OndrejSladky kmercamel issues

OndrejSladky / kmercamel

KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.

MIT License

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issues

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KmerCamel supports k up to 127.

#74 OndrejSladky opened 10 hours ago
0
Include large KmerCamel

#73 OndrejSladky closed 11 hours ago
0
Refactoring AC code to a separate directory to simplify code structure.

#72 GordonHoklinder closed 11 hours ago
0
Draft: Improvements in parser

#71 OndrejSladky closed 1 week ago
0
Runs bug

#70 PavelVesely closed 6 months ago
0
Minimization of number of ones can optionally skip the ILP part.

#69 OndrejSladky closed 6 months ago
0
KmerCamel can compute lower bounds on superstring lengths.

#68 OndrejSladky opened 6 months ago
2
Revert "KmerCamel can compute lower bounds on superstring lengths."

#67 OndrejSladky closed 6 months ago
0
Optimizing the number of runs approximately without running the ILP

#66 PavelVesely closed 6 months ago
3
output of mask optimization is not FASTA

#65 PavelVesely closed 6 months ago
5
Different hashing for k-mers

#64 OndrejSladky closed 7 months ago
3
Fix compilation on OS X with M1

#63 karel-brinda closed 7 months ago
0
Compilation doesn't work on OS X with M1 because of different brew paths

#62 karel-brinda closed 7 months ago
2
KmerCamel can minimize number of runs of ones.

#61 OndrejSladky closed 7 months ago
2
KmerCamel can optimize masks.

#60 OndrejSladky closed 7 months ago
0
KmerCamel can compute lower bounds on superstring lengths.

#59 OndrejSladky closed 6 months ago
3
Added flag for turning off the memory optimizations

#58 OndrejSladky closed 7 months ago
0
Support for k-mers with 31 < k < 64

#57 OndrejSladky closed 7 months ago
0
Project cleanup and reorganization

#56 OndrejSladky closed 7 months ago
0
Using khash in parsing and in local

#55 OndrejSladky closed 7 months ago
0
Put unittests into a separate folder

#54 OndrejSladky closed 7 months ago
1
Use khash in local

#53 OndrejSladky closed 7 months ago
0
Use khash in parser

#52 OndrejSladky closed 7 months ago
0
Add support for larger k-mers

#51 OndrejSladky closed 7 months ago
0
Optimized local

#50 OndrejSladky closed 8 months ago
0
More systematic printing of version and not requiring git

#49 OndrejSladky closed 10 months ago
0
Improved help in convert_superstring

#48 OndrejSladky closed 8 months ago
3
convert_superstring.py

#47 karel-brinda closed 8 months ago
0
Version

#46 OndrejSladky closed 10 months ago
7
Versioning

#45 karel-brinda closed 10 months ago
1
Add general support for parsing .gz files

#44 karel-brinda closed 1 week ago
3
The program cannot read from stdin

#43 karel-brinda closed 1 week ago
0
The example in the program info doesn't work

#42 karel-brinda closed 10 months ago
1
Global algorithm performance improvements

#41 OndrejSladky closed 11 months ago
0
[convert_superstring] Optional reading masked superstring from file

#40 OndrejSladky closed 11 months ago
0
Update README.md

#39 PavelVesely closed 1 year ago
1
Performance improvements

#38 GordonHoklinder closed 11 months ago
0
CLI flags for algorithms renamed.

#37 GordonHoklinder closed 1 year ago
1
AC optimization (reading fasta using kseq.h & slightly improved re-allocations)

#36 GordonHoklinder closed 1 year ago
1
Suboptimal C++ string handling degrades the performance of Ahomaton-based algs

#35 karel-brinda closed 10 months ago
7
Kmercamel should fail when non-sense parameters are used

#34 karel-brinda closed 1 year ago
2
Streaming algorithm

#33 GordonHoklinder closed 1 year ago
0
Create ci.yml

#32 GordonHoklinder closed 1 year ago
0
Cleanup

#31 GordonHoklinder closed 1 year ago
0
Pseudosimplitigs and GREEDY with AC support complements

#30 GordonHoklinder closed 1 year ago
0
Removed time from output fasta header.

#29 GordonHoklinder closed 1 year ago
0
computation is not reproducible even on the same computer

#28 karel-brinda closed 1 year ago
1
make test: ValueError: not enough values to unpack (expected 2, got 0)

#27 karel-brinda closed 11 hours ago
3
error: use of undeclared identifier 'get_current_dir_name'

#26 karel-brinda closed 1 year ago
1
Greedy should now consume less memory

#25 GordonHoklinder closed 1 year ago
0