34

merged 44 commits into from
Nov 18, 2024

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tmaklin
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@tmaklin tmaklin commented Nov 18, 2024

  • Rename to kbo
  • Add crate level documentation.
  • Add gapped alignment to find.
  • Return results as an RLE object from find.
  • Build index in memory by default using the new bpks-mem feature in sbwt v0.3.4.
  • Remove CLI from this repository (will move to a new kbo-cli repo).
  • Minor bug fixes.

tmaklin added 30 commits October 31, 2024 20:30
@tmaklin
Rename sablast to kbo.
a3bb32a
@tmaklin
Tabs -> spaces in refine_translation.
150ff68
@tmaklin
Remove unused import.
95eba77
@tmaklin
Add doc tests for relative_to_ref (1/2 pass).
8e89ea0
@tmaklin
Resolve TODO question (A: works with any).
c3166fc
@tmaklin
Add initial crate documentaiton.
6bc7018
@tmaklin
Restructure read_from_fastx_parser
2a9b1cd
@tmaklin
Rewrite find (allow processign contigs separately)
d35eebc
@tmaklin
Add --detailed to process ref contigs separately.
61c8b25
@tmaklin
Process everything before printing in Find.
def0416
@tmaklin
Add --min-len to filter short alignmentes.
55ecadb
@tmaklin
Update needletail to v0.6.0, enable gz compression
1dee6f0
@tmaklin
Fix test (see #31).
2859d0a
@tmaklin
Return run_lengths as new RLE struct.
3ae23ed
@tmaklin
Use the new RLE return type in find.
3daea1b
@tmaklin
Update run_lengths return type documentation.
0e36001
@tmaklin
Add function to extract gapped run length encoding
e702fcc
@tmaklin
Add gapped run length encodings to find().
3d9a57c
@tmaklin
Move the derandomize opts to lib.rs, differentiate
d064a8e
@tmaklin
Add gapped alignment to CLI.
984e140
@tmaklin
Tabs -> spaces.
d839eee
@tmaklin
Document 2/3 use cases for find.
cfe0ea9
@tmaklin
Fix processing queries with multiple contigs.
90a5016
@tmaklin
Add the last example to find.
18e7a05
@tmaklin
Add example to kbo map.
a22c30f
@tmaklin
Add identity and coverage computation to find.
10bf565
@tmaklin
Update sbwt to 0.3.4.
67fc71b
@tmaklin
Print number of gap opens.
0342b0a
@tmaklin
Use local thread pools for rayon.
9760520
@tmaklin
Enable bitpacked k-mer sorting in memory.
f0dc445
tmaklin
tmaklin commented Nov 18, 2024
View reviewed changes
src/format.rs Outdated Show resolved Hide resolved
@tmaklin tmaklin merged commit 102a2e3 into main Nov 18, 2024
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