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Martinsos
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edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
http://martinsos.github.io/edlib
MIT License
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Idea: share working memory among edlibAlign() calls
#78
Martinsos
opened
7 years ago
3
Make Edlib faster for shorter sequences
#77
Martinsos
opened
7 years ago
7
Improve how testing is done
#76
Martinsos
opened
7 years ago
3
null pointer dereference and segfault in edlibAlign()
#75
geeknik
closed
7 years ago
2
segfault in edlibAlign()
#74
geeknik
closed
7 years ago
6
heap-buffer-overflow in transformSequences()
#73
geeknik
closed
7 years ago
1
heap-buffer-overflow in myersCalcEditDistanceNW()
#72
geeknik
closed
7 years ago
2
stack-buffer-overflow in transformSequences()
#71
geeknik
closed
7 years ago
1
Allow constrained pairwise alignment
#70
rob-p
opened
7 years ago
6
Publish python module on new release automatically.
#69
Martinsos
closed
3 years ago
1
Add table of content README
#68
Martinsos
closed
7 years ago
1
Publish new doxygen docs on new release automatically (Travis CI)
#67
Martinsos
opened
7 years ago
2
Adding feaure to get alignment format (-f NICE) to python?
#66
ksahlin
closed
7 years ago
2
modifications directory paths
#65
ksahlin
closed
7 years ago
1
Installation error with pip
#64
ksahlin
closed
7 years ago
7
Travis: confirm that Python binding builds and works.
#63
Martinsos
closed
7 years ago
1
Provide speed information in README
#62
Martinsos
opened
7 years ago
2
Make edlib usable in Python
#61
Martinsos
closed
7 years ago
4
Idea to significantly speed up the tests
#60
Martinsos
opened
7 years ago
0
Mismatched free() / delete[]
#59
isovic
closed
7 years ago
5
Refactor alignment traceback
#58
Martinsos
opened
7 years ago
0
Wrong CIGAR op in alignment - 1X instead of 1=
#57
isovic
closed
7 years ago
2
Make aligner work on windows
#56
Martinsos
closed
7 years ago
1
Add estimation of edit distance
#55
Martinsos
opened
7 years ago
0
Consider adding an overlap alignment mode
#54
sjackman
closed
7 years ago
4
Move node-edlib code here
#53
Martinsos
closed
3 years ago
1
aligner: Add SAM output format
#52
sjackman
opened
8 years ago
2
aligner: Consider adding characters to show the locations of matches/mismatches
#51
sjackman
closed
8 years ago
2
Name of aligner is too generic
#50
sjackman
closed
8 years ago
2
Replace #defines in edlib.h with enumerations
#49
Martinsos
opened
8 years ago
1
Add more examples in README
#48
Martinsos
closed
7 years ago
1
Document API
#47
Martinsos
closed
8 years ago
1
Add a Gitter chat badge to README.md
#46
gitter-badger
closed
8 years ago
0
Edlib could be faster if starting with bigger k for unsimilar sequences in HW mode
#45
Martinsos
closed
7 years ago
1
Make it easier to prepare sequences for usage
#44
Martinsos
closed
8 years ago
1
Runtime error
#43
hiraksarkar
closed
8 years ago
21
Add progress callback
#42
Martinsos
closed
7 years ago
1
Add helper function for reading fasta files to library
#41
Martinsos
closed
7 years ago
1
Hirschberg
#40
Martinsos
closed
8 years ago
1
Check that allocation of memory is successful
#39
Martinsos
opened
9 years ago
0
Validate function input
#38
Martinsos
opened
9 years ago
2
Segfault because of unsanitazed function parameters
#37
isovic
opened
9 years ago
5
Remove bool from interface
#36
Martinsos
closed
8 years ago
1
Unify all output parameters into one parameter
#35
Martinsos
closed
8 years ago
1
Enable passing NULL for outputs that are not needed
#34
Martinsos
closed
9 years ago
1
Separate code into aligner and library
#33
Martinsos
closed
8 years ago
1
Sometimes alignments start/end with insertions
#32
Martinsos
closed
9 years ago
2
Enable stating that sequence should be consumed in reverse
#31
Martinsos
closed
8 years ago
1
Obtain alignment path for certain best position
#30
Martinsos
opened
9 years ago
0
Return starting position of alignment (but no alignment path)
#29
Martinsos
closed
9 years ago
1
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