isovic / edlib

C/C++ library for sequence alignment using edit distance based on Myers's "Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming"

EDLIB

EDLIB is C/C++ library for sequence alignment using edit distance based on Myers's "Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming".
Implementation combines Myers's bit-vector algorithm with banded approach.
Calculates best score (Levenshtein distance) and all positions of best score. It can also return alignment path, or only starting locations of alignment.

Nodejs

For those who want to use edlib in nodejs there is a nodejs addon, node-edlib!

Alignment modes

There are 3 different modes of alignment:

• NW: Global alignment (Needleman-Wunsch). Appropriate for aligning two sequences of similar length.
• SHW: Semi-global alignment. Gap at query end is not penalized. Appropriate for aligning prefix(query) to sequence(target).
• HW: Semi-global alignment. Gap at query start and gap at query end are not penalized. Appropriate for aligning read(query) to sequence(target) (read is sequence obtained by reading part of larger sequence).

Usage

Include edlib.h in your code and compile it together with myers.cpp.

...
#include "edlib.h"
...

...
int alphabetLength = 9;
int queryLength = 5;
int targetLength = 9;
unsigned char query[5] = {0,1,2,3,4};
unsigned char target[9] = {8,5,0,1,3,4,6,7,5};
int score, numLocations, alignmentLength;
int* startLocations;
int* endLocations;
unsigned char* alignment;

edlibCalcEditDistance(query, queryLength, target, targetLength,
                      alphabetLength, -1, MYERS_MODE_HW, true, true,
                      &score, &endLocations, &startLocations, &numLocations,
                      &alignment, &alignmentLength);

printf("Score %d\n", score);
for (int i = 0; i < numLocations; i++) {
  printf("(%d, %d)\n", startLocations[i], endLocations[i]);
}

if (alignment) {
  for (int i = 0; i < alignmentLength; i++) {
    printf("%d", alignment[i]);
  }
  printf("\n");

  char* cigar;
  edlibAlignmentToCigar(alignment, alignmentLength, EDLIB_CIGAR_EXTENDED, &cigar);
  printf("%s\n", cigar);
  free(cigar);
}

if (endLocations) free(endLocations);
if (startLocations) free(startLocations);
if (alignment) free(alignment);
...

Main function is edlibCalcEditDistance. There is also edlibAlignmentToCigar function, which you can use to convert alignment to cigar format.

For more examples of usage take a look at test.cpp or aligner.cpp.

Running tests

In order to run tests, do following:

cd src
make
./test

Aligner

In order to compile and use simple aligner that uses EDLIB run makefile in src:

cd src
make aligner

Type ./aligner for help.

Example of usage: ./aligner -p ../test_data/query.fasta ../test_data/target.fasta