overlap (semi global) end alignment for two fasta files
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2.3 years ago

Hi there,

I need to find overlaps (semi global alignment) between ends of two strings (two fasta sequences), for that I tried edlib library for c++ but its output is a bit confusing like:

char* query = "AATACTC";
char* target = "ACTCTGAAA";
EdlibAlignResult result = edlibAlign(query, 9,  target, 7 , edlibNewAlignConfig(-1, EDLIB_MODE_SHW, EDLIB_TASK_PATH));

//if (result.status == EDLIB_STATUS_OK) {
    printf("%d\n", result.alignment);
    printf("%d\n", result.alignmentLength);
    printf("%d\n", result.endLocations[0]);

output is:

36934240

9

6

There is code provided in the description as 0 is match etc, but they are up to 3 and i get more numbers in alignment.

Can anyone help me to interpret this result or suggest me any other c++ library which can do this task for me?

Regards,

Madiha

RNA-Seq overlap alignment semi-global edlib • 460 views
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