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OndrejSladky
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fmsi
FMSI is an exact f-masked-superstrings-based index for membership queries and set operations on k-mer sets.
MIT License
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README: include k in the description.
#39
OndrejSladky
closed
5 days ago
0
README: memory requirements.
#38
OndrejSladky
closed
5 days ago
0
README includes info about component files stored.
#37
OndrejSladky
closed
5 days ago
3
FMSI help messages improvements and more robust argument parsing
#36
OndrejSladky
closed
5 days ago
8
Update of README
#35
karel-brinda
closed
6 days ago
0
KmerCamel doesn't need to be included as a submodule
#34
karel-brinda
closed
6 days ago
1
The readme should contain some documentation of the index files, incl. which files are loaded into memory during querying
#33
karel-brinda
closed
5 days ago
0
In version 0.3.0, if klcp not computed && `-s` not used, FMSI doesn't fail (even though it should)
#32
karel-brinda
closed
5 days ago
0
Confused error messages: ./fmsi index` must be run on the provided fasta file beforehand
#31
karel-brinda
closed
5 days ago
1
Memory usage/requirements should be better documented
#30
karel-brinda
closed
5 days ago
1
FMSI should be more verbose
#29
karel-brinda
opened
1 week ago
0
README - better documentation of what FMSI is doing / better failure modes
#28
karel-brinda
closed
5 days ago
0
FMSI is not failing when it should
#27
karel-brinda
closed
5 days ago
0
Chunking in streaming queries in done every sqrt(len) characters.
#26
OndrejSladky
closed
2 weeks ago
0
Loading klcp for query is optional.
#25
OndrejSladky
closed
2 weeks ago
0
Added KmerCamel as a copy to allow deploy on bioconda.
#24
OndrejSladky
closed
3 weeks ago
0
SDSL-lite is integrated as a copy to allow for Bioconda deployment.
#23
OndrejSladky
closed
3 weeks ago
0
Update readme
#22
karel-brinda
closed
1 month ago
0
README more clearly distinguishes which functions are only experimental.
#21
OndrejSladky
closed
1 month ago
0
Restructuring of the documentation
#20
karel-brinda
closed
1 month ago
0
Major FMSI speedup.
#19
OndrejSladky
closed
2 weeks ago
2
Kseq updated to a version from seqtk capable of parsing large inputs.
#18
OndrejSladky
closed
2 months ago
0
Kseq parser updated to work with new version of kseq.
#17
OndrejSladky
closed
2 months ago
0
Fails when reading masked superstrings of length $> 2^{31} = 2147483648$
#16
PavelVesely
closed
2 months ago
6
index: invalid option -- 'k'
#15
PavelVesely
closed
6 months ago
1
Rewrite of the core structure for an order of magnitude speed up
#14
OndrejSladky
closed
6 months ago
0
Add a link to sdsl-lite library
#13
PavelVesely
closed
8 months ago
1
Speeding up queries
#12
PavelVesely
closed
8 months ago
4
Output on a set of queries
#11
PavelVesely
closed
2 weeks ago
0
Merging & normalization
#10
OndrejSladky
closed
9 months ago
0
Computing l-masks from k-masks.
#9
OndrejSladky
closed
1 year ago
0
Add support for different $k$-s
#8
OndrejSladky
closed
1 year ago
0
Add support for different functions
#7
OndrejSladky
closed
1 year ago
0
Representing masks using SDSL bitvectors.
#6
OndrejSladky
closed
1 year ago
1
Fix local sdsl compilation
#5
karel-brinda
closed
1 year ago
5
Working CI
#4
OndrejSladky
closed
1 year ago
0
Infer $k$ from masked superstring if not provided.
#3
OndrejSladky
closed
1 year ago
0
Implement MS-index using SDSL.
#2
OndrejSladky
closed
1 year ago
0
Use bitvectors from SDSL
#1
OndrejSladky
closed
1 year ago
0