Scoring scheme

[pesho-ivanov]

The README file states:
INFO, psgl::parseandSave, scoring scheme = [ match:1 mismatch:1 ins:1 del:1 ]

I guess this is typo as all alignments would receive the same score. For unit costs, the match cost should be zero, I believe.

[cjain7]

Match score reflects positive reward for a match, where as other reflect a penalty value.

cjain7@login1-stampede:PaSGAL$ ./PaSGAL -h
SYNOPSIS
./build/PaSGAL -m (vg|txt) -r <ref> -q <query> -o <output> -t <threads> [-match <N1>] [-mismatch <N2>] [-ins <N3>] [-del <N4>]

    <N1>        match score (default 1)
    <N2>        mismatch penalty (default 1)
    <N3>        insertion penalty (default 1)
    <N4>        deletion penalty (default 1)

[pesho-ivanov]

I see. So, if I understand correctly, this score scheme isn't equivalent to the unit costs (0,1,1,1) in GraphAligner.

I don't think this will make a huge difference, but did you run PaSGAL with (0,1,1,1) costs when comparing to vg-exact and the GraphAligner-exact?

[cjain7]

That is not a valid scoring scheme for local alignments. Here you are trying to maximize alignment score. If you give (0,1,1,1), an empty alignment would achieve the best score.

[pesho-ivanov]

Thank you for underlining that PaSGAL is aligning locally! This means that it solves the same local alignment task by vg, but different from the semi-global alignment task by graphaligner-exact. Is there a way to run PaSGAL for the same task that graphaligner solves?

Can you please share the exact commands and parameters you used to compare PaSGAL, graphaligner-exact and vg-exact? I am especially interested in the scores so that I make sure I reproduce the evaluations for the same data and same problem statement.

[cjain7]

Is there a way to run PaSGAL for the same task that graphaligner solves?

Not at the moment, but in theory, it should be easy to add global alignment algorithm in PaSGAL.

parameters you used to compare PaSGAL, graphaligner-exact and vg-exact?

Parameters to vg-exact: -T0 -e1 -g1 -M1 -m1
Parameters to PaSGAL: default
Parameters to bit-parallel: default