Fix output format in triangle mode

[fplazaonate]

In triangle mode, when an output file is provided, skani generates:

1. A lower triangular matrix without a diagonal by default
2. A lower triangular matrix with a diagonal when --full-matrix is provided

IMO, the correct behaviour should be:

1. A lower triangular matrix with a diagonal by default
2. A full matrix when --full-matrix is provided

What do you think?

[bluenote-1577]

Hi @fplazaonate,

Good to hear from you.

1. I'm a bit confused about the --full-matrix condition: in the latest skani v0.2.1, --full-matrix gives a full matrix, not a lower triangular matrix with a diagonal. Let me know if I misunderstood

2. The choice of not including a diagonal is intentional -- mash outputs lower triangular matrices in this form, and I wanted compatibility between the two software. See https://mothur.org/wiki/phylip-formatted_distance_matrix/ I agree that this matrix format is not ideal, though...

Thanks

[fplazaonate]

Hi @bluenote-1577 ,

Indeed, skani gives the full matrix when the output file is stdout.
The problem occurs with the '-o' option

[bluenote-1577]

@fplazaonate ah, I see. that's indeed a bug.

I'm happy to merge your pull request if you could remove the = condition (so lower triangle matrix don't have diagonal); in this case, I don't think you can comment out the if statement

[fplazaonate]

It should be fixed now.

[bluenote-1577]

Thanks!

[fplazaonate]

BTW, I don't understand why the code for writing to stdout is different than for a regular file.