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OndrejSladky
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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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Suboptimal C++ string handling degrades the performance of Ahomaton-based algs
#35
karel-brinda
closed
1 year 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
2 months 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
Added rule for tests in Makefile.
#24
GordonHoklinder
closed
1 year ago
1
Greedy with complements
#23
GordonHoklinder
closed
1 year ago
0
gtest.h is missing from the repo
#22
karel-brinda
closed
1 year ago
0
Added pragma once and changed extensions to .h
#21
GordonHoklinder
closed
1 year ago
0
Add the "pragma once" directive to header files to avoid multiple inclusions by C++ preprocessor
#20
karel-brinda
closed
1 year ago
0
Make a proper Make rule for kmers
#19
karel-brinda
closed
1 year ago
0
Optional reading from standard input in Python scripts
#18
karel-brinda
closed
1 year ago
7
Reading FASTA in Python
#17
karel-brinda
closed
1 year ago
3
Use kseq for parsing FASTA
#16
GordonHoklinder
closed
1 year ago
1
Testing should be included in the make file
#15
karel-brinda
closed
1 year ago
6
Files that are included using C/C++ preprocessor should have the `.h` suffixes
#14
karel-brinda
closed
1 year ago
0
Basic verification
#13
GordonHoklinder
closed
1 year ago
2
Created fasta file reader.
#12
GordonHoklinder
closed
1 year ago
4
Improvements in help
#11
GordonHoklinder
closed
1 year ago
0
Default argument values should be printed in the help message
#10
karel-brinda
closed
1 year ago
0
Script for converting masked superstring k-mer set representation.
#9
GordonHoklinder
closed
1 year ago
3
Parsing lowercase and unknown characters.
#8
GordonHoklinder
closed
1 year ago
8
std::invalid_argument: cannot convert letter
#7
karel-brinda
closed
1 year ago
1
Fixed error with exiting after first record.
#6
GordonHoklinder
closed
1 year ago
3
Using fixed width integers for k-mer hashing.
#5
GordonHoklinder
closed
1 year ago
2
Verify output correctness using a kmer counter (eg JellyFish)
#4
karel-brinda
closed
1 year ago
0
The results don't seem to be correct
#3
karel-brinda
closed
1 year ago
5
Better to use (u)intX_t for integer data types
#2
karel-brinda
closed
1 year ago
0
Parse cli args using some standard library
#1
karel-brinda
closed
1 year ago
1
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