Question about -debug output

[J-Wall]

Hi,

I was wondering if you could tell me the specification for the stderr output when you run NextPolish with the -debug flag? It looks like it outputs 5 columns, and I have a vague idea what they mean, but I would like to make sure.

For context, I would like to make a file from my NextPolish run which is similar to the file which Pilon outputs when you run it with --changes (see here) and I think I can probably generate this from the -debug output, but to do so, I need to be confident about it's format.

Thanks! And awesome program by the way :)

[moold]

Hi, the following is its format:
seq_ID position(0-based) index new_base original_base

such as:
original_seq:
    >test
    ATGCA
new_seq:
    >test_np1
    ATGGCA
output:
    test_np1 2 1 G -

However, keep in mind that the position is the current input reference, so when you run NextPolish multiple iterations. -debug make no sense, because you can not trace the changes between the final result and the original reference.