Kind of CIGAR

[c0ntradicti0n]

I get with the python binding with pyssw an integer array for the Cigar with few elements depending on gaps in the alignment as the struct for the cigar is defined.

But shouldn't it be a string with the defined diff format or is there some explanation for the encoding? Or is the char* parasail_cigar_decode(parasail_cigar_t *cigar); function missing in the python bindings?

[jeffdaily]

Since this issue is focused on the parasail python bindings it might have been better to file the issue there.

The decode method is part of the cigar object in the python bindings. For example:

>>> import parasail
>>> result = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)
>>> print(result.cigar.seq)
[71]
>>> print(result.cigar.decode)
b'4='

[c0ntradicti0n]

Cool! I see. Thanks!

I did not get the idea of CIGAR referring to traceback until your answer. if this would have happened, I would have found it in the straight documentation for this case...: https://github.com/jeffdaily/parasail-python#tracebacks

Am Mo., 14. Feb. 2022 um 18:46 Uhr schrieb Jeff Daily < @.***>:

Since this issue is focused on the parasail python bindings it might have been better to file the issue there.

The decode method is part of the cigar object in the python bindings. For example:

import parasail>>> result = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)>>> print(result.cigar.seq) [71]>>> print(result.cigar.decode)b'4='

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